Gene loci information

Transcript annotation

  • This transcript has been annotated as Tyrosine-protein phosphatase Lar.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_2 g5546 g5546.t1 isoform g5546.t1 10197766 10208718
chr_2 g5546 g5546.t1 exon g5546.t1.exon1 10197766 10198745
chr_2 g5546 g5546.t1 cds g5546.t1.CDS1 10197766 10198745
chr_2 g5546 g5546.t1 exon g5546.t1.exon2 10198805 10199244
chr_2 g5546 g5546.t1 cds g5546.t1.CDS2 10198805 10199244
chr_2 g5546 g5546.t1 exon g5546.t1.exon3 10199564 10199651
chr_2 g5546 g5546.t1 cds g5546.t1.CDS3 10199564 10199651
chr_2 g5546 g5546.t1 exon g5546.t1.exon4 10202435 10202734
chr_2 g5546 g5546.t1 cds g5546.t1.CDS4 10202435 10202734
chr_2 g5546 g5546.t1 exon g5546.t1.exon5 10203948 10203989
chr_2 g5546 g5546.t1 cds g5546.t1.CDS5 10203948 10203989
chr_2 g5546 g5546.t1 exon g5546.t1.exon6 10204079 10204173
chr_2 g5546 g5546.t1 cds g5546.t1.CDS6 10204079 10204173
chr_2 g5546 g5546.t1 exon g5546.t1.exon7 10204235 10204385
chr_2 g5546 g5546.t1 cds g5546.t1.CDS7 10204235 10204385
chr_2 g5546 g5546.t1 exon g5546.t1.exon8 10204463 10204655
chr_2 g5546 g5546.t1 cds g5546.t1.CDS8 10204463 10204655
chr_2 g5546 g5546.t1 exon g5546.t1.exon9 10204716 10204760
chr_2 g5546 g5546.t1 cds g5546.t1.CDS9 10204716 10204760
chr_2 g5546 g5546.t1 exon g5546.t1.exon10 10204832 10204887
chr_2 g5546 g5546.t1 cds g5546.t1.CDS10 10204832 10204887
chr_2 g5546 g5546.t1 exon g5546.t1.exon11 10205112 10205155
chr_2 g5546 g5546.t1 cds g5546.t1.CDS11 10205112 10205155
chr_2 g5546 g5546.t1 exon g5546.t1.exon12 10205233 10205339
chr_2 g5546 g5546.t1 cds g5546.t1.CDS12 10205233 10205339
chr_2 g5546 g5546.t1 exon g5546.t1.exon13 10205397 10205478
chr_2 g5546 g5546.t1 cds g5546.t1.CDS13 10205397 10205478
chr_2 g5546 g5546.t1 exon g5546.t1.exon14 10205542 10205593
chr_2 g5546 g5546.t1 cds g5546.t1.CDS14 10205542 10205593
chr_2 g5546 g5546.t1 exon g5546.t1.exon15 10205653 10205998
chr_2 g5546 g5546.t1 cds g5546.t1.CDS15 10205653 10205998
chr_2 g5546 g5546.t1 exon g5546.t1.exon16 10206062 10206241
chr_2 g5546 g5546.t1 cds g5546.t1.CDS16 10206062 10206241
chr_2 g5546 g5546.t1 exon g5546.t1.exon17 10206305 10206339
chr_2 g5546 g5546.t1 cds g5546.t1.CDS17 10206305 10206339
chr_2 g5546 g5546.t1 exon g5546.t1.exon18 10206411 10206569
chr_2 g5546 g5546.t1 cds g5546.t1.CDS18 10206411 10206569
chr_2 g5546 g5546.t1 exon g5546.t1.exon19 10207376 10207507
chr_2 g5546 g5546.t1 cds g5546.t1.CDS19 10207376 10207507
chr_2 g5546 g5546.t1 exon g5546.t1.exon20 10208640 10208718
chr_2 g5546 g5546.t1 cds g5546.t1.CDS20 10208640 10208718
chr_2 g5546 g5546.t1 TSS g5546.t1 10209539 10209539
chr_2 g5546 g5546.t1 TTS g5546.t1 NA NA

