Gene loci information

Transcript annotation

  • This transcript has been annotated as Afadin.

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 g2402 g2402.t1 isoform g2402.t1 17656888 17674280
chr_3 g2402 g2402.t1 exon g2402.t1.exon1 17656888 17657298
chr_3 g2402 g2402.t1 cds g2402.t1.CDS1 17656888 17657298
chr_3 g2402 g2402.t1 exon g2402.t1.exon2 17657356 17657497
chr_3 g2402 g2402.t1 cds g2402.t1.CDS2 17657356 17657497
chr_3 g2402 g2402.t1 exon g2402.t1.exon3 17657562 17657845
chr_3 g2402 g2402.t1 cds g2402.t1.CDS3 17657562 17657845
chr_3 g2402 g2402.t1 exon g2402.t1.exon4 17657912 17657993
chr_3 g2402 g2402.t1 cds g2402.t1.CDS4 17657912 17657993
chr_3 g2402 g2402.t1 exon g2402.t1.exon5 17666758 17667107
chr_3 g2402 g2402.t1 cds g2402.t1.CDS5 17666758 17667107
chr_3 g2402 g2402.t1 exon g2402.t1.exon6 17667652 17667773
chr_3 g2402 g2402.t1 cds g2402.t1.CDS6 17667652 17667773
chr_3 g2402 g2402.t1 exon g2402.t1.exon7 17669736 17670017
chr_3 g2402 g2402.t1 cds g2402.t1.CDS7 17669736 17670017
chr_3 g2402 g2402.t1 exon g2402.t1.exon8 17670253 17670928
chr_3 g2402 g2402.t1 cds g2402.t1.CDS8 17670253 17670928
chr_3 g2402 g2402.t1 exon g2402.t1.exon9 17671030 17671554
chr_3 g2402 g2402.t1 cds g2402.t1.CDS9 17671030 17671554
chr_3 g2402 g2402.t1 exon g2402.t1.exon10 17671629 17671748
chr_3 g2402 g2402.t1 cds g2402.t1.CDS10 17671629 17671748
chr_3 g2402 g2402.t1 exon g2402.t1.exon11 17671832 17672018
chr_3 g2402 g2402.t1 cds g2402.t1.CDS11 17671832 17672018
chr_3 g2402 g2402.t1 exon g2402.t1.exon12 17672074 17672133
chr_3 g2402 g2402.t1 cds g2402.t1.CDS12 17672074 17672133
chr_3 g2402 g2402.t1 exon g2402.t1.exon13 17672494 17674280
chr_3 g2402 g2402.t1 cds g2402.t1.CDS13 17672494 17674280
chr_3 g2402 g2402.t1 TSS g2402.t1 NA NA
chr_3 g2402 g2402.t1 TTS g2402.t1 NA NA

