Gene loci information

Transcript annotation

  • This transcript has been annotated as Ephrin type-B receptor 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_3 g68 g68.t1 isoform g68.t1 501206 510520
chr_3 g68 g68.t1 exon g68.t1.exon1 501206 501256
chr_3 g68 g68.t1 cds g68.t1.CDS1 501206 501256
chr_3 g68 g68.t1 exon g68.t1.exon2 501382 501477
chr_3 g68 g68.t1 cds g68.t1.CDS2 501382 501477
chr_3 g68 g68.t1 exon g68.t1.exon3 501709 502190
chr_3 g68 g68.t1 cds g68.t1.CDS3 501709 502190
chr_3 g68 g68.t1 exon g68.t1.exon4 502251 502315
chr_3 g68 g68.t1 cds g68.t1.CDS4 502251 502315
chr_3 g68 g68.t1 exon g68.t1.exon5 502442 502928
chr_3 g68 g68.t1 cds g68.t1.CDS5 502442 502928
chr_3 g68 g68.t1 exon g68.t1.exon6 502982 503158
chr_3 g68 g68.t1 cds g68.t1.CDS6 502982 503158
chr_3 g68 g68.t1 exon g68.t1.exon7 505093 505272
chr_3 g68 g68.t1 cds g68.t1.CDS7 505093 505272
chr_3 g68 g68.t1 exon g68.t1.exon8 505648 506514
chr_3 g68 g68.t1 cds g68.t1.CDS8 505648 506514
chr_3 g68 g68.t1 exon g68.t1.exon9 506572 507238
chr_3 g68 g68.t1 cds g68.t1.CDS9 506572 507238
chr_3 g68 g68.t1 exon g68.t1.exon10 507674 507753
chr_3 g68 g68.t1 cds g68.t1.CDS10 507674 507753
chr_3 g68 g68.t1 exon g68.t1.exon11 510430 510520
chr_3 g68 g68.t1 cds g68.t1.CDS11 510430 510520
chr_3 g68 g68.t1 TSS g68.t1 510943 510943
chr_3 g68 g68.t1 TTS g68.t1 NA NA

Sequences

>g68.t1 Gene=g68 Length=3243
ATGTCTCTGAAAAGAACTAAAAAATTAAATTCTATCGCACCAATTGCACTTCTATTGATC
ATTGCTACGGATATTTGTAATTGTGATCAAGTCGTTTTATTGGATACAACCAAAGAAGCA
ACATTAGAATGGACAAGTTATCCATATGGTCCACAAGCACAACGTCCAGGTTGGATTGAA
GAGTCCTTTACGAATTATGGAAAGGGCATCAACTGGCGTAGTTATGTTGTATGCGATGTT
GCCTATCCTGATGTAAACAATTGGCTTTGGTCACCATTTATTGATCGTGGTCCTGCCAAT
CGACTTTATATTGAAATTCACTTTACAATTCGTGATTGCTCGCTTTTTCCGGGCAATGCA
CTGAGCTGCAAGGAGACATTTAGTCTTCTTTTCTATGAGTTCGATGCACAAACTCGTGAA
CCACCACCATGGCAACCTGAGAGTTATAAGCTTATCGGTCGTATTGCAGCAGGCGAAGGT
CGTTTCAATCACAACTCTGATGTTGATATTAATGTAGAAACAAAGAGTATTGCTGTCAAC
AAGAAGGGTGTTTATTTTGCTTTTCGTGATCAAGGCGCATGCATAAGTGTTTTGGCTGTA
AAAGTCTATTATATCACATGTCCAGCTGTTACAGCCAATTTTGCACATTTTAATGAAACG
CCCACTGGAAAAGAAGTTACTGTGATTGAAAAACAACAAGGCACGTGCGTTGATAATGCT
GAACCAATTGAGCAACCTTACAATCATTGTAAAGGCGATGGAAAATGGACATTGTTATTG
GGTGGATGTCGTTGCAAAGTTGGGTATGAGCCTGATGATGAAAAACAAGCTTGCAAAGTC
TGTCCAGCAGGAACTTTCCGTTCAAGTGAAGTTGCAATGTGCACTTTATGTCCATTGAAT
TCAAAAACAAATAAAGCAGGCTCTAGCTATTGTACATGTGTACAAGGACATTATCGTCAT
CCACTTGATGGCAAACATATGCCATGTCATAAACCACCCGGTGCACCAACAAATCTTACA
GTTCTTTTCTTTGATCAAACCAGTGCAATTTTATCATGGAATCCACCACAAAAATCATCC
GTCGATGACCATTTGATAGATCAACAATTTCGAAATGACGTTGTGTTTCGTGTAAAATGT
CCATCATGCTCAAACAATGTCGTTTTCAATCCATCGAATGATGTATTTAACGAGACAAAA