Sequences

>g5546.t1 Gene=g5546 Length=3606
ATGGGGCTGCATCAAGCAGCAACAAATGTCGTAACAGTGATTGTTCTTTTATGGATAGCT
GAAATTATTAATGCGTCTCATCCACCTGAAATTATTAAAAAACCTGCAAATCAAGGGGTC
AGAGTTGGAGGCGTTGCTACCTTCTTTTGCTCTGCTCGTGGCGATCCGCAACCTACAATT
AATTGGAGAAAAAATGGCAAAAAAGTTTCGAGCACACAGAGTAGATACACCGTCATTGAA
ACAAATGGGATTTCATTGCTGCGAATTGAGCCTGTGAGAGCGGGTCGTGATGATGCCCCT
TATGAGTGCGTAGCAGAGAATGGCGTTGGCGATGCTGTTAGTGCTGAAGCTACGTTGACT
GTTTATGAAGCTGACAAAACTCCAGTTGGATTCCCAACAGTCGAGATACAATCGAACAAT
AGAGTCATTGAAATTGGTCACACAGCAGTTCTTCAATGCAAAGCAAACGGCGCACCGATG
CCTAAAGTTTATTGGTTAAAAGATATGAAAAGAGTCGAATTGACTTCACGCTATACAATT
TTGGATGGATCATTGCAAATATCTCAAAGTGAAGAAGCAGATCAGGGAAAATACGAATGT
GTTGCGGAAAATCAAGTTGGTACTGAACATTCAAAAGCCATAAGCTTGTATGTGAAAATT
CGACGCGTTCCGCCACAATTTTCGCGTCCACCTGATCCCATAAATGAGGTAATGCTAGGT
GGAAGTTTGAATTTGACATGTGTGGCTGTTGGCTCGCCAATGCCTTTCGTAAAATGGCGT
CTGCATGATGAGGATATAACACCAGAACATGAATTACCAGTTGGAAAGAGTGTGCTTCAA
TTAAATGACATTAGAACTAGTGCCAATTATACTTGTGTTGCATCGTCAAGTCTTGGTGTG
ATTGAAGCTAATGCATCGGTTAAAGTCCAATCACTTCCGATTGCTCCAACTGACTTGAAA
ATCTCTGAAGTTACAGCAACAACTGTTCGTTTAGAATGGAGTTATAAAGGAACTGAAGAC
TTGCAATATTATGTTCTTCAACATAAACCAAAGAATGCTAATCAAGCGTATAGTGAGACA
AGTGGAATTATTACTATGTTCTATGTTGTGAGAGGTCTCAGTCCATATACTGAGTATGAG
TTCCATGTGATTGGTGTCAATAACATTGGAAGAGGGCCGCCGTCAGCTCCGGTGTCAGCA
ACGACAGGGGAAACAGAAATGGAAAGTGCTCCCAGAAATATTGAAGTTAGACCATTGAGT
TCATCAACAATGGTCATCACTTGGCAACCTCCTGAAACACCAAATGGTCAAATAAATGGT
TATAAAGTTTATTACACCACAAATCCAAATCAACCTGAAGCTTCATGGAACTCACAAATG
GTCGATAACAGTGAATTGACCACAATTTCTGATCTCACACCGTTAGCCATTTATACAATA
CGCGTACAAGCATTCACGTCAATGGGCGCAGGTCCCATGTCGAATCCGATTCAAGTTAAA
ACACAGCAAGGCGTTCCGTCTCAACCAAGCAATTTTAGAGCAACTGACACTGGTGAGACA
GCTGTGACATTACAGTGGAACAAGCCTTCACATAGTAGTGAAAATATAGTTCATTATGAA
CTATATTGGAATGACACGTACGCCAATGAGCAGCATCATCAACGCATTCCGAATGTTGAG
ACTTATACAATGAGTGGACTTTATCCTGACACATTGTATTATATTTGGTTAGCAGCAAGA
TCACAACGTGGAGAGGGAGCAACAACTCCACCTATCCCTGTTCGTACAAAACAATATGTC
