General information for g569.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as LIM domain-containing protein jub.
Parent gene
- The parent gene g569 is located on chr_3: 4175924..4178557 (- 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_3 | g569 | g569.t1 | TTS | g569.t1 | 4175472 | 4175472 |
| chr_3 | g569 | g569.t1 | isoform | g569.t1 | 4175924 | 4178557 |
| chr_3 | g569 | g569.t1 | exon | g569.t1.exon1 | 4175924 | 4176171 |
| chr_3 | g569 | g569.t1 | cds | g569.t1.CDS1 | 4175924 | 4176171 |
| chr_3 | g569 | g569.t1 | exon | g569.t1.exon2 | 4176232 | 4176310 |
| chr_3 | g569 | g569.t1 | cds | g569.t1.CDS2 | 4176232 | 4176310 |
| chr_3 | g569 | g569.t1 | exon | g569.t1.exon3 | 4176381 | 4176467 |
| chr_3 | g569 | g569.t1 | cds | g569.t1.CDS3 | 4176381 | 4176467 |
| chr_3 | g569 | g569.t1 | exon | g569.t1.exon4 | 4176529 | 4176591 |
| chr_3 | g569 | g569.t1 | cds | g569.t1.CDS4 | 4176529 | 4176591 |
| chr_3 | g569 | g569.t1 | exon | g569.t1.exon5 | 4176655 | 4176683 |
| chr_3 | g569 | g569.t1 | cds | g569.t1.CDS5 | 4176655 | 4176683 |
| chr_3 | g569 | g569.t1 | exon | g569.t1.exon6 | 4176747 | 4176834 |
| chr_3 | g569 | g569.t1 | cds | g569.t1.CDS6 | 4176747 | 4176834 |
| chr_3 | g569 | g569.t1 | exon | g569.t1.exon7 | 4176899 | 4177044 |
| chr_3 | g569 | g569.t1 | cds | g569.t1.CDS7 | 4176899 | 4177044 |
| chr_3 | g569 | g569.t1 | exon | g569.t1.exon8 | 4177106 | 4177150 |
| chr_3 | g569 | g569.t1 | cds | g569.t1.CDS8 | 4177106 | 4177150 |
| chr_3 | g569 | g569.t1 | exon | g569.t1.exon9 | 4177220 | 4178074 |
| chr_3 | g569 | g569.t1 | cds | g569.t1.CDS9 | 4177220 | 4178074 |
| chr_3 | g569 | g569.t1 | exon | g569.t1.exon10 | 4178140 | 4178557 |
| chr_3 | g569 | g569.t1 | cds | g569.t1.CDS10 | 4178140 | 4178557 |
| chr_3 | g569 | g569.t1 | TSS | g569.t1 | NA | NA |
Sequences
>g569.t1 Gene=g569 Length=2058
ATGGCAAATAATCCGAATGATGCACTTCTTTATCGTCTGCAACAAATGAACATTAATAAC
AGCTCGTCTGAGTATCAAAACTATTCTCCAACTGCTTCCTTAAACCGAAGAGTCACTCAA
CCAGCAAATTATCAACAACAACCGCAGCAAGTCTATCAATATTTGCCTCAAGATACTGCA
AGTAGCATATATGAAAATGTCGAATATGCGACCGGAACAAAGATGCAAGTTACAGACTTG
GATGCAGTCGATCATAATTTTGAATCCAGTAATGCAAAAGCGCAACCTCAATTGCGAGCA
CCTAATGGAAATAAACTAAATTATAAACAGGAGCATGAAAATTTACGATATGCACATACA
CCACAACCATCAGAACATGAGACCCAGCCCATTTATGAAAATTTGCAAGTGATTTCAGGT