TTGACAATGACAAACTTAGAGCCTGGTACACAATATGTTGTTCAAATACACACATTGAAT
GGACCATCATATTCACTATTGGGTAGTGGTTATAATCACAGTTTTTCATCAACAATTGAA
GGGACAGAAAGCCCTTTGAAGCGTGGAAATACATTTGATATTAAGTCTGAATATACTGAA
ATAACATTCACAACTGAATCGACAATTTTGAGTACAGTTTTTAATGTAAAAGTTACAACA
ATAACAAGTAAAGAAGTTGAATTAACATGGGACAATCCATTACATATTGACTCACCAATT
GAGTTTTATGAAGTCCGTTGGTTCCCAAAATCTGAAGTTGATTCACTTAATAAAACCACA
CAAAGTACGAAAGAGACGAAAATTTTGATAAATGATTTATCAGAAAACACAGAATATGGC
TTTCAAATTCGATGCAAGACAACAAGTGGATGGGGAACTTATAGCAATATTGTCTATGCT
CAAACTTTGCAAAGTATCACACCAGTATTTAACGAATCATCAATTCAAAATCGATTAGTC
GCCGGTGCAACAGTGCTGATAGTTTTCATCGTAGTGCTCGCAATTGTCGCAACAGTTCTT
GTTCTACGTACGAAAAATCAAGATGATTTGGATAAGAAAACTAGTAATCATTTGCCATTA
CCTTTAGATTACGCTAGCAATGAAGAAGGTGGCTATAAATATTATTCTTCTGCTCGTCGT
AATCATTTTGCAGTGACAACACCACTTTTTGGTGGCAATCGAAGTTATGTTGATCCACAT
ACATATGAAGATCCAAATCAAGCCATTCGAGAGTTTGCAAGAGAAATTGATGCTGGTTAT
ATCACTATTGAAGCAATTATTGGTGGAGGAGAATTCGGTGATGTATGTCGTGGTCGATTG
AAAATTCCACCAAGTTTTATTCAAGAAATTGATGTTGCCATTAAAACACTAAAGCCGGGA
TCAAGTGAAAAAGCTCGCTGTGATTTTCTCACAGAAGCATCAATCATGGGACAATTTGAT
CATCCCAATGTGATTTATCTACAAGGTGTTGTTACTCGATCGAATCCTGTCATGATAATC
ACAGAATATATGGAAAATGGAAGTCTTGATACATTCTTGCGTGCAAATGATGGAAAATTT
CAAACAATTCAGTTAATTGGTATGCTTAGAGGTATTGCAGCTGGAATGTCATACCTCAGT
GACATGAACTATGTCCATCGTGATTTGGCTGCGCGCAACGTTCTTGTCAATGCATCACTT
ATCTGTAAAATTGCTGACTTTGGTCTTTCACGTGAAATTGAAAATGCCAGTGATGCTTAT
ACAACACGTGGAGGAAAAATCCCAGTGAGATGGACAGCGCCAGAAGCGATTGCATTCCGT
AAATTTACATCAGCCAGTGATGTGTGGTCATATGGTGTTGTTTTATGGGAAGTCATGTCA
TATGGTGAACGTCCTTATTGGAATTGGTCAAATCAAGATGTCATTAAAAGTATCGAAAAA
GGCTATCGTTTGCCTGCACCTATGGACTGTCCTGAAGCTCTCTATCAACTCATGCTTGAC
TGCTGGCAGAAACAACGAACACATCGACCAACATTTGCCAGCATTACACAAACACTCGAC
AATCTAGCACGACAACCACAACTCCTGCTTACGATACGAAATTCACCGACAGGAGATCAA
CAGGGTCCAGATTTCCATCAAACGCCAACTTCATCTTCTTCATCGCATGGTCAACAGCCA
CAATTAATCATGGGTCATACGATGGATAGTAGATGTGGAACAATGGGAGCAACAGCCGAC
ATTGTTTTTAATTCAACTGATCAATGGTTGAGCGATATTAAAATGGGACGATATGCTCAA
CATTTTAAAGAAGCTGGCCTAATAACACCTCAACAGGTTGCACGTCTCACAGCTCAACAA
CTTTCTGACATGGGCATCACACTTGTTGGACATCAAAAGAAAATTCTTCATCAGGCTCGA
CAATTGGATACTAACATTGAAATGGATAATTTTTTGGCAACTCCAACTTCCATGTTTGTA
TGA

>g68.t1 Gene=g68 Length=1080
MSLKRTKKLNSIAPIALLLIIATDICNCDQVVLLDTTKEATLEWTSYPYGPQAQRPGWIE
ESFTNYGKGINWRSYVVCDVAYPDVNNWLWSPFIDRGPANRLYIEIHFTIRDCSLFPGNA
LSCKETFSLLFYEFDAQTREPPPWQPESYKLIGRIAAGEGRFNHNSDVDINVETKSIAVN
KKGVYFAFRDQGACISVLAVKVYYITCPAVTANFAHFNETPTGKEVTVIEKQQGTCVDNA
EPIEQPYNHCKGDGKWTLLLGGCRCKVGYEPDDEKQACKVCPAGTFRSSEVAMCTLCPLN
SKTNKAGSSYCTCVQGHYRHPLDGKHMPCHKPPGAPTNLTVLFFDQTSAILSWNPPQKSS
VDDHLIDQQFRNDVVFRVKCPSCSNNVVFNPSNDVFNETKLTMTNLEPGTQYVVQIHTLN
GPSYSLLGSGYNHSFSSTIEGTESPLKRGNTFDIKSEYTEITFTTESTILSTVFNVKVTT
