Gene loci information

Transcript annotation

  • This transcript has been annotated as Laminin subunit alpha-1.

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 g5874 g5874.t1 isoform g5874.t1 12540820 12555629
chr_2 g5874 g5874.t1 exon g5874.t1.exon1 12540820 12541504
chr_2 g5874 g5874.t1 cds g5874.t1.CDS1 12540820 12541504
chr_2 g5874 g5874.t1 exon g5874.t1.exon2 12541568 12543543
chr_2 g5874 g5874.t1 cds g5874.t1.CDS2 12541568 12543543
chr_2 g5874 g5874.t1 exon g5874.t1.exon3 12550120 12550457
chr_2 g5874 g5874.t1 cds g5874.t1.CDS3 12550120 12550457
chr_2 g5874 g5874.t1 exon g5874.t1.exon4 12555377 12555629
chr_2 g5874 g5874.t1 cds g5874.t1.CDS4 12555377 12555629
chr_2 g5874 g5874.t1 TSS g5874.t1 12555952 12555952
chr_2 g5874 g5874.t1 TTS g5874.t1 NA NA

Sequences

>g5874.t1 Gene=g5874 Length=3252
ATGAGGAAATTTAAAAATCGAGCATTAATGTGCTTTATAGTTTTAATTTTAATAATCGTT
CGCGTTTCATCCGCTCAAAGTTCGCGATCGAATCGAAAAAAGTCGCAAAATAATAACTTA
CAAAATTTAAGTTTCGATATTAATAATAAAGACACAAGCAATGATGGATTATTAGCGCAT
CAACAAAATCGCCCATCGAGACCGAACACGGGACAAAAGAGAAGACGAAAGGGTCATCAG
CGAAATGAGTATGATTTGCGACAGCTACCAGACAGTACACATCCGTTTCAGCGCTTTGTC
GAATCAGCACCGAATGGCGGTTTATTTCCAAAACCTTTTAATATTGCTGCAAAAGCTAAA
ATTACAGCAAATGCAACATGTGGTAGTATTGAGGATGAAGAATTTTGTCGAATGGCTGAT
ATTTATTCACCAAGGCAGCAATCGATGTGTGAATTATGTGATGCTAGTGATATTGATTCG
AGCCACCCAATAGAGAATGCAATTGATGGTACACATTCGTTCTGGCAGTCACCTACACTG
GCTATGGGCAGTGAATATGAATTTGTTACAATTGATATTGATTTAGGACAGATTTACGAG
ATCTATTCAATAAAAATAAAATCTGCCGAATCACCATTGCCTAAAGCATGGATACTAGAG
AAATCGATCGATGGTGAAAATTATAATGAATGGCAATATTTTGCCTCTAGCAATGCCGAC
TGTTTATCACGCTACAACCGCCCAGGTCGCAATTTAAATTATACACTGCAAAGTAATGAA
GAAATCATTTGTACTACACAATACTCGGAGTCAATTCGTCTCAAATATGGCGAGGCAAAA
TTTGTCGTAATGTCACAACGCAACTATGATGATTCTATGCTTAATTTTACTCTTGCCAGT
CACATACGGCTACGATTTCAAGGTTTAGTGAAAGATATTATTGAAATTGAAAATGATAGA
ACACCAAAGTGGCAACCAGATCAAGAAGATTTACTTAAAAGAAGTTATTATTCAATTCAA
TCGATCATGGTGGTAGGTCGCTGCTACTGTTCTGGTCATGCTGCAAAATGTCGTGAAAGT
GATACCGAATCAAGTCTAAAATTACCTCAATGCGAATGCATGCACAATACATGCGGGAAA
AATTGCGATAAATGCTGTCCATTATATAATCAACGTCCATTTCGTGCTGGAACACCTCAG
