General information for g4002.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Actin-binding LIM protein 1.
Parent gene
- The parent gene g4002 is located on chr_3: 29452331..29453298 (+ 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 | g4002 | g4002.t1 | TSS | g4002.t1 | 29446813 | 29446813 |
| chr_3 | g4002 | g4002.t1 | isoform | g4002.t1 | 29446933 | 29452331 |
| chr_3 | g4002 | g4002.t1 | exon | g4002.t1.exon1 | 29446933 | 29446936 |
| chr_3 | g4002 | g4002.t1 | cds | g4002.t1.CDS1 | 29446933 | 29446936 |
| chr_3 | g4002 | g4002.t1 | exon | g4002.t1.exon2 | 29448317 | 29448627 |
| chr_3 | g4002 | g4002.t1 | cds | g4002.t1.CDS2 | 29448317 | 29448627 |
| chr_3 | g4002 | g4002.t1 | exon | g4002.t1.exon3 | 29448747 | 29449030 |
| chr_3 | g4002 | g4002.t1 | cds | g4002.t1.CDS3 | 29448747 | 29449030 |
| chr_3 | g4002 | g4002.t1 | exon | g4002.t1.exon4 | 29449097 | 29449445 |
| chr_3 | g4002 | g4002.t1 | cds | g4002.t1.CDS4 | 29449097 | 29449445 |
| chr_3 | g4002 | g4002.t1 | exon | g4002.t1.exon5 | 29449661 | 29449726 |
| chr_3 | g4002 | g4002.t1 | cds | g4002.t1.CDS5 | 29449661 | 29449726 |
| chr_3 | g4002 | g4002.t1 | exon | g4002.t1.exon6 | 29449860 | 29450545 |
| chr_3 | g4002 | g4002.t1 | cds | g4002.t1.CDS6 | 29449860 | 29450545 |
| chr_3 | g4002 | g4002.t1 | exon | g4002.t1.exon7 | 29450610 | 29450746 |
| chr_3 | g4002 | g4002.t1 | cds | g4002.t1.CDS7 | 29450610 | 29450746 |
| chr_3 | g4002 | g4002.t1 | exon | g4002.t1.exon8 | 29450837 | 29450922 |
| chr_3 | g4002 | g4002.t1 | cds | g4002.t1.CDS8 | 29450837 | 29450922 |
| chr_3 | g4002 | g4002.t1 | exon | g4002.t1.exon9 | 29451781 | 29451847 |
| chr_3 | g4002 | g4002.t1 | cds | g4002.t1.CDS9 | 29451781 | 29451847 |
| chr_3 | g4002 | g4002.t1 | exon | g4002.t1.exon10 | 29451909 | 29452189 |
| chr_3 | g4002 | g4002.t1 | cds | g4002.t1.CDS10 | 29451909 | 29452189 |
| chr_3 | g4002 | g4002.t1 | exon | g4002.t1.exon11 | 29452257 | 29452331 |
| chr_3 | g4002 | g4002.t1 | cds | g4002.t1.CDS11 | 29452257 | 29452331 |
| chr_3 | g4002 | g4002.t1 | TTS | g4002.t1 | 29453141 | 29453141 |
Sequences
>g4002.t1 Gene=g4002 Length=2346
ATGGGTAAAACAAAAATTTACTGCGCGAAATGCCAGAAAAAGTGTTCAGGTGAAGTGCTG
CGAGTTACTGACAAATATTTTCACAAAGCGTGCTTTCAGTGTGTTAAATGCAGCAAATCA
TTAGCAGCAGGCGGCTTTTTTGCAAAAGATAATAGCTACTACTGTGTAGTCGATTATCAG