CCTGGAGCACCTCCTCAGAATAATACATGTCAAGCAACAAGTCCGACAACAATCAAAGTA
TCTTGGAAGCCACCACCACAAGATCGCTCAAATGGTCGTATAACATATTACAAACTTTTC
TTTGTCGAAGAAGGACGATCAGATAATGAAGCTGATTCGATAAAAATTTGGAACACAACA
GAGTTCACACTTGATGAATTGAAGCGTTGGACTGAATATAAAATTTGGATTTTAGCAGGA
ACCATTGTTGGAAATGGACCTAGAACTCAACCTATCAAATGCAGGACACATGAAGACGTG
CCTGGTGAACCAACGTCTGTGAGAGCAATTCCAGTCAATTCAACGACAATCCACGTTTCG
TGGCGACCACCTGCGGAGAAAGATAGAAACGGAATTATTCGTGGTTACCACATTCATGTA
CATGAAACTAAAGAGGAAGGAAAAAGTTTCCTCAATGAGCCTATGAAGTTTGAAGTGCCC
GATGGCGTTCTCGATTATAACATTAGCGGTTTACAGCCAGACACAAAATATTCTGTGCAA
GTTGCCGCATTGACACGCAAGGGCGATGGCGATCGAAGCAATGCGATATCAGTAAAAACG
CCAGGTGGTGTGCCAATTCGACCCATCGTCCGATTAAAAGTTTTAGAACGCGATCCAACT
GTATCTATTGAACTTGAATGGGAGCGACCAATGCAAACCTATGGTGAATTACGAGGTTAT
CGCGTCAGATGGGGTGTCAAAGATCATCATAAACTACATGAAACCATGTTGGGCCCTGAC
GCTACAACAAAAAATATTAAAGATCTTGAGCGTGGCATTGAATACGAATTCCGAATTGCT
GGCACAAATCATATTGGCGTTGGACAAGAGGCGGTCAAATATTATACTACACCCGAGGGA
ACGCCTTCAGGAGCACCAACAAACATTACTTATCGTTTCCAGACGCCAGACGTACTATGT
GTGACATGGGATTCACCCATTAGAGAGCATAGAAATGGGCAAATTCTTCGTTATGACATT
CAATTTCACAAGAAAATTGATCATGGATTGGGCACTGAAAGAAACACAACGGTTCGTAAA
GCAGTTTTTGCAAATCTCGATGAAAATACTGAATATGTAGTGAGAATAAGAGCTTATACA
AAGCAAGGAGCTGGTCCATTTAGTGAAAAGATTATAATTGAAACTGAAAAAGATATGGGT
CGAGCACCAATGATGGTTCAAGCAATTGCAACATCAGAACAAACAGTTGAAGTATGGTGG
GAATCTGTTCCATCACGTGGACGACTTATTGGTTACAAAATTTTTTATACAATGACTGCT
GTCGAAGATCTTGATGAATGGCAAACAAAAATTGTCGGTCTTACAGAATCAGCCGATTTA
GTCAATTTGGAAAAGCAAGCACAATATGCAATAGCAATAGCAGCTCGTTTCAAGACAGGT
CTTGGAAGACTGAGTGAAAAAATTACTGTCAAAATAAAGCCAGAAGATGTTCCACTTAAT
TTAAGAGCACAAGATGTGAGCACACATTCAATGACTTTGACATGGTCTCCACCCAATCGA
CTTAATCCAATACATTATAAAATAAGTTTTGATGCAATAAAAGTATTTGTCGATGCACAA
GGAATCACTCAAACTCAAACTATACCACGACGGGAAATTATAATTCAACAGCACAAAACG
TCGCATACAATTAATGAGCTCTCACCATTCACGACTTATTATGTGAATGTATCAGCGGTT
CCTGCAGACTTAACATATAAGCCACCGACAAAAATTAGCGTAACAACACAGGTAAGAAAA
AGATAA