CAACAAGCTCAACCTCAAGCATCGCCTGCAAATAAATCGATTTATTATTATGAACGTAGC
GGTTCAAATAGCCCTCAAATACCATATCATATGCAGCAGCGCGATCATCTTGCATCTGAC
TCTCTAGTTCTCAATGCAACTGCTAGCTCAAAATATGTCAATCTCACAAGCAGCAATAGT
ATTGCCAATGTTGGTAGCGGTCAAAATGTAATTTATCAACATCTTGCTTCTGCATCACTT
CCAGCACAGAATAGCTTGCCTCCAAAATCTCTTGCACAACAGCATCTTCAACAGAAAATT
ATCCTCTCTCCTCAATCTCCTAACAAGGACTATGTCCAAATAAATTCCCCAAACATTTAT
GCAAATCAACCGCAACAACAGTCACAACAATCTCATAGTCCATCACCATCAAGATCTCTT
AATCGTGCTTATAATCATCAGTCTCCAACCAAGTCACTAAGTGGCAGCACTGGATCACGA
ACAGCTCTCAATGATGATATTAATGGCTCTGACTATGTGTGCATGAACAGTGGAACACTT
ACGAAACAATTACAACAAACAAATGGAAAACAGCCTGCAAATCAAATTTCATCATCACAA
GTTATTTATCAACGACCACCAGCTGTTGCACCTCTAACGAATATCAATTTGAAAACAAAT
TATACGACACCAGCAAATGAACTTCCACAAGCTCAATATTCAACAGCTGCTAATCAACAA
ATTGATGCAATTGCTGTCGCAAAACAATCTGTGAATCTTAATAAAATTTCAAACTCACCA
GTTGTCAATACTAAACCATCATCTTCACCAACGCCTTCAACTGGTAGTACTGGCTCTGCA
CCACCTGGAAAAATGAAATTTAAAAACTTACTTCCATATAGTGTGACTTCAAGACCAGCT
GGTAAAACTGATGCTGAAAGAAAAATTGAAGAATTAACCCGTGCATTAGAAGAGGAAATG
GAGAAAAACGAAGAGCAAGGAGAATATTTTGGAATTTGTCATACTTGTAAATTAAAAGTT
ACAGGAGCAAATCAAGCATGTCAGGCTATGGGAAATTTATATCATACAGCATGCTTTATT
TGCTGTCAATGTGGAAGAGCACTTCGTGGAAAAGCTTTTTATAATGTTCTTGGACGTGTT
TATTGTGAAGAAGACTATTTGTATTCTGGCTTCCAACAAACATCTGAGAAATGCAACATA
TGTGGACATTTAATTATGGAAATGATACTTCATGCAATGGGAAAATCATATCATCCTGGT
TGCTTTAGATGTTGCGTTTGTAATGAATGCCTAGATGGAGTGCCATTTACGGTTGATGTT
GACAATAAAATTTATTGTGTAAACGATTATCATCATTTGTATGCTCCAAAATGTAGTGGA
TGCAAAAAGAGTATAACACCATTGTCGGATAGTGAAGACAATGAAACTGTCAGAGTAGTT
TCTATGGATAAAGATTATCACATTGATTGCTATGTTTGTGAATCGTGCAACATGCAGTTG
ACTGATGAACCAGATAAGAGATGTTATCCTTTAGATTCCCATTTATTATGCAGAAACTGC
CATTTGGAACGCATTAGTGTTCATAATCGCATGACAGAGCCAGCTTCTGCCTCTATAAGT
TATCAATTTTTGGGCTAA
>g569.t1 Gene=g569 Length=685
MANNPNDALLYRLQQMNINNSSSEYQNYSPTASLNRRVTQPANYQQQPQQVYQYLPQDTA
SSIYENVEYATGTKMQVTDLDAVDHNFESSNAKAQPQLRAPNGNKLNYKQEHENLRYAHT
PQPSEHETQPIYENLQVISGQQAQPQASPANKSIYYYERSGSNSPQIPYHMQQRDHLASD
SLVLNATASSKYVNLTSSNSIANVGSGQNVIYQHLASASLPAQNSLPPKSLAQQHLQQKI
ILSPQSPNKDYVQINSPNIYANQPQQQSQQSHSPSPSRSLNRAYNHQSPTKSLSGSTGSR
TALNDDINGSDYVCMNSGTLTKQLQQTNGKQPANQISSSQVIYQRPPAVAPLTNINLKTN
YTTPANELPQAQYSTAANQQIDAIAVAKQSVNLNKISNSPVVNTKPSSSPTPSTGSTGSA
PPGKMKFKNLLPYSVTSRPAGKTDAERKIEELTRALEEEMEKNEEQGEYFGICHTCKLKV
TGANQACQAMGNLYHTACFICCQCGRALRGKAFYNVLGRVYCEEDYLYSGFQQTSEKCNI
CGHLIMEMILHAMGKSYHPGCFRCCVCNECLDGVPFTVDVDNKIYCVNDYHHLYAPKCSG