AAGTTATTTGGCACAAAGTGTGCTGTATGTCAGCAATATGTTGAAGGCGAAGTTGTGTCA
ACAATGGGCAATACATACCATCAAAAGTGTTTCACATGCACTCGCTGTAGTCTGCCTTTT
GAATCTGGTAGTAAGGTCACAAATACCGGAAAAGAAATTTTATGTGAGAAATGTGTTGAG
GGTAAACCAGTTGTGGCTAAACCAATTGTCCAACAACAACAGCAGCATCAGCAACAACAA
AAGCAGCTGCATTCTAGTCCAACAAAAGCTACAGCTCAGCAGCAGCATCACGAAACTCTA
CAGAAACCAATGAGTCCAAAGGATATTGATCCAAACAATTGTGCCGGTTGTAATGCAGAA
TTAAAGGAGGGTCAGGCACTCATCGCTTTAGATAGGCAGTGGCATATTTGGTGCTTCCGT
TGTATGGTGTGTGGACAAGTATTAAGTGGCGAATACATGGGTAAAGACGGACAACCGTAT
TGCGAAAAAGATTACCAGAAATCATTTGGTGTCAAGTGCGCTTATTGCGAACGCTACATA
AGTGGAAAAGTTCTGCAAGCGGGTGATAATCATCATTTTCATCCTACCTGTGCTCGTTGC
TCTAAATGTGGTGATCCTTTCGGTGATGGCGAAGAAATGTACTTGCAGGGAACTGCAATT
TGGCATCCTCGTTGTGGACCTCATCCATCAGAAAATAATGGCACAATTTTCAATGGAACT
TCGGCTGCTGAAGTTGATAGAATAAGTAATAGCGCGAGCGAAATACAATTTTCATTACGT
TCACGCACGCCTAGTTTAAGTGGATCAGTTTGTAGTCCTTATACTGGTAGAAAATATCAT
CGTACAACAAGCCCTGGTTTAGTGTTACGTGAATATAATCAATCTAATTATAGCGAGGAT
ATTTCACGTATTTATACCTATAGTTATTTAACTGAAGAAGTTGCTGGTTTAAAAAAACCA
ATTGATCCATATGATAAGAAGCCAGTTTCGCCACATTTTCATCGACCGAACTATGTTTCT
TCATCGTCGAGACCACCATCACGTCCTCAATCACGCAGTCGTTCGGCAATGAGAGTTTTA
GTAGATAGTATTCGCACTGAAGCACCTCGACCAAAAAGTCCTGCAATGAATAATGAAGAA
CCAATTGAAATGAGCCATTATCCTGGTGGTAAAAAACCAAATCCTAATGAAAAACCAAAA
ATCGAGCGTGACGACTTTCCTGCTCCTCCTTATCCATATACTGATCCAGAGAGAAGACGC
CGATATTCAGATTCTTATAAAGGTGTTCAAACTTCAGATGATGAAGATCAGGTTGATAAA
GCAGCCGAAATTGAAAATATTGAACCACAGCTGAAACGTGAGGAAGAAGAACTTAAAAAG
ATAAATTCGGGTATGAGCAAGGTCATCTTGAAAGACATAAAAGAACGACAAAAGTATAAG
ATATGGAAACAAAACAATCTTGACCCTCGCAATGCATCACGATTTCCTTCAGCTTCAAAA
GAGCCCGTTTATAAAATGAGATATGAAAGTCCAGTTGGTGCAAGTCCAAGTAGAAATCTC
GATCACTCTCGTCCATTTGAGGACGAGTTGTTTGATCGATCAATTAGCTATAGAGGATCA
GTTGGTCGTGCTATTGGTGCTGGCAACAGTTACAATGCAATAAATTCATATCGATCGCCA
AAGCCAGGAAGTAGCTATAAGCATTCGACTCTTCCATCATCAATTCGAAACGGTTACAGT
TCTGATTTTTCATTTGGTCCATTAGGTGACAAAACGCACAGTACAGAATTTTCATGTGGA
AAATCAGATATTTCAGTTGAAGAGTCAATAACAGAAGGTGACAGAAGAGCACTTGGTGCC
GATATTCCAGTCTCTAGTACATATTCAGGTGCAATTTATAATCAATATCCACAATCGGGT
CTGACAAGAAGATCGTTGCCTAATATGGCACATTCAATACTCGTTCATGAGCCAGCAAAA
ATTTATCCCTATCACTTGCTACTAGTCTCCAATTATAGATTGCCAGCTGATGTTGATCGT
TGTAATTTAGAACGTCATTTATCAGATACTGAATTTGAAGCAATTTGTGGGTGCTCAAGA
GCAGAATTCTATCGCATGCCACAGTGGAAGCGAAATGACATCAAAAGACGCGCCCGACTA
TTTTAA
>g4002.t1 Gene=g4002 Length=781