>g5546.t1 Gene=g5546 Length=1201
MGLHQAATNVVTVIVLLWIAEIINASHPPEIIKKPANQGVRVGGVATFFCSARGDPQPTI
NWRKNGKKVSSTQSRYTVIETNGISLLRIEPVRAGRDDAPYECVAENGVGDAVSAEATLT
VYEADKTPVGFPTVEIQSNNRVIEIGHTAVLQCKANGAPMPKVYWLKDMKRVELTSRYTI
LDGSLQISQSEEADQGKYECVAENQVGTEHSKAISLYVKIRRVPPQFSRPPDPINEVMLG
GSLNLTCVAVGSPMPFVKWRLHDEDITPEHELPVGKSVLQLNDIRTSANYTCVASSSLGV
IEANASVKVQSLPIAPTDLKISEVTATTVRLEWSYKGTEDLQYYVLQHKPKNANQAYSET
SGIITMFYVVRGLSPYTEYEFHVIGVNNIGRGPPSAPVSATTGETEMESAPRNIEVRPLS
SSTMVITWQPPETPNGQINGYKVYYTTNPNQPEASWNSQMVDNSELTTISDLTPLAIYTI
RVQAFTSMGAGPMSNPIQVKTQQGVPSQPSNFRATDTGETAVTLQWNKPSHSSENIVHYE
LYWNDTYANEQHHQRIPNVETYTMSGLYPDTLYYIWLAARSQRGEGATTPPIPVRTKQYV
PGAPPQNNTCQATSPTTIKVSWKPPPQDRSNGRITYYKLFFVEEGRSDNEADSIKIWNTT
EFTLDELKRWTEYKIWILAGTIVGNGPRTQPIKCRTHEDVPGEPTSVRAIPVNSTTIHVS
WRPPAEKDRNGIIRGYHIHVHETKEEGKSFLNEPMKFEVPDGVLDYNISGLQPDTKYSVQ
VAALTRKGDGDRSNAISVKTPGGVPIRPIVRLKVLERDPTVSIELEWERPMQTYGELRGY
RVRWGVKDHHKLHETMLGPDATTKNIKDLERGIEYEFRIAGTNHIGVGQEAVKYYTTPEG
TPSGAPTNITYRFQTPDVLCVTWDSPIREHRNGQILRYDIQFHKKIDHGLGTERNTTVRK
AVFANLDENTEYVVRIRAYTKQGAGPFSEKIIIETEKDMGRAPMMVQAIATSEQTVEVWW
ESVPSRGRLIGYKIFYTMTAVEDLDEWQTKIVGLTESADLVNLEKQAQYAIAIAARFKTG
LGRLSEKITVKIKPEDVPLNLRAQDVSTHSMTLTWSPPNRLNPIHYKISFDAIKVFVDAQ
GITQTQTIPRREIIIQQHKTSHTINELSPFTTYYVNVSAVPADLTYKPPTKISVTTQVRK
R

