Gene loci information

Transcript annotation

  • This transcript has been annotated as Tyrosine kinase receptor Cad96Ca.

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
HiC_scaffold_385 g17832 g17832.t1 isoform g17832.t1 22843 24405
HiC_scaffold_385 g17832 g17832.t1 exon g17832.t1.exon1 22843 23127
HiC_scaffold_385 g17832 g17832.t1 cds g17832.t1.CDS1 22843 23127
HiC_scaffold_385 g17832 g17832.t1 exon g17832.t1.exon2 23365 24405
HiC_scaffold_385 g17832 g17832.t1 cds g17832.t1.CDS2 23365 24405
HiC_scaffold_385 g17832 g17832.t1 TSS g17832.t1 NA NA
HiC_scaffold_385 g17832 g17832.t1 TTS g17832.t1 NA NA

Sequences

>g17832.t1 Gene=g17832 Length=1326
ATGAGACAAATTCACACTTTAGTATTTATTTTGTTGCTTCTTGCAACAAAATTCTCACGA
GGTTCCGGTCCAGGGACAATTTCAGTTGATAGAAACTGGAGTGTTCCGGAATCAACGAAA
ATTGGACAAATTGTAAAGACTGTGAGGGTCACTGGTGTTGGAAATCGAAGTGTTAGCTAT
TCTTTAGAGACTGACGACACGCTGGGCTTTGGAAATTTTGAAAGTCCATTTTGGATTAAT
CCAAGCACTGGATATGTTTATTTGAATAAAAGTCTTGAAGGATGGAAATCACCAAATCCC
TTCATTTTATCAGTAGCAGCAGATGATGGAAATATTCCAGTAAAAAACCAAGTTCTTGTT
CGAATAATTCCATCAAATGGTCAACAAAATTATCCAAATAGTTTTGAGCCACCATCAAGA
ATTCCATCATTGCCTGATTTTACATCACTTCCATTACCACCAATTCCACCACCATATCAG
ACAACAACAAAAGTCATAACAAAACAACCTAAAATTCGACAAAATAAAACTTATATCGAT
GAAACTACAACCACAACAACAACATCAACGACAATCATCACAACAACAGAGGCTGCAAAG
ACAAAAAATGCCGGCATAAGTCAGCAAACTGCTCTTGTTACAATTCTCATTGCAATTATT
ACAATTTTCCTCATTGCTGCACTTATTGCTATGATAATTTTCCGTAAGCAATTAATGCGA
CCATTTAGTCGAAAATTCAAGAAAAGTAAAGTTGATAAAGCCAAAAAGAGCAACCAAAGT
ATTCAAATTATTACATTATCAAATGAAAGCAGTCGAAATTCAATGGTCATGCAGCACTGG
CAAGGACCATTGGCATACAACAATCGTTATACACCATGGGCTCATGATGACATTCATGGT
CAAATTTCAAATTCAAGTTTCACTTATAGTAGTGGAAATGACATAAAAGTACCAGGTTAT
GACCGTTGGGAATTTCCGCGTCATCGACTGAAGGTTTTTAATATTCTCGGTGAAGGAGCT
TTTGGTCAAGTTTGGCGATGTGAAGCTGCTGATATTGATGGTGTTGAAGGAACTTCAATT
GTAGCATTAAAAACATTGAAAGAAAATGCAACAGAAAGCGAAAAAAAAGATCTCATTTCA
GAACTTCAAGTAATGAAAACACTTGAGCCGCACATCAATGTTGTTCGACTTCTTGGTTGT
TGCACTGAAAAAGATCCAATTTTTGTGATAATCGAATATGTTGCATTAGGAAAATTACAA
ACATTCTTAAGAAATTCAAGAGTTGAAAAAATTATCATAATGCAAGTGGAAAGTCAAAAA
CTTTAA

>g17832.t1 Gene=g17832 Length=441
MRQIHTLVFILLLLATKFSRGSGPGTISVDRNWSVPESTKIGQIVKTVRVTGVGNRSVSY
SLETDDTLGFGNFESPFWINPSTGYVYLNKSLEGWKSPNPFILSVAADDGNIPVKNQVLV
RIIPSNGQQNYPNSFEPPSRIPSLPDFTSLPLPPIPPPYQTTTKVITKQPKIRQNKTYID
ETTTTTTTSTTIITTTEAAKTKNAGISQQTALVTILIAIITIFLIAALIAMIIFRKQLMR
PFSRKFKKSKVDKAKKSNQSIQIITLSNESSRNSMVMQHWQGPLAYNNRYTPWAHDDIHG
QISNSSFTYSSGNDIKVPGYDRWEFPRHRLKVFNILGEGAFGQVWRCEAADIDGVEGTSI
VALKTLKENATESEKKDLISELQVMKTLEPHINVVRLLGCCTEKDPIFVIIEYVALGKLQ
TFLRNSRVEKIIIMQVESQKL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g17832.t1 CDD cd11304 Cadherin_repeat 34 126 6.77467E-10
8 g17832.t1 Gene3D G3DSA:2.60.40.60 Cadherins 26 123 1.7E-8
7 g17832.t1 Gene3D G3DSA:3.30.200.20 Phosphorylase Kinase; domain 1 286 413 1.8E-37
2 g17832.t1 PANTHER PTHR24416:SF537 TYROSINE KINASE RECEPTOR CAD96CA 146 430 2.7E-88
3 g17832.t1 PANTHER PTHR24416 TYROSINE-PROTEIN KINASE RECEPTOR 146 430 2.7E-88
1 g17832.t1 Pfam PF07714 Protein tyrosine and serine/threonine kinase 332 430 2.6E-24
11 g17832.t1 Phobius SIGNAL_PEPTIDE Signal peptide region 1 21 -
12 g17832.t1 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 5 -
13 g17832.t1 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 6 16 -
15 g17832.t1 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 17 21 -
10 g17832.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 22 210 -
14 g17832.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 211 234 -
9 g17832.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 235 441 -
18 g17832.t1 ProSitePatterns PS00107 Protein kinases ATP-binding region signature. 336 364 -
20 g17832.t1 ProSiteProfiles PS50268 Cadherins domain profile. 34 147 10.024
21 g17832.t1 ProSiteProfiles PS50011 Protein kinase domain profile. 330 441 16.499
19 g17832.t1 SMART SM00219 tyrkin_6 330 441 7.8E-4
4 g17832.t1 SUPERFAMILY SSF49313 Cadherin-like 32 122 1.27E-7
5 g17832.t1 SUPERFAMILY SSF56112 Protein kinase-like (PK-like) 306 428 2.53E-24
6 g17832.t1 SignalP_EUK SignalP-noTM SignalP-noTM 1 21 -
17 g17832.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 212 234 -

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:0016020 membrane CC
GO:0004713 protein tyrosine kinase activity MF
GO:0005524 ATP binding MF
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules BP
GO:0005509 calcium ion binding MF
GO:0004672 protein kinase activity MF
GO:0006468 protein phosphorylation BP

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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