General information for g12512.t1
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.t1 | TSS | g12512.t1 | 24200696 | 24200696 |
| chr_1 | g12512 | g12512.t1 | isoform | g12512.t1 | 24201514 | 24208593 |
| chr_1 | g12512 | g12512.t1 | exon | g12512.t1.exon1 | 24201514 | 24201579 |
| chr_1 | g12512 | g12512.t1 | cds | g12512.t1.CDS1 | 24201514 | 24201579 |
| chr_1 | g12512 | g12512.t1 | exon | g12512.t1.exon2 | 24205446 | 24205568 |
| chr_1 | g12512 | g12512.t1 | cds | g12512.t1.CDS2 | 24205446 | 24205568 |
| chr_1 | g12512 | g12512.t1 | exon | g12512.t1.exon3 | 24205644 | 24205892 |
| chr_1 | g12512 | g12512.t1 | cds | g12512.t1.CDS3 | 24205644 | 24205892 |
| chr_1 | g12512 | g12512.t1 | exon | g12512.t1.exon4 | 24205954 | 24206459 |
| chr_1 | g12512 | g12512.t1 | cds | g12512.t1.CDS4 | 24205954 | 24206459 |
| chr_1 | g12512 | g12512.t1 | exon | g12512.t1.exon5 | 24206530 | 24206597 |
| chr_1 | g12512 | g12512.t1 | cds | g12512.t1.CDS5 | 24206530 | 24206597 |
| chr_1 | g12512 | g12512.t1 | exon | g12512.t1.exon6 | 24206668 | 24206772 |
| chr_1 | g12512 | g12512.t1 | cds | g12512.t1.CDS6 | 24206668 | 24206772 |
| chr_1 | g12512 | g12512.t1 | exon | g12512.t1.exon7 | 24206831 | 24206920 |
| chr_1 | g12512 | g12512.t1 | cds | g12512.t1.CDS7 | 24206831 | 24206920 |
| chr_1 | g12512 | g12512.t1 | exon | g12512.t1.exon8 | 24206987 | 24207054 |
| chr_1 | g12512 | g12512.t1 | cds | g12512.t1.CDS8 | 24206987 | 24207054 |
| chr_1 | g12512 | g12512.t1 | exon | g12512.t1.exon9 | 24208334 | 24208411 |
| chr_1 | g12512 | g12512.t1 | cds | g12512.t1.CDS9 | 24208334 | 24208411 |
| chr_1 | g12512 | g12512.t1 | exon | g12512.t1.exon10 | 24208552 | 24208593 |
| chr_1 | g12512 | g12512.t1 | cds | g12512.t1.CDS10 | 24208552 | 24208593 |
| chr_1 | g12512 | g12512.t1 | TTS | g12512.t1 | 24209151 | 24209151 |
Sequences
>g12512.t1 Gene=g12512 Length=1395
ATGAATGCTTGGAGGAGGCTGATAGAGTTACGACTCAAAAATAACAATAACATTGTTGTT
GAAAAGTCTGGCGTAAATGGGAACGCTATAAGTGAGGGTAGTGACTTCTCAGAAGATCAA
GATTCACCCAAAATCAACCACAAACCATTCTTCCGACGCCTTTCATTTAAAGCTTTACGA
AAGGGAAAGGTACCGTTTCAAACGATATTTCAGAAACAGCATTCAGATGATCTTGATGTA
TCGGGTTCGGGTCAAAATAAAAAGAAATTGGCTAAGATTGTTGTAGAATGTCGAAAAGAA
GGAAATGTAAATTACATTCCGCCCGAGTCTCTCGATCAAACAAACGACAACAACAAATGG
GAAAAGTGTAGATTAGTGCTAGTTAAAACTGTAAGCGGATATATGCTCGAGTTTTATAGT
CCACCAAAAGCTCCAAAGCCTAAAAGCGGTCTTTTTTGTGGTGTCTTGTGTGAAGCAAGA
CAAACAATTCCACTTGAAATGCCTGACAAGGAAAATACATTTGTGCTTAAGGCAAATGAT
CAAGAATATGTCATAGAAGCAAAAGACGCTGCAGACATGAAAAGTTGGCTTGCAACAATT
CGATATTGCATGAAAAGCACACCAACATCACAAATGCCGCCATCACTTCCACTCAACGAT
TCTTCCAATAATTCATGTCTACTGAATGAAGCAGCATCGACTAATGCCCAAGCGTCTTCA
TCCGCAGCAGTGGGAGCAACAAGTGCGGCAGCCTCAGATACATTAAATAATAGCTTAAAT
AATAATAATACAAACACTAATAATAACAATGTAAATAGCACAAATAATAATAATCAGCCT
GAAATTCCTCCACGACGACCGGAGTCTTCAAGTCATTTTCATTTAGAGGAGGAAGATCTC
TTACATGATTCTGACCTAACGGCGATGATGATGGAATATCCATGGTTTCATGGAACACTT
