Gene loci information

Transcript annotation

  • This transcript has been annotated as Cytoplasmic protein NCK1.

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 g4463 g4463.t1 TSS g4463.t1 2709021 2709021
chr_2 g4463 g4463.t1 isoform g4463.t1 2710068 2711446
chr_2 g4463 g4463.t1 exon g4463.t1.exon1 2710068 2710095
chr_2 g4463 g4463.t1 cds g4463.t1.CDS1 2710068 2710095
chr_2 g4463 g4463.t1 exon g4463.t1.exon2 2710164 2710586
chr_2 g4463 g4463.t1 cds g4463.t1.CDS2 2710164 2710586
chr_2 g4463 g4463.t1 TTS g4463.t1 2710329 2710329
chr_2 g4463 g4463.t1 exon g4463.t1.exon3 2710642 2711171
chr_2 g4463 g4463.t1 cds g4463.t1.CDS3 2710642 2711171
chr_2 g4463 g4463.t1 exon g4463.t1.exon4 2711234 2711446
chr_2 g4463 g4463.t1 cds g4463.t1.CDS4 2711234 2711446

Sequences

>g4463.t1 Gene=g4463 Length=1194
ATGGCAGGAACAGGAAACATGAGACAAGAAGACACAGCAACATACGTCGTCGCGAAGTAT
GATTATTCCGCACAAGGTGCACAAGAATTAGATTTAAGAAAAAATGAAAGATATTTACTG
CTTGATGATAGCAAACATTGGTGGCGTGTTCAAGATGCTCGTAATCAATCGGGCTATGTG
CCGAGCAATTATGTGAAAAAAGAGAAAAAATCGGTTTCGCTTTTTGATAGTTTCAAGAAA
AAAGTGAAAAAAGGCACAAACTCACGAACCCTTCCTAATTCATCGCCATCAAGGCAAGTA
GATTCACCAACTATGGGTCGAAAGTTGCCACCTGATCCTTCTGAAGCCATTGGCACTGCC
ATAGTAAAATATAATTATCAAGCTCAACAAGCAGATGAATTGTCGCTAACTAAAGGCACA
AGAATTTTAATACTTGAAAAAAGCAATGATGGATGGTGGAGAGGACAAAATGGAAGTCAA
ACAGGATGGTTTCCAAGTAATTATACAACTGAAGAAAATGACAATGATGAACTTCATACT
TATGCCATGGCTGAAAATGTTCTCGATATTGTGGTTGCACTTTACTCATTTAACTCTAAT
AATGATACAGAACTTTCATTTGAGAAAGGTGATCGATTGGAAATTATTGATAGACCACCA
TCTGATCCAGAATGGTATAGGGCGCGTAATCAGAAAGGTCAAATTGGTCTAGTGCCACGA
AATTATCTTCAGGAGCTTCAGGAATATCTGAATACACCATATCGAGATGGACCTGATTCA
CTGGGTAGGAGAAATGATAGTGGCGGTTCAACAATGCAAAGTACACATGGTTCACATGGA
AATGGCACGAGTCAGTTAGAAAGGCCAGTCTTAAGTGGTAAAAGTTGGTATTATGGAGCC
ATTACAAGAAGTCAATGCGATACAGTGCTAAATTCGCATGGTCACGATGGTGATTTTCTG
ATTCGTGACTCAGAAACTAATACTGGAGATTTTTCTGTATCACTAAAAGCCCCAGGACGT
AATAAACATTTTCGAGTGCATGTTGAAGGAAATATGTATTGCATAGGACAACGAAAATTC
CATAATTTGGATCAACTTGTCGATCATTACCAAAGAGCGCCAATTTATACGAATAAACAA
GGTGAGAAATTGTATTTGGTGCGACCTCTGCCTAAAGCATCCAATGGCACTTAA