Sequences

>g2402.t1 Gene=g2402 Length=5028
ATGTCATTGAACGAAAAACGAATGCTGGATCGCGAAGCATTGCGTTCAGTAATTCAGCAA
TGGAATGCAAATCGACTAGATTTATTTGAATTGTCAGAGCCAAGTGAAAATCTTGAATTC
CATGGCGTAATGCGTTTCTATTTTCAAGATGTTGGTCAGAAAGTCGCTACCAAATGTATA
CGCGTGCAATCTGATGCAACAGTTGCCGATGTGATCGAGACATTAATCGAAAAATTCCGT
CCTGATATGCGCATGTTATCCGTCCCAAATTATGCACTTTATGAAGTGCATGCAAATGGT
GAGGAAAGAAAATTAAATCCAGATGAAAAGCCATTGCTTGTGCAGCTCAATTGGCACGTC
GATGACCGCGAAGGAAGGTTTTTATTGAAAGATCTCGATCAAAAACCAACTACATTAGAC
AACACAGACACAAACTTTAAACGAAAATTATCGAAACGTGAAAAGAAGGAGCAAAAGAAG
AAGGAAAAATTGCAAAAACTCAACTCAAATGCTGACGAGTCAGAAAACCATGTTGCTGAA
AAATTGTATACCGAGCTTCCAGAAACATCGTTTACGCGCTCAATATCAAATCCAGAAGCA
GTCATGCGACGAAGAAGACAGCAAAAACTTGAGAAGAAATTGCAACAATTTAGATCAAGA
GATGGAGGGCCTGATACGGGTGGAACGTTAAAAATTTATGGTGAAAGTCTCTGCCGCGAT
GTGCCTTATAAAACACTACTGCTGTCAATACGTGATTGCGCACAAGCAGTTGTTAGAGAA
ATGTTGGCAAAATATGGTATGGACAAAGCTGATCCACTACATTATTGTCTTGTGCAGGTT
AATAGTGATGGCTCCGAATATATTCTTGATGATGATGAATGTCCATTATCAATACTAATG
AATCATCCGACGTCTAGAGGATCCATCATGTTCCACGTTCGTCGGCGTCCAGCTGATTCA
CAGCCGCGACGTAGGAAGAAAAAACCATTGGGTATTAGTAATGGTGGCAACATGACAACA
GAACGCGAAGGACCAATGCTCATTGAAATTACACACGCGGGCGATGGTGGTCGAAGGGTT
AAATTGACGACGGAACCTATTGAGGTTGGTTCTGCAAATACAAATGCTCTACAGTTGTTT
GGACCGTCAATTCAACCTCGCCACTGTCTTATATCGCTGCATGAAGGTGTTTGTACTGTA
ACACCGCTTCATGCTGATGGTTTGACGTTTGTTAATGGACATCATATTACGCAGCCAACA
ATTTTGCATAACGGTTCCGTTGTGATGTTTGGACGTGCTGCATCATATCGTTTTATCGAT
ATACCAACTGATGGCCGCTACAACTTGGCATTATCACAATCGCAATTAGATTCAGCTTAT
CTTTATGAGAATCGTTCGTCGACAAATCCACCATCATGGCATGAGGAAGAAGATACTAGT
ATAACTAGCTCCAATTACACGAAAAAGCAACAAGGTTTTCCACAAAAAGGAATGCAATCG
GCACCGCAACAACAGCCGACACAATCACAACAACAACAGCACAGTCCAGGAAGCAATGAA
CTAAAATTAAGCACCGCACAGCAATCAAGCGATGATAAGTCACTGTTCGATAATGATGCC
GGCAATCTTGAAAACGAAACAAAATCTGTGTCGAGTATGAGGAGTCAGGACAGTCGTTCA
CAATCATTTGCAAAGCAGCCAGCAGGAATGTCTGCTGCAACACCAACAATGGAACCACAA
GGACAGGAGGCGATTTTACCGGCAGTTCTTGAGTTTCCCGAGCATAGCCAGGAACAATTT
TTAAAAGCTGTCATTACTGATCTCGATGTGAATGCTCCAAATTTTAAACTCGCGCCCGTT
TATACACTTTATTTGTGTGCGCGATATCGTGCCTCAACACATTACCGTCCCGACCTGCAG
CCAACTGAACGTGCTCACAAATTGACTGTTTTTCTTCACCATGTGGCAAATCTTATTCAT
AACATCATTCAAGAGAAATATAACGATCCAAAAATTCTCTCATTTTGGATGGCCAACAGC
AGCGAATTTTTGCATTTCCTAAAATCTGACCGACATATTTCGGCTTTCAGTGTGCAAGCA
CAGGAAGTATTAGCCGAATGTGTACAAGCAGCTTTTCAAAATCTCGTATCGATTTTCCAT
TCAGAATTATCACAAACACTCAATCAATTTCTGTCGGAAAATATTGACCATGATTCGGCC
GCTGGACTTGTGCTTTCAGTTCTTGGATCTGCGATGGCATTGCTGAGGAGATGCCGTGTA
AATGCAGCACTCACTATTCAGCTATTTTCGCAATTGTTCCATTATATAAATGTTGTTTGT
TTCAATAAGTTTGTCACAACATCACATTTATGTACGAATGTATGGGGAAAAGCATTAAGT
GATAGACTAGCATTGCTAGAATTGTGGGCAGAAAAACAAGGACTTGAGCTTGCAGCTGAT
TGTCATCTAGCCAAAATCAACCAGTGTGCCGAGTTTTTACAAGCACCAAAAACATCAGTC
