General information for g12512.t10
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative SH2B adapter protein 1.
Parent gene
- The parent gene g12512 is located on chr_1: 24208421..24209668 (+ strand)
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_1 | g12512 | g12512.t10 | TSS | g12512.t10 | 24205445 | 24205445 |
| chr_1 | g12512 | g12512.t10 | isoform | g12512.t10 | 24206064 | 24209163 |
| chr_1 | g12512 | g12512.t10 | exon | g12512.t10.exon1 | 24206064 | 24206459 |
| chr_1 | g12512 | g12512.t10 | cds | g12512.t10.CDS1 | 24206092 | 24206459 |
| chr_1 | g12512 | g12512.t10 | exon | g12512.t10.exon2 | 24206530 | 24206597 |
| chr_1 | g12512 | g12512.t10 | cds | g12512.t10.CDS2 | 24206530 | 24206597 |
| chr_1 | g12512 | g12512.t10 | exon | g12512.t10.exon3 | 24206668 | 24206772 |
| chr_1 | g12512 | g12512.t10 | cds | g12512.t10.CDS3 | 24206668 | 24206772 |
| chr_1 | g12512 | g12512.t10 | exon | g12512.t10.exon4 | 24206831 | 24206920 |
| chr_1 | g12512 | g12512.t10 | cds | g12512.t10.CDS4 | 24206831 | 24206920 |
| chr_1 | g12512 | g12512.t10 | exon | g12512.t10.exon5 | 24206987 | 24207054 |
| chr_1 | g12512 | g12512.t10 | cds | g12512.t10.CDS5 | 24206987 | 24207054 |
| chr_1 | g12512 | g12512.t10 | exon | g12512.t10.exon6 | 24208334 | 24208411 |
| chr_1 | g12512 | g12512.t10 | cds | g12512.t10.CDS6 | 24208334 | 24208411 |
| chr_1 | g12512 | g12512.t10 | exon | g12512.t10.exon7 | 24208552 | 24209163 |
| chr_1 | g12512 | g12512.t10 | cds | g12512.t10.CDS7 | 24208552 | 24208593 |
| chr_1 | g12512 | g12512.t10 | TTS | g12512.t10 | 24209151 | 24209151 |
Sequences
>g12512.t10 Gene=g12512 Length=1417
TGTCATAGAAGCAAAAGACGCTGCAGACATGAAAAGTTGGCTTGCAACAATTCGATATTG
CATGAAAAGCACACCAACATCACAAATGCCGCCATCACTTCCACTCAACGATTCTTCCAA
TAATTCATGTCTACTGAATGAAGCAGCATCGACTAATGCCCAAGCGTCTTCATCCGCAGC
AGTGGGAGCAACAAGTGCGGCAGCCTCAGATACATTAAATAATAGCTTAAATAATAATAA
TACAAACACTAATAATAACAATGTAAATAGCACAAATAATAATAATCAGCCTGAAATTCC
TCCACGACGACCGGAGTCTTCAAGTCATTTTCATTTAGAGGAGGAAGATCTCTTACATGA
TTCTGACCTAACGGCGATGATGATGGAATATCCATGGTTTCATGGAACACTTGCTAGAAG
TGATGCTAGTGCAATGGTCCTTCATGGTGGAGTATCTAGTCATGGTGTTTTTCTCGTTCG
ACAAAGTGAAACTCGTAAAGGAGAATATGTGTTAACATTCAACTTCCAAGGACGTGCAAA
ACATTTACGAATGACATTAAATGACTTAGGCCAATGTCGTGTACAACATCTATGGTTTCC
AAGTATAACTGAAATGCTCGAGCATTTTAGACAAAATCCTATTCCGCTGGAACAAGGAGG
TGTTGCTGATGTGAGGCTTACCGAATACGTAATTGCAAACACACAATCATTAGCATCCCC
