Gene loci information

Transcript annotation

  • This transcript has been annotated as Catenin alpha.

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 g3109 g3109.t1 TSS g3109.t1 22855445 22855445
chr_3 g3109 g3109.t1 isoform g3109.t1 22855709 22859490
chr_3 g3109 g3109.t1 exon g3109.t1.exon1 22855709 22855749
chr_3 g3109 g3109.t1 cds g3109.t1.CDS1 22855709 22855749
chr_3 g3109 g3109.t1 exon g3109.t1.exon2 22855809 22855921
chr_3 g3109 g3109.t1 cds g3109.t1.CDS2 22855809 22855921
chr_3 g3109 g3109.t1 exon g3109.t1.exon3 22856121 22857856
chr_3 g3109 g3109.t1 cds g3109.t1.CDS3 22856121 22857856
chr_3 g3109 g3109.t1 exon g3109.t1.exon4 22858202 22858274
chr_3 g3109 g3109.t1 cds g3109.t1.CDS4 22858202 22858274
chr_3 g3109 g3109.t1 exon g3109.t1.exon5 22858383 22858450
chr_3 g3109 g3109.t1 cds g3109.t1.CDS5 22858383 22858450
chr_3 g3109 g3109.t1 exon g3109.t1.exon6 22858646 22859068
chr_3 g3109 g3109.t1 cds g3109.t1.CDS6 22858646 22859068
chr_3 g3109 g3109.t1 exon g3109.t1.exon7 22859132 22859248
chr_3 g3109 g3109.t1 cds g3109.t1.CDS7 22859132 22859248
chr_3 g3109 g3109.t1 exon g3109.t1.exon8 22859326 22859490
chr_3 g3109 g3109.t1 cds g3109.t1.CDS8 22859326 22859490
chr_3 g3109 g3109.t1 TTS g3109.t1 22860146 22860146