>g4463.t1 Gene=g4463 Length=397
MAGTGNMRQEDTATYVVAKYDYSAQGAQELDLRKNERYLLLDDSKHWWRVQDARNQSGYV
PSNYVKKEKKSVSLFDSFKKKVKKGTNSRTLPNSSPSRQVDSPTMGRKLPPDPSEAIGTA
IVKYNYQAQQADELSLTKGTRILILEKSNDGWWRGQNGSQTGWFPSNYTTEENDNDELHT
YAMAENVLDIVVALYSFNSNNDTELSFEKGDRLEIIDRPPSDPEWYRARNQKGQIGLVPR
NYLQELQEYLNTPYRDGPDSLGRRNDSGGSTMQSTHGSHGNGTSQLERPVLSGKSWYYGA
ITRSQCDTVLNSHGHDGDFLIRDSETNTGDFSVSLKAPGRNKHFRVHVEGNMYCIGQRKF
HNLDQLVDHYQRAPIYTNKQGEKLYLVRPLPKASNGT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
29 g4463.t1 CDD cd11765 SH3_Nck_1 15 65 1.04199E-27
27 g4463.t1 CDD cd11766 SH3_Nck_2 119 171 6.82277E-29
28 g4463.t1 CDD cd11767 SH3_Nck_3 190 245 2.95726E-30
30 g4463.t1 CDD cd09943 SH2_Nck_family 294 386 9.30263E-59
24 g4463.t1 Gene3D G3DSA:2.30.30.40 SH3 Domains 7 71 9.1E-19
22 g4463.t1 Gene3D G3DSA:2.30.30.40 SH3 Domains 110 184 3.0E-25
23 g4463.t1 Gene3D G3DSA:2.30.30.40 SH3 Domains 186 249 7.8E-22
21 g4463.t1 Gene3D G3DSA:3.30.505.40 - 294 348 7.8E-20
25 g4463.t1 Gene3D G3DSA:3.30.505.10 SHC Adaptor Protein 350 390 3.2E-22
36 g4463.t1 MobiDBLite mobidb-lite consensus disorder prediction 83 112 -
37 g4463.t1 MobiDBLite mobidb-lite consensus disorder prediction 87 102 -
35 g4463.t1 MobiDBLite mobidb-lite consensus disorder prediction 265 286 -
6 g4463.t1 PANTHER PTHR19969:SF14 DREADLOCKS, ISOFORM B 15 77 1.2E-128
8 g4463.t1 PANTHER PTHR19969 SH2-SH3 ADAPTOR PROTEIN-RELATED 15 77 1.2E-128
5 g4463.t1 PANTHER PTHR19969:SF14 DREADLOCKS, ISOFORM B 85 390 1.2E-128
7 g4463.t1 PANTHER PTHR19969 SH2-SH3 ADAPTOR PROTEIN-RELATED 85 390 1.2E-128
26 g4463.t1 PIRSF PIRSF037874 NCK 10 392 3.4E-185
15 g4463.t1 PRINTS PR00452 SH3 domain signature 14 24 2.8E-10
14 g4463.t1 PRINTS PR00452 SH3 domain signature 132 147 2.8E-10
13 g4463.t1 PRINTS PR00452 SH3 domain signature 149 158 2.8E-10
16 g4463.t1 PRINTS PR00452 SH3 domain signature 160 172 2.8E-10
12 g4463.t1 PRINTS PR00401 SH2 domain signature 296 310 1.0E-10
10 g4463.t1 PRINTS PR00401 SH2 domain signature 316 326 1.0E-10
11 g4463.t1 PRINTS PR00401 SH2 domain signature 328 339 1.0E-10
9 g4463.t1 PRINTS PR00401 SH2 domain signature 359 373 1.0E-10
2 g4463.t1 Pfam PF00018 SH3 domain 17 62 6.6E-13
1 g4463.t1 Pfam PF00018 SH3 domain 121 166 7.3E-17
3 g4463.t1 Pfam PF00018 SH3 domain 192 239 8.9E-13
4 g4463.t1 Pfam PF00017 SH2 domain 296 370 3.4E-21
40 g4463.t1 ProSiteProfiles PS50002 Src homology 3 (SH3) domain profile. 11 70 24.096
39 g4463.t1 ProSiteProfiles PS50002 Src homology 3 (SH3) domain profile. 115 174 27.563
38 g4463.t1 ProSiteProfiles PS50002 Src homology 3 (SH3) domain profile. 186 248 28.663
41 g4463.t1 ProSiteProfiles PS50001 Src homology 2 (SH2) domain profile. 296 390 20.771
33 g4463.t1 SMART SM00326 SH3_2 14 69 2.1E-16
31 g4463.t1 SMART SM00326 SH3_2 118 173 5.6E-23
32 g4463.t1 SMART SM00326 SH3_2 189 247 2.9E-20
34 g4463.t1 SMART SM00252 SH2_5 294 376 4.3E-30
20 g4463.t1 SUPERFAMILY SSF50044 SH3-domain 13 69 2.49E-17
18 g4463.t1 SUPERFAMILY SSF50044 SH3-domain 110 174 2.23E-23
19 g4463.t1 SUPERFAMILY SSF50044 SH3-domain 182 264 8.93E-20
17 g4463.t1 SUPERFAMILY SSF55550 SH2 domain 289 389 1.35E-26

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: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