ITSKEVELTWDNPLHIDSPIEFYEVRWFPKSEVDSLNKTTQSTKETKILINDLSENTEYG
FQIRCKTTSGWGTYSNIVYAQTLQSITPVFNESSIQNRLVAGATVLIVFIVVLAIVATVL
VLRTKNQDDLDKKTSNHLPLPLDYASNEEGGYKYYSSARRNHFAVTTPLFGGNRSYVDPH
TYEDPNQAIREFAREIDAGYITIEAIIGGGEFGDVCRGRLKIPPSFIQEIDVAIKTLKPG
SSEKARCDFLTEASIMGQFDHPNVIYLQGVVTRSNPVMIITEYMENGSLDTFLRANDGKF
QTIQLIGMLRGIAAGMSYLSDMNYVHRDLAARNVLVNASLICKIADFGLSREIENASDAY
TTRGGKIPVRWTAPEAIAFRKFTSASDVWSYGVVLWEVMSYGERPYWNWSNQDVIKSIEK
GYRLPAPMDCPEALYQLMLDCWQKQRTHRPTFASITQTLDNLARQPQLLLTIRNSPTGDQ
QGPDFHQTPTSSSSSHGQQPQLIMGHTMDSRCGTMGATADIVFNSTDQWLSDIKMGRYAQ
HFKEAGLITPQQVARLTAQQLSDMGITLVGHQKKILHQARQLDTNIEMDNFLATPTSMFV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
41 g68.t1 CDD cd10319 EphR_LBD 31 206 2.48239E-77
39 g68.t1 CDD cd00063 FN3 333 425 5.91448E-9
40 g68.t1 CDD cd00063 FN3 475 562 3.94332E-17
38 g68.t1 CDD cd05033 PTKc_EphR 676 942 0.0
27 g68.t1 Gene3D G3DSA:2.60.120.260 - 27 207 1.6E-56
24 g68.t1 Gene3D G3DSA:2.60.40.1770 ephrin a2 ectodomain 208 263 6.4E-20
26 g68.t1 Gene3D G3DSA:2.10.50.10 Tumor Necrosis Factor Receptor 264 332 3.0E-12
23 g68.t1 Gene3D G3DSA:2.60.40.10 Immunoglobulins 333 428 2.5E-12
22 g68.t1 Gene3D G3DSA:2.60.40.10 Immunoglobulins 456 570 2.7E-19
25 g68.t1 Gene3D G3DSA:3.30.200.20 Phosphorylase Kinase; domain 1 655 763 8.1E-38
28 g68.t1 Gene3D G3DSA:1.10.510.10 Transferase(Phosphotransferase) domain 1 764 951 6.9E-58
29 g68.t1 Gene3D G3DSA:1.10.150.50 Transcription Factor 997 1072 5.7E-17
52 g68.t1 MobiDBLite mobidb-lite consensus disorder prediction 959 980 -
7 g68.t1 PANTHER PTHR24416:SF539 EPH RECEPTOR TYROSINE KINASE, ISOFORM C 33 423 2.1E-288
9 g68.t1 PANTHER PTHR24416 TYROSINE-PROTEIN KINASE RECEPTOR 33 423 2.1E-288
8 g68.t1 PANTHER PTHR24416:SF539 EPH RECEPTOR TYROSINE KINASE, ISOFORM C 463 1060 2.1E-288
10 g68.t1 PANTHER PTHR24416 TYROSINE-PROTEIN KINASE RECEPTOR 463 1060 2.1E-288
37 g68.t1 PIRSF PIRSF000666 TyrPK_ephrin_receptor 1 1074 0.0
14 g68.t1 PRINTS PR00109 Tyrosine kinase catalytic domain signature 761 774 6.9E-37
13 g68.t1 PRINTS PR00109 Tyrosine kinase catalytic domain signature 798 816 6.9E-37
15 g68.t1 PRINTS PR00109 Tyrosine kinase catalytic domain signature 847 857 6.9E-37
12 g68.t1 PRINTS PR00109 Tyrosine kinase catalytic domain signature 866 888 6.9E-37
11 g68.t1 PRINTS PR00109 Tyrosine kinase catalytic domain signature 910 932 6.9E-37
1 g68.t1 Pfam PF01404 Ephrin receptor ligand binding domain 31 207 6.1E-50
6 g68.t1 Pfam PF00041 Fibronectin type III domain 335 422 3.8E-9
5 g68.t1 Pfam PF00041 Fibronectin type III domain 472 555 2.2E-12
2 g68.t1 Pfam PF14575 Ephrin type-A receptor 2 transmembrane domain 582 678 5.7E-19
