General information for g12512.t2
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.t2 | TSS | g12512.t2 | 24192871 | 24192871 |
| chr_1 | g12512 | g12512.t2 | isoform | g12512.t2 | 24193246 | 24208593 |
| chr_1 | g12512 | g12512.t2 | exon | g12512.t2.exon1 | 24193246 | 24193494 |
| chr_1 | g12512 | g12512.t2 | cds | g12512.t2.CDS1 | 24193246 | 24193494 |
| chr_1 | g12512 | g12512.t2 | exon | g12512.t2.exon2 | 24205446 | 24205568 |
| chr_1 | g12512 | g12512.t2 | cds | g12512.t2.CDS2 | 24205446 | 24205568 |
| chr_1 | g12512 | g12512.t2 | exon | g12512.t2.exon3 | 24205644 | 24205892 |
| chr_1 | g12512 | g12512.t2 | cds | g12512.t2.CDS3 | 24205644 | 24205892 |
| chr_1 | g12512 | g12512.t2 | exon | g12512.t2.exon4 | 24205954 | 24206459 |
| chr_1 | g12512 | g12512.t2 | cds | g12512.t2.CDS4 | 24205954 | 24206459 |
| chr_1 | g12512 | g12512.t2 | exon | g12512.t2.exon5 | 24206530 | 24206597 |
| chr_1 | g12512 | g12512.t2 | cds | g12512.t2.CDS5 | 24206530 | 24206597 |
| chr_1 | g12512 | g12512.t2 | exon | g12512.t2.exon6 | 24206668 | 24206772 |
| chr_1 | g12512 | g12512.t2 | cds | g12512.t2.CDS6 | 24206668 | 24206772 |
| chr_1 | g12512 | g12512.t2 | exon | g12512.t2.exon7 | 24206831 | 24206920 |
| chr_1 | g12512 | g12512.t2 | cds | g12512.t2.CDS7 | 24206831 | 24206920 |
| chr_1 | g12512 | g12512.t2 | exon | g12512.t2.exon8 | 24206987 | 24207054 |
| chr_1 | g12512 | g12512.t2 | cds | g12512.t2.CDS8 | 24206987 | 24207054 |
| chr_1 | g12512 | g12512.t2 | exon | g12512.t2.exon9 | 24208334 | 24208411 |
| chr_1 | g12512 | g12512.t2 | cds | g12512.t2.CDS9 | 24208334 | 24208411 |
| chr_1 | g12512 | g12512.t2 | exon | g12512.t2.exon10 | 24208552 | 24208593 |
| chr_1 | g12512 | g12512.t2 | cds | g12512.t2.CDS10 | 24208552 | 24208593 |
| chr_1 | g12512 | g12512.t2 | TTS | g12512.t2 | 24209151 | 24209151 |
Sequences
>g12512.t2 Gene=g12512 Length=1578
ATGGAATCAACACCAGAAGTAGTAGTAGCTCACGAATTAGGAACAGGCTGGATTGAATTT
TCTGAGCGTCATGCAAGAGCTGCAAGTAGTGATTTTGCTAGATCTGTCGTGCAATATTTT
AATTCAACACTTCAACCTGAAGCAAGATCACAAATTTCACATAAAGAGCTCTTAAAAAAA
TTTATCGAATGTTTTTCGGAGAATTTTGAATATGAATTCTTGAGACGTAGCGTGCAGCAA
GGAAATAAGTCTGGCGTAAATGGGAACGCTATAAGTGAGGGTAGTGACTTCTCAGAAGAT
CAAGATTCACCCAAAATCAACCACAAACCATTCTTCCGACGCCTTTCATTTAAAGCTTTA
CGAAAGGGAAAGGTACCGTTTCAAACGATATTTCAGAAACAGCATTCAGATGATCTTGAT
GTATCGGGTTCGGGTCAAAATAAAAAGAAATTGGCTAAGATTGTTGTAGAATGTCGAAAA
GAAGGAAATGTAAATTACATTCCGCCCGAGTCTCTCGATCAAACAAACGACAACAACAAA
TGGGAAAAGTGTAGATTAGTGCTAGTTAAAACTGTAAGCGGATATATGCTCGAGTTTTAT
AGTCCACCAAAAGCTCCAAAGCCTAAAAGCGGTCTTTTTTGTGGTGTCTTGTGTGAAGCA
AGACAAACAATTCCACTTGAAATGCCTGACAAGGAAAATACATTTGTGCTTAAGGCAAAT
GATCAAGAATATGTCATAGAAGCAAAAGACGCTGCAGACATGAAAAGTTGGCTTGCAACA
ATTCGATATTGCATGAAAAGCACACCAACATCACAAATGCCGCCATCACTTCCACTCAAC
GATTCTTCCAATAATTCATGTCTACTGAATGAAGCAGCATCGACTAATGCCCAAGCGTCT
TCATCCGCAGCAGTGGGAGCAACAAGTGCGGCAGCCTCAGATACATTAAATAATAGCTTA
AATAATAATAATACAAACACTAATAATAACAATGTAAATAGCACAAATAATAATAATCAG
CCTGAAATTCCTCCACGACGACCGGAGTCTTCAAGTCATTTTCATTTAGAGGAGGAAGAT