ACAGAAGTTCAACAACTTGCATGCTCATGTTTCCGACTAAATTCACTGCAAATGGCAGCT
CTACTTTCACAAGAAACAATTCCAAGAGCTTTAATTGATGCTACAGTCAGAATGGCTGAG
TCAGTTGCTGATGAATTGACACGCGCCGATGGTCGTGAAATTAGATTGGAAGAGTCTCCG
GACTTGCCATTAGCTTTGCTTTTGCCGGTCGATGGCTTCAGTTGTGATGTCGTGCGTGGA
ATCCCTGCTGGTCTTGTTGATTTTCTCGCTCCATTCCAGTCGGCAGGATACTGTCGTCTA
GCATCGCAACCAACAAGTATTGGCTTATGGACAGTTTATATGCATCAATTTAATGGTCGC
TCACCAAGCGTTTTATCATCAAAAATGCCACAACCGGAAGTGCAAACAATCAAACTTCAT
AAAAACACAAACGGCATGGGTCTTTCTATTGTTGCTGCCAAGGGTGCAGGTCAAGAACGT
TTGGGAATTTATATTAAATCTGTTGTTGCTGGAGGAGCAGCTGACGCAGATGGAAGACTT
CAAGCTGGTGATCAATTACTAAGAGTTGATGGTCAAAGCTTAATTGGAATTACACAAGAA
CGTGCAGCAGATTATTTAGTCAGAACTGGACCAATTGTTACATTAGAAGTTGCTAAACAA
GGTGCCATTTTTCATGGTTTGGCGACACTTTTACAACAACCAAGTCCAGTCATTCAAAGA
GATGAAAATTTGTATCGTTCTGATTCGGATGAAAGCATACGTAGATATCGTTTAGGTCAC
GTTCCAATTCATCAACAACATCTAATACCGCGTCCCCAAAGTACCTTATCGCTCAATCAA
TTAACGTACAGACGCAGTTCCAATCCAGACATTTATCCAGGTGCACGGCGCTTTAGCACC
TCATATTCTGACGAGGACATTCTCTCAAACGACCAATTAGATCAGATACATTTTGATCCT
CGTTATCGTGACTATCGTTCAGCCTCTAGTCTTAATAATTCAAATTATCGTACGCGTAGC
AATAGTTTGCATTCGATGCATAGTGGAGGTAGCAATATTGGTATGAGTGCCCTTATGCCT
CAATATCAACCCTTTCGTCGTGTCTCGAGCACATCTCCGCCGCTTATTTCTGTTCCATTG
ATGCCTCAGAAGCGTTGGAATACGAATCCTTCTATATTCATTGAAGAATATTGTGATGAT
GAGCATAAAACGGAATCAGTCAAGAGTGAGGTTGAAGAAACAAGAAATACTTCGAAAGAG
ACCCTATGTACAAGTAATGAATCATTGCAAACGCCAGCATTGAGTGTTTATGACATAAAA
TCTTTCGGTGATCTTAGCCAAATTCCATTTATTGACGATGATTCTAATGACTCGGCGCCC
TGTCGTGTACTCAGTGATACTGAAATTTGCCACAAGGATGATAAAAAACGTGATACATGC
CGTAAGACTGTGAGTTTTGACGTGATAAAAACAGGCACTGCACAGCAGCATCTATACAGT
CGCAGCTCGAGTCATGGTAAAAATTTCCCCCCAATTTCCTCCCTTCATACTAAGACATTT
AATGACACTGATCCCAAAAAATTGTTTCATGCTGGCATCAGAGCAATGAGCGATATACGA
ACATCGAAAGACGGCTATGTAGATAGAGTGCGCTCAGTTTCTATCAAACCATCATCAGCA
TCACTTTCATCACTTCATTATCGCGAGACAAACGATCACTGCATACTTGTTGATAAGCTT
ATTCAAATGAGACGAGAAGAAAAAGAGGAACGGCATTGTGCCAAAACTTGTAAGCTAAAT
AACTACAAAATTAAATGGGATGAAATCAAGGGTAATGAAAGTACAAAGAATGACGATTCG
ATTATTCGTTCTGGCAAAGTGAAAGCATTAACAACATTTTTCAATACACTGCCATATATA
ACAAATGATTGCACTTGTCCCAAAAGCTCAATTCATCATTCAACGCCAGATTTAAGAGAT
GGTGGTGATAAATTGACTGATGAAGAAATGACGTGCGTGAAAAAACAATTGAAAGAATGG
AGCGAATACAGATTACCATCAAAGGAGAAACTTGTATGCACTTTCATGAAAAGAGCCAAT
TCTTCACCTGTAATATGCTTGGAAAATGAAGCATATAGTGATTGCAATCGCTATCACGAT
GTTTTAAATCGGTTGGATAAAGTGCACAAGCAAAAGCACTGCAATAACCATCGTCACCAC
CATCATCATCATCAATGTGAGAATCCTTGCTTGCCAGACTGCTTTATACTACGTAAAAAA
CTCCATTGCCATCCCTCATGCAATAACATCGAAAACATTCCAATAGAAGTCAAGGCTACA
ACTGACTTGACTGAAGTTACACCCTTTAAATCAGAGAAACATCGATGTAGATCTGCATGT
TTCAATATCAAGGACCCAGCAAAGAAAAGAAAAAAGAAATTGATGAAAATCAAGGCAATG
CAACAACAAAAGAATTTAGAGGATGACAACGAGAGTCTCATAATCTGA