MGKTKIYCAKCQKKCSGEVLRVTDKYFHKACFQCVKCSKSLAAGGFFAKDNSYYCVVDYQ
KLFGTKCAVCQQYVEGEVVSTMGNTYHQKCFTCTRCSLPFESGSKVTNTGKEILCEKCVE
GKPVVAKPIVQQQQQHQQQQKQLHSSPTKATAQQQHHETLQKPMSPKDIDPNNCAGCNAE
LKEGQALIALDRQWHIWCFRCMVCGQVLSGEYMGKDGQPYCEKDYQKSFGVKCAYCERYI
SGKVLQAGDNHHFHPTCARCSKCGDPFGDGEEMYLQGTAIWHPRCGPHPSENNGTIFNGT
SAAEVDRISNSASEIQFSLRSRTPSLSGSVCSPYTGRKYHRTTSPGLVLREYNQSNYSED
ISRIYTYSYLTEEVAGLKKPIDPYDKKPVSPHFHRPNYVSSSSRPPSRPQSRSRSAMRVL
VDSIRTEAPRPKSPAMNNEEPIEMSHYPGGKKPNPNEKPKIERDDFPAPPYPYTDPERRR
RYSDSYKGVQTSDDEDQVDKAAEIENIEPQLKREEEELKKINSGMSKVILKDIKERQKYK
IWKQNNLDPRNASRFPSASKEPVYKMRYESPVGASPSRNLDHSRPFEDELFDRSISYRGS
VGRAIGAGNSYNAINSYRSPKPGSSYKHSTLPSSIRNGYSSDFSFGPLGDKTHSTEFSCG
KSDISVEESITEGDRRALGADIPVSSTYSGAIYNQYPQSGLTRRSLPNMAHSILVHEPAK
IYPYHLLLVSNYRLPADVDRCNLERHLSDTEFEAICGCSRAEFYRMPQWKRNDIKRRARL
F
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 19 | g4002.t1 | CDD | cd09327 | LIM1_abLIM | 8 | 59 | 6.31188E-25 |
| 22 | g4002.t1 | CDD | cd09328 | LIM2_abLIM | 64 | 119 | 9.24772E-27 |
| 21 | g4002.t1 | CDD | cd09329 | LIM3_abLIM | 174 | 225 | 1.82224E-29 |
| 20 | g4002.t1 | CDD | cd09330 | LIM4_abLIM | 233 | 287 | 9.48417E-32 |
| 15 | g4002.t1 | Gene3D | G3DSA:2.10.110.10 | Cysteine Rich Protein | 1 | 59 | 2.9E-14 |
| 18 | g4002.t1 | Gene3D | G3DSA:2.10.110.10 | Cysteine Rich Protein | 60 | 124 | 2.7E-19 |
| 17 | g4002.t1 | Gene3D | G3DSA:2.10.110.10 | Cysteine Rich Protein | 158 | 230 | 3.6E-23 |
| 16 | g4002.t1 | Gene3D | G3DSA:2.10.110.10 | Cysteine Rich Protein | 231 | 295 | 1.2E-15 |
| 14 | g4002.t1 | Gene3D | G3DSA:1.10.950.10 | Villin Headpiece Domain; Chain A | 718 | 781 | 3.0E-25 |
| 32 | g4002.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 136 | 165 | - |
| 35 | g4002.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 136 | 160 | - |
| 34 | g4002.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 394 | 506 | - |
| 33 | g4002.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 395 | 417 | - |
| 31 | g4002.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 474 | 506 | - |
| 6 | g4002.t1 | PANTHER | PTHR24213:SF9 | UNCOORDINATED 115A, ISOFORM B-RELATED | 3 | 781 | 6.0E-257 |
| 7 | g4002.t1 | PANTHER | PTHR24213 | ACTIN-BINDING LIM PROTEIN | 3 | 781 | 6.0E-257 |
| 5 | g4002.t1 | Pfam | PF00412 | LIM domain | 8 | 62 | 9.1E-12 |