CTCTTACATGATTCTGACCTAACGGCGATGATGATGGAATATCCATGGTTTCATGGAACA
CTTGCTAGAAGTGATGCTAGTGCAATGGTCCTTCATGGTGGAGTATCTAGTCATGGTGTT
TTTCTCGTTCGACAAAGTGAAACTCGTAAAGGAGAATATGTGTTAACATTCAACTTCCAA
GGACGTGCAAAACATTTACGAATGACATTAAATGACTTAGGCCAATGTCGTGTACAACAT
CTATGGTTTCCAAGTATAACTGAAATGCTCGAGCATTTTAGACAAAATCCTATTCCGCTG
GAACAAGGAGGTGTTGCTGATGTGAGGCTTACCGAATACGTAATTGCAAACACACAATCA
TTAGCATCCCCTCGACATCAAAATCAAATTATCACAATGGCTGGCAGTGTACGAATTAAG
ACATGCGATTTAGATTTGATGATGCAAGAGCCACAGGATACCGAGCGAGCCGTCTCAAAT
GAGTATTCATTTGTGTAA
>g12512.t2 Gene=g12512 Length=525
MESTPEVVVAHELGTGWIEFSERHARAASSDFARSVVQYFNSTLQPEARSQISHKELLKK
FIECFSENFEYEFLRRSVQQGNKSGVNGNAISEGSDFSEDQDSPKINHKPFFRRLSFKAL
RKGKVPFQTIFQKQHSDDLDVSGSGQNKKKLAKIVVECRKEGNVNYIPPESLDQTNDNNK
WEKCRLVLVKTVSGYMLEFYSPPKAPKPKSGLFCGVLCEARQTIPLEMPDKENTFVLKAN
DQEYVIEAKDAADMKSWLATIRYCMKSTPTSQMPPSLPLNDSSNNSCLLNEAASTNAQAS
SSAAVGATSAAASDTLNNSLNNNNTNTNNNNVNSTNNNNQPEIPPRRPESSSHFHLEEED
LLHDSDLTAMMMEYPWFHGTLARSDASAMVLHGGVSSHGVFLVRQSETRKGEYVLTFNFQ
GRAKHLRMTLNDLGQCRVQHLWFPSITEMLEHFRQNPIPLEQGGVADVRLTEYVIANTQS
LASPRHQNQIITMAGSVRIKTCDLDLMMQEPQDTERAVSNEYSFV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g12512.t2 | CDD | cd01231 | PH_SH2B_family | 157 | 265 | 2.60564E-51 |
| 16 | g12512.t2 | CDD | cd10346 | SH2_SH2B_family | 367 | 463 | 5.80348E-68 |
| 13 | g12512.t2 | Gene3D | G3DSA:2.30.29.30 | - | 142 | 272 | 2.3E-47 |
| 14 | g12512.t2 | Gene3D | G3DSA:3.30.505.10 | SHC Adaptor Protein | 368 | 476 | 6.9E-29 |
| 19 | g12512.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 322 | 354 | - |
| 20 | g12512.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 322 | 346 | - |
| 4 | g12512.t2 | PANTHER | PTHR10872 | SH2B ADAPTER PROTEIN | 12 | 491 | 7.5E-182 |
| 5 | g12512.t2 | PANTHER | PTHR10872:SF2 | LNK, ISOFORM D | 12 | 491 | 7.5E-182 |
| 6 | g12512.t2 | PRINTS | PR00401 | SH2 domain signature | 376 | 390 | 1.4E-8 |
| 9 | g12512.t2 | PRINTS | PR00401 | SH2 domain signature | 398 | 408 | 1.4E-8 |
| 8 | g12512.t2 | PRINTS | PR00401 | SH2 domain signature | 410 | 421 | 1.4E-8 |
| 7 | g12512.t2 | PRINTS | PR00401 | SH2 domain signature | 442 | 456 | 1.4E-8 |
| 2 | g12512.t2 | Pfam | PF08916 | Phenylalanine zipper | 16 | 73 | 8.4E-15 |
| 3 | g12512.t2 | Pfam | PF00169 | PH domain | 174 | 265 | 1.1E-8 |
| 1 | g12512.t2 | Pfam | PF00017 | SH2 domain | 376 | 453 | 1.9E-13 |
| 22 | g12512.t2 | ProSiteProfiles | PS50003 | PH domain profile. | 232 | 266 | 7.15 |
| 21 | g12512.t2 | ProSiteProfiles | PS50001 | Src homology 2 (SH2) domain profile. | 376 | 474 | 17.478 |
| 17 | g12512.t2 | SMART | SM00233 | PH_update | 158 | 268 | 7.2E-4 |
| 18 | g12512.t2 | SMART | SM00252 | SH2_5 | 374 | 459 | 5.0E-21 |
| 12 | g12512.t2 | SUPERFAMILY | SSF109805 | Phenylalanine zipper | 16 | 77 | 7.85E-14 |
| 10 | g12512.t2 | SUPERFAMILY | SSF50729 | PH domain-like | 146 | 269 | 1.29E-33 |
| 11 | g12512.t2 | SUPERFAMILY | SSF55550 | SH2 domain | 373 | 477 | 4.04E-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.