Sequences

>g3109.t1 Gene=g3109 Length=2736
ATGGAAAATAACGCATTAATGGGCTCAATTGCAGCCCGATGGGATCCAAAGAATCTTGAA
ATTCGTACAATGTCAGTTGAAAAGACTCTTGAGCCATTAGTACTTCAAGTTACAACACTT
GTCAACAGCAAATCAACAACTAAGAAAAAGAAAGGTAAATCCAAACGTGCTTCAGCTCTT
GTTGCGGCTGTTGAAAAAGCAACAGAAAATTTTATTGAAAGAGGAGAACAAATTGCCTAT
GAGAATCCAGACATAACTCAAGAAATGTTGACAGCAGTTGAAGAAGTTCGCAAAACTGGA
CTTTCAATGAGCACTGCTGCTCGTGAGTTTAGTGAAGATCCATGCAGTTCATTGAAGCGT
GGAAATATGGTGCGAGCAGCTAGAAATTTACTTTCAGCTGTCACACGCTTGTTGATTCTT
GCTGACATGGTTGATGTTCATCTTTTACTCAAATCACTTCATGTTGTTGAGGATGATTTA
GATAAACTTCGTGATGCATCAAGTCAAGATGAATTAATCTCAAATATGCGTCAATTCGGT
CGCAACGCTAATGAACTTATTAAACAAGCAGCTAAACGTCAACATGAATTAAAAGATCCG
CAATTGCGTGATGATTTAGCAGCAGCTCGTGCTATTCTTAAGAAACACTCAACAATGCTT
TTGACAGCATCAAAAGTTTATGTTCGTCATCCAGAACTTGATTTGGCTAAAATCAATCGA
GATTATGTTTTGAAGCAAGTTTGTGAAGCTGTCAATACAATCAGTGATGTAGCACAAGGA
AAAGCTTCAACACCACAAGATACATTCAATGGTGCAGGTGAACTTGCTGCCGCTCTTGAT
GACTTTGATGAAGGAATAATTATGGATCCATTGGTCTATAATGAAGTTCGTTCGAGACCA
TCATTGGAAGAACGTTTGGAAAGCATTATAAGTGCTGCTGCGTTGATGGCTGATGCTGAT
TGCACTCGTGATGAGCGTCGTGAAAGAATCGTTGCTGAATGTAATGCTGTACGTCAAGCA
TTGCAAGATCTATTGTCTGAATACATGTCTAATATGGGTACAAAAGATCGTACTCCAGAA
CTTGAGCGTGCAATTGGACAAATGTATCGTAAAACCAAGGACTTACGTCGTCAATTGAGA
AAGGCCGTTGTTGATCATGTTTCTGACTCATTTTTGGAAACAAATATGCCATTGTTGGAT
TTAATCGAGGCCGCACGCTCTGGACAAGAAAAGAAAGTTCACGAACGTGCTGAAGTTTTC
ACAAAACATGCTGAAAAATTAGTTGAAGTTGCTAATTTGGTCTGCAGTATGTCAAATAAT
GAAGATGGTGTCAAAATGGTTCGCTATGCAGCAGCACAAATTGAAACTTTATGCCCTCAA
GTCATCAATGCTGCTCTCATTCTTGCTGCTCGTCCAAATTCAAAAGTAGCACAAGAAAAT
ATGGATTCATATAGACAAGCATGGGAAAATCAAGTTCGAATTTTGACTGAAGCTGTTGAT
GACATAACAACAATTGATGATTTCCTTGCTGTCTCTGAAAATCACATTCTTGAAGATGTC
AACAAATGTGTGCTTGCATTGCAAGAGGGTGATGCTTTGGATCTTCGTAATACTGCTGGT
GCAATTCAAGGTAGATCAGCACGTGTCTGTCATGTTGTTGAAGCTGAAATGGACAATTAT
GAGCCATGCATTTATACCAAGCGTGTACTCGAAGCTGTCAAAGTATTGCGTGATCAAGTC
ATGTCAAAATTCGCACAACGAGTCGATGTTGCTGTAAATGCGCTGTCAAGCAACTCACCC
AAGGATGTCGATGAAAATGATTTTATTGACGCATCTCGATTAGTCTATGATGGTGTACGT
GAAATAAGACGTGCTGTTCTAATGAATCGCAGCTCAGAAGAATTGGATACAGACACAGAG
TTTGAGCCAGTAGAAGATATGACAATTGAAACACGTAGTCGTTCAAGCGCTCATACAGGC
GATCAAACAATTGATGAATATCCTGATATTAGTGGAATTACAACAGCAAGAGAAGCGATG
CGCAAGATGAATGAGGAAGACAAGCAAAAGATTATGCAACAAGTCGAGTTATTCCGTAGA
GAAAAACTCACATTCGATTCAGAAGTTGCTAAATGGGACGACACTGGCAATGATATCATC
TATCTTGCTAAACATATGTGTATGATTATGATGGAAATGACTGATTTCACACGTGGTCGT
GGTCCATTAAAGACAACTATGGATGTCATCAATGCAGCTAAGAAAATTTCAGAAGCTGGA
ACAAAACTTGATAAATTAACTCGCGAAATTGCTGATCAATGTCCTGAAAGTTCTACAAAG
AAAGATCTTTTGGCCTACATTCAACGAATCGTTCTCTATTGTCATCAAATTCAAATTACG
TCGAAGGTCAAAGCTGATGTGCAAAATATTTCTGGTGAATTGATTGTTTCTGGGCTCGAC
AGTGCAACATCCTTGATTCAAGCTGCCAAAAATTTAATGAATGCTGTCGTTTATACGGTA
AAATATTCCTATGTAGCATCAACTAAATACACCAGACAAGGAACAGTTTCGTCACCAATA
GTTGTATGGAAGATGAAAGCACCAGAAAAGAAACCACTTGTAAGGCCTGAAAAACCTGAA
GAAGTTCGTGCAAAAGTCAGACGAGCATCACAGAAAAAGACACAAAATCCAGTGCACGCC
CTTTCGGAATTTCAGAGCCCTGCCGACAACATTTAA