AAGGAAAATAAGTGCGAAAAGTGTCAATGCTATGGACATGCTACAGAATGTCGTTATAGT
TCTGATATTGATGAACGAAATTTAAGTCAAAACATAAAGGGCAAAATGAGTGGCGGCGGT
GTTTGTGTAAATTGTACAAAATTTACGACTGGCATTAACTGCGAAAAATGCATGTCTGGC
TATTATCGGCCTTATGATCGCGCACCTGATGATGATGAGCCATGCATTGCATGTAATTGC
AGTCAAAAAGGATCAATTGGAGTTTGTAATGAAGTTGGTGGTGAATGCATTTGTAAGCCA
GGTTTTAGTGGACCAAAATGTGACATTTGTGCAGTTGGATATGGTGGAAATGATTGCGAA
AAATGCAGTTGCGATGTTCGTGGAACAATTCCTGGTGGTGAATGTGATGAATCATGTCAA
TGTAAACCTCATGTAACTGGTGAAAAATGCGACACTTGCAAAGATGGATATTTTGCTTTA
TCTTATGACAATCCGGATGGTTGTTTGAAATGCATTTGTTCTGGACTTAATATAACTTGT
GAAAGTCATTCAATTGAAAGAAGTTTTATTGAATCACTTGAAGGATGGGTTGTAACCGAT
ATTTCTAAAACACAAATTGCTTATCCAACTAGAGATGTTGATACTGGTTTTTATGTATTT
GGAATGTATGAATTATCAGATGTGGAAGCAGTTTATTGGTCAGCACCAGAAGTTTATTTG
GGAAATAGATTAGAAAATTATGGCTCACATTTCATCTTTCAAATTGATTATGTTATTGTT
CGAGGTGATACGAGCGGCAAACCAACAAATGGACCGAATTTCATTCTTATTGGCAAAAAT
GGAATGAAAATTGCATTTGGTGATGGAATTTTTACAAATTCAAATGCTAGTGTGAAAGTA
CCATTAATGGAAACAAATTGGTATCATGTACCAAAGAATGTTAAAGATATAATAACACGA
TTAAGAAGAACAGATTATAAAGGCGATCCAGTGACGAGAACTCAATTTATGTCAGTCATT
AGTGACATTGATAGTATTTTAATTAGAGGAACTTATCACACAGATCAGGCTGAAGCAATT
CTTAGACGTGCTATACTTTATTCGGGCGATTTAATGACATCAAATGAAGTTATTGAAAAC
ACTGATGAAAATTCTTTGAGTTTTGTTGAAAAATGTCATTGCCCAATTGGCTATACTGGA
CTGTCTTGCGAATCTTGCATGTTTGGTCACATTTCAATTATTGAAAATTCTTCAACTCAT
GAGAAAATATTGAAATGTTTGCCATGCAACTGCAACGGACACTCAGAAACGTGTGACGTG
GTGAATAATCAATGTGGTGAATGCATTCATAATACAACTGGAGAAAGATGTGAAAAATGT
AAAATTGGTTTTTATGGCGACGCAACAAAAGGAACGCCTGAAGATTGTAAAAAATGTGCG
TGTCCATTGAACATTGACTCGAATAATTTTAGTGATAAATGCAAATTAACAAATGATGGT
GATTATGTCTGTCTTAATTGTCCATTAGGTCACAGTGGTCCATTAGGTCATTGTGAAAAG
TGTGAAGATGGCTATTATGGAAATCCATTAGAAATTGGATCAAAATGTATTCGTTGTGAA
TGTAATGAAGATGAATCATGCGATAAAATAACAGGAAAATGCATAAAATGTGAAGGAAAT
ACTGAAGGTTGGCGTTGTGATAAATGCAAAAAAGGATACTTTGGTGATCCAAATATCGGT
TGTGAAGTTTGTGAATGCAGTGAATATGGATCAGTGAATAATCTTTGTGATTCAATAACA
GGAAAATGTTTATGTAAAGAAAATTATAAAGGAAAGAATTGTGATCAATGTGAAATAGGA
TTTGTCAATATTTCATTAGCGTGTGTTTCATGTGATTGTAATAAAAATGGCTCAAGAGAT
CAAAATTGTGACTCAAACAGTGGACAATGCGATTGCAAACCAAATGTTCATGGATTAAAG
TGTGATGAATGTGATGAACTTTTCTTTGGATTAAATTTTGATGGCTGCGAAGGTGAGTTA
CAAAAAATTTAA