>g2402.t1 Gene=g2402 Length=1675
MSLNEKRMLDREALRSVIQQWNANRLDLFELSEPSENLEFHGVMRFYFQDVGQKVATKCI
RVQSDATVADVIETLIEKFRPDMRMLSVPNYALYEVHANGEERKLNPDEKPLLVQLNWHV
DDREGRFLLKDLDQKPTTLDNTDTNFKRKLSKREKKEQKKKEKLQKLNSNADESENHVAE
KLYTELPETSFTRSISNPEAVMRRRRQQKLEKKLQQFRSRDGGPDTGGTLKIYGESLCRD
VPYKTLLLSIRDCAQAVVREMLAKYGMDKADPLHYCLVQVNSDGSEYILDDDECPLSILM
NHPTSRGSIMFHVRRRPADSQPRRRKKKPLGISNGGNMTTEREGPMLIEITHAGDGGRRV
KLTTEPIEVGSANTNALQLFGPSIQPRHCLISLHEGVCTVTPLHADGLTFVNGHHITQPT
ILHNGSVVMFGRAASYRFIDIPTDGRYNLALSQSQLDSAYLYENRSSTNPPSWHEEEDTS
ITSSNYTKKQQGFPQKGMQSAPQQQPTQSQQQQHSPGSNELKLSTAQQSSDDKSLFDNDA
GNLENETKSVSSMRSQDSRSQSFAKQPAGMSAATPTMEPQGQEAILPAVLEFPEHSQEQF
LKAVITDLDVNAPNFKLAPVYTLYLCARYRASTHYRPDLQPTERAHKLTVFLHHVANLIH
NIIQEKYNDPKILSFWMANSSEFLHFLKSDRHISAFSVQAQEVLAECVQAAFQNLVSIFH
SELSQTLNQFLSENIDHDSAAGLVLSVLGSAMALLRRCRVNAALTIQLFSQLFHYINVVC
FNKFVTTSHLCTNVWGKALSDRLALLELWAEKQGLELAADCHLAKINQCAEFLQAPKTSV
TEVQQLACSCFRLNSLQMAALLSQETIPRALIDATVRMAESVADELTRADGREIRLEESP
DLPLALLLPVDGFSCDVVRGIPAGLVDFLAPFQSAGYCRLASQPTSIGLWTVYMHQFNGR
SPSVLSSKMPQPEVQTIKLHKNTNGMGLSIVAAKGAGQERLGIYIKSVVAGGAADADGRL
QAGDQLLRVDGQSLIGITQERAADYLVRTGPIVTLEVAKQGAIFHGLATLLQQPSPVIQR
DENLYRSDSDESIRRYRLGHVPIHQQHLIPRPQSTLSLNQLTYRRSSNPDIYPGARRFST
SYSDEDILSNDQLDQIHFDPRYRDYRSASSLNNSNYRTRSNSLHSMHSGGSNIGMSALMP
QYQPFRRVSSTSPPLISVPLMPQKRWNTNPSIFIEEYCDDEHKTESVKSEVEETRNTSKE
TLCTSNESLQTPALSVYDIKSFGDLSQIPFIDDDSNDSAPCRVLSDTEICHKDDKKRDTC
RKTVSFDVIKTGTAQQHLYSRSSSHGKNFPPISSLHTKTFNDTDPKKLFHAGIRAMSDIR
TSKDGYVDRVRSVSIKPSSASLSSLHYRETNDHCILVDKLIQMRREEKEERHCAKTCKLN
NYKIKWDEIKGNESTKNDDSIIRSGKVKALTTFFNTLPYITNDCTCPKSSIHHSTPDLRD
GGDKLTDEEMTCVKKQLKEWSEYRLPSKEKLVCTFMKRANSSPVICLENEAYSDCNRYHD
VLNRLDKVHKQKHCNNHRHHHHHHQCENPCLPDCFILRKKLHCHPSCNNIENIPIEVKAT
TDLTEVTPFKSEKHRCRSACFNIKDPAKKRKKKLMKIKAMQQQKNLEDDNESLII