3 g68.t1 Pfam PF07714 Protein tyrosine and serine/threonine kinase 682 939 1.8E-97
4 g68.t1 Pfam PF00536 SAM domain (Sterile alpha motif) 1004 1062 1.4E-16
32 g68.t1 Phobius SIGNAL_PEPTIDE Signal peptide region 1 28 -
33 g68.t1 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 11 -
34 g68.t1 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 12 23 -
36 g68.t1 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 24 28 -
31 g68.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 29 578 -
35 g68.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 579 602 -
30 g68.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 603 1080 -
49 g68.t1 ProSitePatterns PS00790 Receptor tyrosine kinase class V signature 1. 188 208 -
51 g68.t1 ProSitePatterns PS00107 Protein kinases ATP-binding region signature. 687 715 -
50 g68.t1 ProSitePatterns PS00109 Tyrosine protein kinases specific active-site signature. 804 816 -
56 g68.t1 ProSiteProfiles PS51550 Eph receptor ligand-binding domain profile. 29 212 49.802
53 g68.t1 ProSiteProfiles PS50853 Fibronectin type-III domain profile. 335 445 13.397
54 g68.t1 ProSiteProfiles PS50853 Fibronectin type-III domain profile. 472 565 19.953
57 g68.t1 ProSiteProfiles PS50011 Protein kinase domain profile. 681 948 37.262
55 g68.t1 ProSiteProfiles PS50105 SAM domain profile. 1001 1065 16.106
45 g68.t1 SMART SM00615 eph 30 207 3.0E-76
47 g68.t1 SMART SM01411 GCC2_GCC3_2 268 311 2.7E-5
43 g68.t1 SMART SM00060 FN3_2 333 425 1.1E-9
44 g68.t1 SMART SM00060 FN3_2 470 552 5.6E-8
46 g68.t1 SMART SM00219 tyrkin_6 681 939 7.4E-134
48 g68.t1 SMART SM00454 SAM_4 998 1065 4.2E-14
16 g68.t1 SUPERFAMILY SSF49785 Galactose-binding domain-like 31 205 3.53E-47
19 g68.t1 SUPERFAMILY SSF57184 Growth factor receptor domain 257 391 2.16E-5
18 g68.t1 SUPERFAMILY SSF49265 Fibronectin type III 332 565 5.61E-28
20 g68.t1 SUPERFAMILY SSF56112 Protein kinase-like (PK-like) 673 958 6.79E-80
17 g68.t1 SUPERFAMILY SSF47769 SAM/Pointed domain 1002 1062 2.55E-15
21 g68.t1 SignalP_EUK SignalP-noTM SignalP-noTM 1 28 -
42 g68.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 580 602 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005524 ATP binding MF
GO:0006468 protein phosphorylation BP
GO:0004713 protein tyrosine kinase activity MF
GO:0007169 transmembrane receptor protein tyrosine kinase signaling pathway BP
GO:0005515 protein binding MF
GO:0005887 integral component of plasma membrane CC
GO:0004672 protein kinase activity MF
GO:0016021 integral component of membrane CC
GO:0005003 ephrin receptor activity 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