CKKSITPLSDSEDNETVRVVSMDKDYHIDCYVCESCNMQLTDEPDKRCYPLDSHLLCRNC
HLERISVHNRMTEPASASISYQFLG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g569.t1 | CDD | cd09352 | LIM1_Ajuba_like | 473 | 526 | 5.04764E-28 |
| 14 | g569.t1 | CDD | cd09355 | LIM2_Ajuba_like | 538 | 590 | 1.46894E-36 |
| 12 | g569.t1 | CDD | cd09438 | LIM3_Ajuba_like | 598 | 661 | 1.16432E-33 |
| 11 | g569.t1 | Coils | Coil | Coil | 442 | 469 | - |
| 10 | g569.t1 | Gene3D | G3DSA:2.10.110.10 | Cysteine Rich Protein | 461 | 528 | 2.9E-15 |
| 8 | g569.t1 | Gene3D | G3DSA:2.10.110.10 | Cysteine Rich Protein | 529 | 594 | 5.5E-17 |
| 9 | g569.t1 | Gene3D | G3DSA:2.10.110.10 | Cysteine Rich Protein | 595 | 670 | 2.8E-18 |
| 20 | g569.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 262 | 299 | - |
| 18 | g569.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 397 | 423 | - |
| 19 | g569.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 397 | 420 | - |
| 4 | g569.t1 | PANTHER | PTHR24219:SF4 | LIM DOMAIN-CONTAINING PROTEIN JUB | 53 | 677 | 6.0E-147 |
| 5 | g569.t1 | PANTHER | PTHR24219 | LIM DOMAIN-CONTAINING PROTEIN JUB | 53 | 677 | 6.0E-147 |
| 3 | g569.t1 | Pfam | PF00412 | LIM domain | 473 | 527 | 2.2E-11 |
| 2 | g569.t1 | Pfam | PF00412 | LIM domain | 538 | 592 | 9.5E-10 |
| 1 | g569.t1 | Pfam | PF00412 | LIM domain | 598 | 663 | 2.3E-9 |
| 22 | g569.t1 | ProSiteProfiles | PS50023 | LIM domain profile. | 471 | 532 | 12.088 |
| 21 | g569.t1 | ProSiteProfiles | PS50023 | LIM domain profile. | 536 | 596 | 13.296 |
| 23 | g569.t1 | ProSiteProfiles | PS50023 | LIM domain profile. | 599 | 667 | 10.92 |
| 16 | g569.t1 | SMART | SM00132 | lim_4 | 472 | 525 | 3.5E-13 |
| 17 | g569.t1 | SMART | SM00132 | lim_4 | 537 | 589 | 3.1E-16 |
| 15 | g569.t1 | SMART | SM00132 | lim_4 | 597 | 660 | 5.8E-15 |
| 7 | g569.t1 | SUPERFAMILY | SSF57716 | Glucocorticoid receptor-like (DNA-binding domain) | 501 | 568 | 5.95E-11 |
| 6 | g569.t1 | SUPERFAMILY | SSF57716 | Glucocorticoid receptor-like (DNA-binding domain) | 563 | 637 | 1.67E-14 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g569/g569.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g569.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K16682 (LIM domain-containing protein)
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.