TCGACATCAAAATCAAATTATCACAATGGCTGGCAGTGTACGAATTAAGACATGCGATTT
AGATTTGATGATGCAAGAGCCACAGGATACCGAGCGAGCCGTCTCAAATGAGTATTCATT
TGTGTAAACATAAACACATACAATTTAAAGAAAATGAAATTATCTACTATTAATGATTGT
TGAAAATCCACATGAAAAAAAAATTATAAAGAAGATCTACCTACTTAGTTTTTCATTTCC
TCAAGTGTGCATGTCGCTGTTGTTCGGCATGAATTTCCTACTGATTTTTTTTCTAATATT
CCTTGCAATATTTTTTGTTGCGTTCCTTTTTTGATAGTAAAGAAAAAAATTTTTTTTCTG
CCAGCATGACTTAATATGATGATAATTTAAAAAGAGATGATGAAAATAAAAATTCCTTAA
TTGACATAAATACTTTAAAATACAAGAAGAAAATAAAATAGAATCATTTAAAATCTGATA
CTTGGACATGGTAAGCAGAAGTGATTCTCTTTAAAATTGATATCGACTTATGCTTATTGA
ATTCCATATCTCAGATTTGATGTGTATTTTTTGACGATGAATAAAAATTGAAATTATTGT
GCCATAAAATTTTTATTTTATGCAAGAAAGAACATATAAATCTAATTTAAAAATAAAACG
ATGAAATCTTTAATGTAAATTTCACGAAAAAAAAAGA
>g12512.t10 Gene=g12512 Length=272
MKSWLATIRYCMKSTPTSQMPPSLPLNDSSNNSCLLNEAASTNAQASSSAAVGATSAAAS
DTLNNSLNNNNTNTNNNNVNSTNNNNQPEIPPRRPESSSHFHLEEEDLLHDSDLTAMMME
YPWFHGTLARSDASAMVLHGGVSSHGVFLVRQSETRKGEYVLTFNFQGRAKHLRMTLNDL
GQCRVQHLWFPSITEMLEHFRQNPIPLEQGGVADVRLTEYVIANTQSLASPRHQNQIITM
AGSVRIKTCDLDLMMQEPQDTERAVSNEYSFV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g12512.t10 | CDD | cd10346 | SH2_SH2B_family | 114 | 210 | 2.65909E-68 |
| 9 | g12512.t10 | Gene3D | G3DSA:3.30.505.10 | SHC Adaptor Protein | 115 | 223 | 2.0E-29 |
| 12 | g12512.t10 | MobiDBLite | mobidb-lite | consensus disorder prediction | 69 | 101 | - |
| 13 | g12512.t10 | MobiDBLite | mobidb-lite | consensus disorder prediction | 69 | 93 | - |
| 2 | g12512.t10 | PANTHER | PTHR10872 | SH2B ADAPTER PROTEIN | 1 | 239 | 4.1E-85 |
| 3 | g12512.t10 | PANTHER | PTHR10872:SF2 | LNK, ISOFORM D | 1 | 239 | 4.1E-85 |
| 6 | g12512.t10 | PRINTS | PR00401 | SH2 domain signature | 123 | 137 | 1.6E-9 |
| 5 | g12512.t10 | PRINTS | PR00401 | SH2 domain signature | 145 | 155 | 1.6E-9 |
| 7 | g12512.t10 | PRINTS | PR00401 | SH2 domain signature | 157 | 168 | 1.6E-9 |
| 4 | g12512.t10 | PRINTS | PR00401 | SH2 domain signature | 189 | 203 | 1.6E-9 |
| 1 | g12512.t10 | Pfam | PF00017 | SH2 domain | 123 | 200 | 6.2E-14 |
| 14 | g12512.t10 | ProSiteProfiles | PS50001 | Src homology 2 (SH2) domain profile. | 123 | 221 | 17.478 |
| 11 | g12512.t10 | SMART | SM00252 | SH2_5 | 121 | 206 | 5.0E-21 |
| 8 | g12512.t10 | SUPERFAMILY | SSF55550 | SH2 domain | 120 | 224 | 1.16E-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:0035591 | signaling adaptor activity | MF |
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.