Protein features from InterProScan

Transcript Database ID Name Start End E.value
53 g5546.t1 CDD cd00063 FN3 313 402 5.42704E-16
55 g5546.t1 CDD cd00063 FN3 409 501 2.4204E-18
50 g5546.t1 CDD cd00063 FN3 506 596 4.8758E-16
56 g5546.t1 CDD cd00063 FN3 604 696 1.83722E-13
51 g5546.t1 CDD cd00063 FN3 701 800 3.20781E-16
49 g5546.t1 CDD cd00063 FN3 808 891 6.34932E-8
52 g5546.t1 CDD cd00063 FN3 904 995 3.06368E-11
54 g5546.t1 CDD cd00063 FN3 1096 1196 6.86605E-9
43 g5546.t1 Gene3D G3DSA:2.60.40.10 Immunoglobulins 24 124 7.2E-28
38 g5546.t1 Gene3D G3DSA:2.60.40.10 Immunoglobulins 125 221 9.2E-24
41 g5546.t1 Gene3D G3DSA:2.60.40.10 Immunoglobulins 222 312 1.2E-20
33 g5546.t1 Gene3D G3DSA:2.60.40.10 Immunoglobulins 313 398 1.6E-19
37 g5546.t1 Gene3D G3DSA:2.60.40.10 Immunoglobulins 399 501 8.7E-31
32 g5546.t1 Gene3D G3DSA:2.60.40.10 Immunoglobulins 502 596 1.2E-19
36 g5546.t1 Gene3D G3DSA:2.60.40.10 Immunoglobulins 597 693 3.1E-24
39 g5546.t1 Gene3D G3DSA:2.60.40.10 Immunoglobulins 694 798 5.3E-28
40 g5546.t1 Gene3D G3DSA:2.60.40.10 Immunoglobulins 799 894 5.5E-13
35 g5546.t1 Gene3D G3DSA:2.60.40.10 Immunoglobulins 895 999 6.3E-21
42 g5546.t1 Gene3D G3DSA:2.60.40.10 Immunoglobulins 1000 1095 2.0E-13
34 g5546.t1 Gene3D G3DSA:2.60.40.10 Immunoglobulins 1096 1200 1.4E-14
15 g5546.t1 PANTHER PTHR19134 RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE 96 175 2.1E-242
18 g5546.t1 PANTHER PTHR19134:SF203 RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE F 96 175 2.1E-242
14 g5546.t1 PANTHER PTHR19134 RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE 182 875 2.1E-242
17 g5546.t1 PANTHER PTHR19134:SF203 RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE F 182 875 2.1E-242
13 g5546.t1 PANTHER PTHR19134 RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE 866 1179 2.1E-242
16 g5546.t1 PANTHER PTHR19134:SF203 RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE F 866 1179 2.1E-242
19 g5546.t1 PRINTS PR00014 Fibronectin type III repeat signature 422 431 4.3E-5
21 g5546.t1 PRINTS PR00014 Fibronectin type III repeat signature 435 445 4.3E-5
22 g5546.t1 PRINTS PR00014 Fibronectin type III repeat signature 759 777 4.3E-5
20 g5546.t1 PRINTS PR00014 Fibronectin type III repeat signature 875 889 4.3E-5
2 g5546.t1 Pfam PF07679 Immunoglobulin I-set domain 29 121 4.1E-17
3 g5546.t1 Pfam PF07679 Immunoglobulin I-set domain 132 213 3.9E-15
1 g5546.t1 Pfam PF13927 Immunoglobulin domain 224 295 1.5E-8
12 g5546.t1 Pfam PF00041 Fibronectin type III domain 315 395 5.1E-14
5 g5546.t1 Pfam PF00041 Fibronectin type III domain 409 494 4.9E-18
11 g5546.t1 Pfam PF00041 Fibronectin type III domain 507 587 2.4E-16
7 g5546.t1 Pfam PF00041 Fibronectin type III domain 604 688 3.2E-11
6 g5546.t1 Pfam PF00041 Fibronectin type III domain 703 793 2.5E-16
10 g5546.t1 Pfam PF00041 Fibronectin type III domain 812 890 7.8E-9
8 g5546.t1 Pfam PF00041 Fibronectin type III domain 905 988 7.8E-12
9 g5546.t1 Pfam PF00041 Fibronectin type III domain 1002 1085 7.2E-7
4 g5546.t1 Pfam PF00041 Fibronectin type III domain 1097 1183 4.8E-9