GCTAGAAGTGATGCTAGTGCAATGGTCCTTCATGGTGGAGTATCTAGTCATGGTGTTTTT
CTCGTTCGACAAAGTGAAACTCGTAAAGGAGAATATGTGTTAACATTCAACTTCCAAGGA
CGTGCAAAACATTTACGAATGACATTAAATGACTTAGGCCAATGTCGTGTACAACATCTA
TGGTTTCCAAGTATAACTGAAATGCTCGAGCATTTTAGACAAAATCCTATTCCGCTGGAA
CAAGGAGGTGTTGCTGATGTGAGGCTTACCGAATACGTAATTGCAAACACACAATCATTA
GCATCCCCTCGACATCAAAATCAAATTATCACAATGGCTGGCAGTGTACGAATTAAGACA
TGCGATTTAGATTTGATGATGCAAGAGCCACAGGATACCGAGCGAGCCGTCTCAAATGAG
TATTCATTTGTGTAA
>g12512.t1 Gene=g12512 Length=464
MNAWRRLIELRLKNNNNIVVEKSGVNGNAISEGSDFSEDQDSPKINHKPFFRRLSFKALR
KGKVPFQTIFQKQHSDDLDVSGSGQNKKKLAKIVVECRKEGNVNYIPPESLDQTNDNNKW
EKCRLVLVKTVSGYMLEFYSPPKAPKPKSGLFCGVLCEARQTIPLEMPDKENTFVLKAND
QEYVIEAKDAADMKSWLATIRYCMKSTPTSQMPPSLPLNDSSNNSCLLNEAASTNAQASS
SAAVGATSAAASDTLNNSLNNNNTNTNNNNVNSTNNNNQPEIPPRRPESSSHFHLEEEDL
LHDSDLTAMMMEYPWFHGTLARSDASAMVLHGGVSSHGVFLVRQSETRKGEYVLTFNFQG
RAKHLRMTLNDLGQCRVQHLWFPSITEMLEHFRQNPIPLEQGGVADVRLTEYVIANTQSL
ASPRHQNQIITMAGSVRIKTCDLDLMMQEPQDTERAVSNEYSFV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g12512.t1 | CDD | cd01231 | PH_SH2B_family | 96 | 204 | 6.54689E-52 |
| 14 | g12512.t1 | CDD | cd10346 | SH2_SH2B_family | 306 | 402 | 1.53524E-69 |
| 11 | g12512.t1 | Gene3D | G3DSA:2.30.29.30 | - | 81 | 211 | 1.8E-47 |
| 12 | g12512.t1 | Gene3D | G3DSA:3.30.505.10 | SHC Adaptor Protein | 307 | 415 | 5.6E-29 |
| 17 | g12512.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 261 | 293 | - |
| 18 | g12512.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 261 | 285 | - |
| 3 | g12512.t1 | PANTHER | PTHR10872 | SH2B ADAPTER PROTEIN | 21 | 430 | 4.0E-161 |
| 4 | g12512.t1 | PANTHER | PTHR10872:SF2 | LNK, ISOFORM D | 21 | 430 | 4.0E-161 |
| 5 | g12512.t1 | PRINTS | PR00401 | SH2 domain signature | 315 | 329 | 9.2E-9 |
| 6 | g12512.t1 | PRINTS | PR00401 | SH2 domain signature | 337 | 347 | 9.2E-9 |
| 7 | g12512.t1 | PRINTS | PR00401 | SH2 domain signature | 349 | 360 | 9.2E-9 |
| 8 | g12512.t1 | PRINTS | PR00401 | SH2 domain signature | 381 | 395 | 9.2E-9 |
| 2 | g12512.t1 | Pfam | PF00169 | PH domain | 113 | 204 | 9.2E-9 |
| 1 | g12512.t1 | Pfam | PF00017 | SH2 domain | 315 | 392 | 1.6E-13 |
| 20 | g12512.t1 | ProSiteProfiles | PS50003 | PH domain profile. | 171 | 205 | 7.15 |
| 19 | g12512.t1 | ProSiteProfiles | PS50001 | Src homology 2 (SH2) domain profile. | 315 | 413 | 17.478 |
| 15 | g12512.t1 | SMART | SM00233 | PH_update | 97 | 207 | 7.2E-4 |
| 16 | g12512.t1 | SMART | SM00252 | SH2_5 | 313 | 398 | 5.0E-21 |
| 9 | g12512.t1 | SUPERFAMILY | SSF50729 | PH domain-like | 85 | 208 | 1.04E-33 |
| 10 | g12512.t1 | SUPERFAMILY | SSF55550 | SH2 domain | 312 | 416 | 3.37E-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:0035591 | signaling adaptor activity | MF |
KEGG
Orthology
- This transcript has been annotated with K07193 (SH2B adapter protein 2)
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.