>g3109.t1 Gene=g3109 Length=911
MENNALMGSIAARWDPKNLEIRTMSVEKTLEPLVLQVTTLVNSKSTTKKKKGKSKRASAL
VAAVEKATENFIERGEQIAYENPDITQEMLTAVEEVRKTGLSMSTAAREFSEDPCSSLKR
GNMVRAARNLLSAVTRLLILADMVDVHLLLKSLHVVEDDLDKLRDASSQDELISNMRQFG
RNANELIKQAAKRQHELKDPQLRDDLAAARAILKKHSTMLLTASKVYVRHPELDLAKINR
DYVLKQVCEAVNTISDVAQGKASTPQDTFNGAGELAAALDDFDEGIIMDPLVYNEVRSRP
SLEERLESIISAAALMADADCTRDERRERIVAECNAVRQALQDLLSEYMSNMGTKDRTPE
LERAIGQMYRKTKDLRRQLRKAVVDHVSDSFLETNMPLLDLIEAARSGQEKKVHERAEVF
TKHAEKLVEVANLVCSMSNNEDGVKMVRYAAAQIETLCPQVINAALILAARPNSKVAQEN
MDSYRQAWENQVRILTEAVDDITTIDDFLAVSENHILEDVNKCVLALQEGDALDLRNTAG
AIQGRSARVCHVVEAEMDNYEPCIYTKRVLEAVKVLRDQVMSKFAQRVDVAVNALSSNSP
KDVDENDFIDASRLVYDGVREIRRAVLMNRSSEELDTDTEFEPVEDMTIETRSRSSAHTG
DQTIDEYPDISGITTAREAMRKMNEEDKQKIMQQVELFRREKLTFDSEVAKWDDTGNDII
YLAKHMCMIMMEMTDFTRGRGPLKTTMDVINAAKKISEAGTKLDKLTREIADQCPESSTK
KDLLAYIQRIVLYCHQIQITSKVKADVQNISGELIVSGLDSATSLIQAAKNLMNAVVYTV
KYSYVASTKYTRQGTVSSPIVVWKMKAPEKKPLVRPEKPEEVRAKVRRASQKKTQNPVHA
LSEFQSPADNI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
23 g3109.t1 Gene3D G3DSA:1.20.120.230 - 20 147 2.2E-49
26 g3109.t1 Gene3D G3DSA:1.20.120.230 - 148 266 1.1E-45
22 g3109.t1 Gene3D G3DSA:1.20.120.810 - 295 503 1.0E-63
25 g3109.t1 Gene3D G3DSA:1.20.120.230 - 504 629 4.0E-52
24 g3109.t1 Gene3D G3DSA:1.20.120.230 - 671 866 9.3E-79
19 g3109.t1 MobiDBLite mobidb-lite consensus disorder prediction 871 888 -
20 g3109.t1 MobiDBLite mobidb-lite consensus disorder prediction 871 911 -
21 g3109.t1 MobiDBLite mobidb-lite consensus disorder prediction 891 911 -
3 g3109.t1 PANTHER PTHR18914:SF9 CATENIN ALPHA 10 908 0.0
4 g3109.t1 PANTHER PTHR18914 ALPHA CATENIN 10 908 0.0
13 g3109.t1 PRINTS PR00805 Alpha-catenin signature 13 37 5.7E-129
6 g3109.t1 PRINTS PR00805 Alpha-catenin signature 109 127 5.7E-129
10 g3109.t1 PRINTS PR00805 Alpha-catenin signature 128 146 5.7E-129
14 g3109.t1 PRINTS PR00805 Alpha-catenin signature 302 326 5.7E-129
11 g3109.t1 PRINTS PR00805 Alpha-catenin signature 370 390 5.7E-129
7 g3109.t1 PRINTS PR00805 Alpha-catenin signature 491 515 5.7E-129
12 g3109.t1 PRINTS PR00805 Alpha-catenin signature 606 630 5.7E-129
5 g3109.t1 PRINTS PR00805 Alpha-catenin signature 718 740 5.7E-129
8 g3109.t1 PRINTS PR00805 Alpha-catenin signature 782 806 5.7E-129
9 g3109.t1 PRINTS PR00805 Alpha-catenin signature 859 877 5.7E-129
2 g3109.t1 Pfam PF01044 Vinculin family 20 344 1.4E-93
1 g3109.t1 Pfam PF01044 Vinculin family 335 871 5.2E-210
18 g3109.t1 SUPERFAMILY SSF47220 alpha-catenin/vinculin-like 57 259 2.67E-63
17 g3109.t1 SUPERFAMILY SSF47220 alpha-catenin/vinculin-like 374 503 3.51E-44
15 g3109.t1 SUPERFAMILY SSF47220 alpha-catenin/vinculin-like 505 628 5.76E-54
16 g3109.t1 SUPERFAMILY SSF47220 alpha-catenin/vinculin-like 685 866 1.26E-52

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:0051015 actin filament binding MF
GO:0007155 cell adhesion BP
GO:0045296 cadherin 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