Protein features from InterProScan

Transcript Database ID Name Start End E.value
18 g2402.t1 CDD cd01782 RA1_Afadin 21 130 1.04438E-76
21 g2402.t1 CDD cd01781 RA2_Afadin 227 317 4.68136E-52
20 g2402.t1 CDD cd00060 FHA 348 438 7.03803E-10
17 g2402.t1 CDD cd15471 Myo5p-like_CBD_afadin 596 899 1.26792E-159
19 g2402.t1 CDD cd00992 PDZ_signaling 974 1058 1.8708E-17
16 g2402.t1 Coils Coil Coil 147 177 -
12 g2402.t1 Gene3D G3DSA:3.10.20.90 - 27 165 8.8E-18
13 g2402.t1 Gene3D G3DSA:3.10.20.90 - 219 322 1.8E-35
14 g2402.t1 Gene3D G3DSA:2.60.200.20 - 336 443 1.2E-21
15 g2402.t1 Gene3D G3DSA:2.30.42.10 - 964 1065 4.0E-26
27 g2402.t1 MobiDBLite mobidb-lite consensus disorder prediction 140 176 -
31 g2402.t1 MobiDBLite mobidb-lite consensus disorder prediction 145 176 -
30 g2402.t1 MobiDBLite mobidb-lite consensus disorder prediction 194 226 -
28 g2402.t1 MobiDBLite mobidb-lite consensus disorder prediction 199 219 -
29 g2402.t1 MobiDBLite mobidb-lite consensus disorder prediction 315 338 -
32 g2402.t1 MobiDBLite mobidb-lite consensus disorder prediction 466 578 -
6 g2402.t1 PANTHER PTHR10398 AFADIN 7 1312 0.0
7 g2402.t1 PANTHER PTHR10398:SF1 CANOE, ISOFORM E 7 1312 0.0
4 g2402.t1 Pfam PF00788 Ras association (RalGDS/AF-6) domain 41 130 1.8E-17
3 g2402.t1 Pfam PF00788 Ras association (RalGDS/AF-6) domain 228 317 1.6E-20
2 g2402.t1 Pfam PF00498 FHA domain 368 431 3.4E-8
1 g2402.t1 Pfam PF01843 DIL domain 767 864 1.7E-23
5 g2402.t1 Pfam PF00595 PDZ domain 977 1057 2.1E-15
35 g2402.t1 ProSiteProfiles PS50200 Ras-associating (RA) domain profile. 40 134 30.884
34 g2402.t1 ProSiteProfiles PS50200 Ras-associating (RA) domain profile. 226 318 31.091
33 g2402.t1 ProSiteProfiles PS51126 Dilute domain profile. 653 881 33.259
36 g2402.t1 ProSiteProfiles PS50106 PDZ domain profile. 976 1061 21.953
25 g2402.t1 SMART SM00314 RA_5 40 134 2.4E-22
24 g2402.t1 SMART SM00314 RA_5 226 318 5.2E-27
22 g2402.t1 SMART SM00240 FHA_2 366 416 0.0037
26 g2402.t1 SMART SM01132 DIL_2 767 871 3.1E-26
23 g2402.t1 SMART SM00228 pdz_new 984 1061 1.2E-19
10 g2402.t1 SUPERFAMILY SSF54236 Ubiquitin-like 41 131 2.58E-19
9 g2402.t1 SUPERFAMILY SSF54236 Ubiquitin-like 227 317 2.69E-24
11 g2402.t1 SUPERFAMILY SSF49879 SMAD/FHA domain 345 438 2.36E-19
8 g2402.t1 SUPERFAMILY SSF50156 PDZ domain-like 961 1064 2.37E-24

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:0007165 signal transduction BP
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