>g5874.t1 Gene=g5874 Length=1083
MRKFKNRALMCFIVLILIIVRVSSAQSSRSNRKKSQNNNLQNLSFDINNKDTSNDGLLAH
QQNRPSRPNTGQKRRRKGHQRNEYDLRQLPDSTHPFQRFVESAPNGGLFPKPFNIAAKAK
ITANATCGSIEDEEFCRMADIYSPRQQSMCELCDASDIDSSHPIENAIDGTHSFWQSPTL
AMGSEYEFVTIDIDLGQIYEIYSIKIKSAESPLPKAWILEKSIDGENYNEWQYFASSNAD
CLSRYNRPGRNLNYTLQSNEEIICTTQYSESIRLKYGEAKFVVMSQRNYDDSMLNFTLAS
HIRLRFQGLVKDIIEIENDRTPKWQPDQEDLLKRSYYSIQSIMVVGRCYCSGHAAKCRES
DTESSLKLPQCECMHNTCGKNCDKCCPLYNQRPFRAGTPQKENKCEKCQCYGHATECRYS
SDIDERNLSQNIKGKMSGGGVCVNCTKFTTGINCEKCMSGYYRPYDRAPDDDEPCIACNC
SQKGSIGVCNEVGGECICKPGFSGPKCDICAVGYGGNDCEKCSCDVRGTIPGGECDESCQ
CKPHVTGEKCDTCKDGYFALSYDNPDGCLKCICSGLNITCESHSIERSFIESLEGWVVTD
ISKTQIAYPTRDVDTGFYVFGMYELSDVEAVYWSAPEVYLGNRLENYGSHFIFQIDYVIV
RGDTSGKPTNGPNFILIGKNGMKIAFGDGIFTNSNASVKVPLMETNWYHVPKNVKDIITR
LRRTDYKGDPVTRTQFMSVISDIDSILIRGTYHTDQAEAILRRAILYSGDLMTSNEVIEN
TDENSLSFVEKCHCPIGYTGLSCESCMFGHISIIENSSTHEKILKCLPCNCNGHSETCDV
VNNQCGECIHNTTGERCEKCKIGFYGDATKGTPEDCKKCACPLNIDSNNFSDKCKLTNDG
DYVCLNCPLGHSGPLGHCEKCEDGYYGNPLEIGSKCIRCECNEDESCDKITGKCIKCEGN
TEGWRCDKCKKGYFGDPNIGCEVCECSEYGSVNNLCDSITGKCLCKENYKGKNCDQCEIG
FVNISLACVSCDCNKNGSRDQNCDSNSGQCDCKPNVHGLKCDECDELFFGLNFDGCEGEL
QKI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
49 g5874.t1 CDD cd00055 EGF_Lam 347 398 3.2323E-5
44 g5874.t1 CDD cd00055 EGF_Lam 477 524 5.32144E-7
47 g5874.t1 CDD cd00055 EGF_Lam 522 568 1.10023E-6
48 g5874.t1 CDD cd00055 EGF_Lam 828 871 1.93508E-9
45 g5874.t1 CDD cd00055 EGF_Lam 938 980 4.63832E-7
46 g5874.t1 CDD cd00055 EGF_Lam 984 1031 2.91959E-9
50 g5874.t1 CDD cd00055 EGF_Lam 1030 1077 2.39117E-11
30 g5874.t1 Gene3D G3DSA:2.60.120.1490 - 91 373 4.9E-61
37 g5874.t1 Gene3D G3DSA:2.10.25.10 Laminin 374 481 2.2E-33
33 g5874.t1 Gene3D G3DSA:2.10.25.10 Laminin 482 520 5.0E-6
32 g5874.t1 Gene3D G3DSA:2.10.25.10 Laminin 521 569 9.9E-11
38 g5874.t1 Gene3D G3DSA:2.170.300.10 - 771 871 2.7E-14
31 g5874.t1 Gene3D G3DSA:2.10.25.10 Laminin 879 938 1.5E-11
35 g5874.t1 Gene3D G3DSA:2.10.25.10 Laminin 939 982 5.8E-11
34 g5874.t1 Gene3D G3DSA:2.10.25.10 Laminin 983 1029 4.1E-10
36 g5874.t1 Gene3D G3DSA:2.10.25.10 Laminin 1030 1077 2.8E-12
72 g5874.t1 MobiDBLite mobidb-lite consensus disorder prediction 58 90 -
12 g5874.t1 PANTHER PTHR10574 NETRIN/LAMININ-RELATED 105 1079 0.0
13 g5874.t1 PANTHER PTHR10574:SF405 WING BLISTER, ISOFORM B 105 1079 0.0