| 4 | g4002.t1 | Pfam | PF00412 | LIM domain | 67 | 119 | 2.3E-10 |
| 3 | g4002.t1 | Pfam | PF00412 | LIM domain | 174 | 229 | 9.7E-15 |
| 2 | g4002.t1 | Pfam | PF00412 | LIM domain | 233 | 275 | 6.7E-7 |
| 1 | g4002.t1 | Pfam | PF02209 | Villin headpiece domain | 746 | 781 | 5.1E-14 |
| 25 | g4002.t1 | ProSitePatterns | PS00478 | LIM zinc-binding domain signature. | 8 | 41 | - |
| 23 | g4002.t1 | ProSitePatterns | PS00478 | LIM zinc-binding domain signature. | 67 | 100 | - |
| 24 | g4002.t1 | ProSitePatterns | PS00478 | LIM zinc-binding domain signature. | 233 | 267 | - |
| 39 | g4002.t1 | ProSiteProfiles | PS50023 | LIM domain profile. | 6 | 65 | 13.355 |
| 38 | g4002.t1 | ProSiteProfiles | PS50023 | LIM domain profile. | 66 | 125 | 9.197 |
| 37 | g4002.t1 | ProSiteProfiles | PS50023 | LIM domain profile. | 172 | 231 | 14.157 |
| 36 | g4002.t1 | ProSiteProfiles | PS50023 | LIM domain profile. | 232 | 295 | 6.801 |
| 40 | g4002.t1 | ProSiteProfiles | PS51089 | Headpiece (HP) domain profile. | 716 | 781 | 19.507 |
| 30 | g4002.t1 | SMART | SM00132 | lim_4 | 7 | 58 | 6.4E-14 |
| 29 | g4002.t1 | SMART | SM00132 | lim_4 | 66 | 118 | 9.8E-14 |
| 28 | g4002.t1 | SMART | SM00132 | lim_4 | 173 | 224 | 3.4E-15 |
| 27 | g4002.t1 | SMART | SM00132 | lim_4 | 232 | 285 | 2.3E-7 |
| 26 | g4002.t1 | SMART | SM00153 | VHP_1 | 746 | 781 | 2.3E-12 |
| 13 | g4002.t1 | SUPERFAMILY | SSF57716 | Glucocorticoid receptor-like (DNA-binding domain) | 33 | 96 | 4.96E-17 |
| 9 | g4002.t1 | SUPERFAMILY | SSF57716 | Glucocorticoid receptor-like (DNA-binding domain) | 91 | 121 | 1.77E-5 |
| 11 | g4002.t1 | SUPERFAMILY | SSF57716 | Glucocorticoid receptor-like (DNA-binding domain) | 169 | 199 | 2.16E-7 |
| 12 | g4002.t1 | SUPERFAMILY | SSF57716 | Glucocorticoid receptor-like (DNA-binding domain) | 200 | 263 | 2.75E-14 |
| 10 | g4002.t1 | SUPERFAMILY | SSF57716 | Glucocorticoid receptor-like (DNA-binding domain) | 260 | 289 | 1.12E-10 |
| 8 | g4002.t1 | SUPERFAMILY | SSF47050 | VHP, Villin headpiece domain | 713 | 781 | 6.02E-22 |
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:0003779 | actin binding | MF |
| GO:0007010 | cytoskeleton organization | BP |
KEGG
Orthology
- This transcript has been annotated with K07520 (actin-binding LIM 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.