45 g5546.t1 Phobius SIGNAL_PEPTIDE Signal peptide region 1 25 -
46 g5546.t1 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 9 -
47 g5546.t1 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 10 20 -
48 g5546.t1 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 21 25 -
44 g5546.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 26 1201 -
83 g5546.t1 ProSiteProfiles PS50835 Ig-like domain profile. 29 120 13.983
82 g5546.t1 ProSiteProfiles PS50835 Ig-like domain profile. 132 215 13.639
81 g5546.t1 ProSiteProfiles PS50835 Ig-like domain profile. 225 308 10.335
73 g5546.t1 ProSiteProfiles PS50853 Fibronectin type-III domain profile. 315 405 19.637
74 g5546.t1 ProSiteProfiles PS50853 Fibronectin type-III domain profile. 410 504 23.874
72 g5546.t1 ProSiteProfiles PS50853 Fibronectin type-III domain profile. 508 599 21.199
77 g5546.t1 ProSiteProfiles PS50853 Fibronectin type-III domain profile. 604 699 22.391
79 g5546.t1 ProSiteProfiles PS50853 Fibronectin type-III domain profile. 703 803 22.785
78 g5546.t1 ProSiteProfiles PS50853 Fibronectin type-III domain profile. 808 904 14.067
76 g5546.t1 ProSiteProfiles PS50853 Fibronectin type-III domain profile. 905 998 19.172
80 g5546.t1 ProSiteProfiles PS50853 Fibronectin type-III domain profile. 1002 1095 13.894
75 g5546.t1 ProSiteProfiles PS50853 Fibronectin type-III domain profile. 1097 1199 15.053
59 g5546.t1 SMART SM00409 IG_3c 35 122 7.1E-9
71 g5546.t1 SMART SM00408 igc2_5 41 110 2.2E-9
57 g5546.t1 SMART SM00409 IG_3c 138 219 1.8E-9
70 g5546.t1 SMART SM00408 igc2_5 144 207 1.5E-13
58 g5546.t1 SMART SM00409 IG_3c 232 310 1.2E-7
69 g5546.t1 SMART SM00408 igc2_5 238 299 3.5E-5
68 g5546.t1 SMART SM00060 FN3_2 313 392 2.9E-12
64 g5546.t1 SMART SM00060 FN3_2 408 491 1.5E-12
61 g5546.t1 SMART SM00060 FN3_2 506 586 1.4E-13
65 g5546.t1 SMART SM00060 FN3_2 601 686 7.3E-10
67 g5546.t1 SMART SM00060 FN3_2 701 790 2.9E-14
63 g5546.t1 SMART SM00060 FN3_2 805 888 6.5E-6
60 g5546.t1 SMART SM00060 FN3_2 903 985 6.8E-9
66 g5546.t1 SMART SM00060 FN3_2 1000 1082 0.19
62 g5546.t1 SMART SM00060 FN3_2 1095 1187 2.1E-8
30 g5546.t1 SUPERFAMILY SSF48726 Immunoglobulin 28 128 2.38E-20
28 g5546.t1 SUPERFAMILY SSF48726 Immunoglobulin 129 219 7.45E-19
29 g5546.t1 SUPERFAMILY SSF48726 Immunoglobulin 224 310 9.52E-14
27 g5546.t1 SUPERFAMILY SSF49265 Fibronectin type III 313 506 6.25E-42
23 g5546.t1 SUPERFAMILY SSF49265 Fibronectin type III 504 701 3.3E-42
25 g5546.t1 SUPERFAMILY SSF49265 Fibronectin type III 699 889 1.93E-33
26 g5546.t1 SUPERFAMILY SSF49265 Fibronectin type III 893 1003 3.14E-21
24 g5546.t1 SUPERFAMILY SSF49265 Fibronectin type III 1002 1196 2.99E-21
31 g5546.t1 SignalP_EUK SignalP-noTM SignalP-noTM 1 25 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5546/g5546.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5546.t1.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005515 protein binding MF

KEGG

Orthology

Pathway

  • This transcript belongs to the following pathways

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.

Raw TPM values