15 g5874.t1 PRINTS PR00011 Type III EGF-like signature 489 507 5.6E-18
14 g5874.t1 PRINTS PR00011 Type III EGF-like signature 532 550 5.6E-18
16 g5874.t1 PRINTS PR00011 Type III EGF-like signature 967 995 5.6E-18
17 g5874.t1 PRINTS PR00011 Type III EGF-like signature 1043 1061 5.6E-18
1 g5874.t1 Pfam PF00055 Laminin N-terminal (Domain VI) 109 346 1.9E-48
5 g5874.t1 Pfam PF00053 Laminin EGF domain 408 464 0.0027
8 g5874.t1 Pfam PF00053 Laminin EGF domain 478 517 1.1E-5
10 g5874.t1 Pfam PF00053 Laminin EGF domain 522 568 1.6E-7
11 g5874.t1 Pfam PF00052 Laminin B (Domain IV) 632 770 2.8E-24
7 g5874.t1 Pfam PF00053 Laminin EGF domain 791 813 0.034
3 g5874.t1 Pfam PF00053 Laminin EGF domain 829 876 1.9E-7
9 g5874.t1 Pfam PF00053 Laminin EGF domain 879 936 0.0039
6 g5874.t1 Pfam PF00053 Laminin EGF domain 939 978 1.8E-6
4 g5874.t1 Pfam PF00053 Laminin EGF domain 984 1024 7.3E-10
2 g5874.t1 Pfam PF00053 Laminin EGF domain 1031 1073 2.2E-10
40 g5874.t1 Phobius SIGNAL_PEPTIDE Signal peptide region 1 25 -
41 g5874.t1 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 7 -
42 g5874.t1 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 8 20 -
43 g5874.t1 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 21 25 -
39 g5874.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 26 1083 -
71 g5874.t1 ProSitePatterns PS01248 Laminin-type EGF-like (LE) domain signature. 496 524 -
70 g5874.t1 ProSitePatterns PS01248 Laminin-type EGF-like (LE) domain signature. 954 986 -
69 g5874.t1 ProSitePatterns PS01248 Laminin-type EGF-like (LE) domain signature. 1050 1076 -
83 g5874.t1 ProSiteProfiles PS51117 Laminin N-terminal domain profile. 104 347 33.648
80 g5874.t1 ProSiteProfiles PS50027 Laminin-type EGF-like (LE) domain profile. 348 407 7.342
79 g5874.t1 ProSiteProfiles PS50027 Laminin-type EGF-like (LE) domain profile. 408 477 8.313
77 g5874.t1 ProSiteProfiles PS50027 Laminin-type EGF-like (LE) domain profile. 478 521 15.758
82 g5874.t1 ProSiteProfiles PS50027 Laminin-type EGF-like (LE) domain profile. 522 570 16.481
73 g5874.t1 ProSiteProfiles PS51115 Laminin IV type A domain profile. 591 791 28.293
81 g5874.t1 ProSiteProfiles PS50027 Laminin-type EGF-like (LE) domain profile. 829 878 16.862
75 g5874.t1 ProSiteProfiles PS50027 Laminin-type EGF-like (LE) domain profile. 879 938 7.38
74 g5874.t1 ProSiteProfiles PS50027 Laminin-type EGF-like (LE) domain profile. 939 983 15.377
76 g5874.t1 ProSiteProfiles PS50027 Laminin-type EGF-like (LE) domain profile. 984 1030 15.567
78 g5874.t1 ProSiteProfiles PS50027 Laminin-type EGF-like (LE) domain profile. 1031 1078 18.786
68 g5874.t1 SMART SM00136 LamNT_2 102 346 3.5E-40
58 g5874.t1 SMART SM00180 lamegf_3 348 405 0.2
53 g5874.t1 SMART SM00180 lamegf_3 408 475 1.7E-5
61 g5874.t1 SMART SM00180 lamegf_3 478 519 2.0E-6
67 g5874.t1 SMART SM00181 egf_5 479 520 34.0
60 g5874.t1 SMART SM00180 lamegf_3 522 568 3.7E-8
66 g5874.t1 SMART SM00181 egf_5 534 569 210.0
52 g5874.t1 SMART SM00281 LamB_3a 627 771 2.4E-11
54 g5874.t1 SMART SM00180 lamegf_3 829 876 5.7E-8
65 g5874.t1 SMART SM00181 egf_5 837 877 33.0
59 g5874.t1 SMART SM00180 lamegf_3 879 936 0.23
57 g5874.t1 SMART SM00180 lamegf_3 939 981 2.4E-8
62 g5874.t1 SMART SM00181 egf_5 946 982 16.0
56 g5874.t1 SMART SM00180 lamegf_3 984 1028 8.8E-11
64 g5874.t1 SMART SM00181 egf_5 985 1018 200.0
55 g5874.t1 SMART SM00180 lamegf_3 1031 1076 3.5E-11
63 g5874.t1 SMART SM00181 egf_5 1032 1077 130.0
18 g5874.t1 SUPERFAMILY SSF49785 Galactose-binding domain-like 152 238 3.76E-8
25 g5874.t1 SUPERFAMILY SSF57196 EGF/Laminin 348 410 1.84E-5
21 g5874.t1 SUPERFAMILY SSF57196 EGF/Laminin 408 464 2.79E-5
20 g5874.t1 SUPERFAMILY SSF57196 EGF/Laminin 478 518 9.21E-5
26 g5874.t1 SUPERFAMILY SSF57196 EGF/Laminin 536 573 2.54E-5
24 g5874.t1 SUPERFAMILY SSF57196 EGF/Laminin 829 872 1.67E-8
19 g5874.t1 SUPERFAMILY SSF57196 EGF/Laminin 886 941 1.28E-6
23 g5874.t1 SUPERFAMILY SSF57196 EGF/Laminin 939 979 3.07E-6
27 g5874.t1 SUPERFAMILY SSF57196 EGF/Laminin 984 1025 4.46E-8
22 g5874.t1 SUPERFAMILY SSF57196 EGF/Laminin 1031 1072 5.3E-7
29 g5874.t1 SignalP_EUK SignalP-noTM SignalP-noTM 1 25 -
28 g5874.t1 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 25 -
51 g5874.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 7 25 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5874/g5874.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5874.t1.fa.iupred3.txt does not exist

GO terms from InterProScan

There are no GO annotations for this transcript.

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