Gene loci information

Transcript annotation

  • This transcript has been annotated as Actin-binding LIM protein 1.

Parent gene

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.t4 TSS g4002.t4 29446813 29446813
chr_3 g4002 g4002.t4 isoform g4002.t4 29446933 29449445
chr_3 g4002 g4002.t4 exon g4002.t4.exon1 29446933 29446936
chr_3 g4002 g4002.t4 cds g4002.t4.CDS1 29446933 29446936
chr_3 g4002 g4002.t4 exon g4002.t4.exon2 29448317 29448627
chr_3 g4002 g4002.t4 cds g4002.t4.CDS2 29448317 29448627
chr_3 g4002 g4002.t4 exon g4002.t4.exon3 29448747 29449030
chr_3 g4002 g4002.t4 cds g4002.t4.CDS3 29448747 29449030
chr_3 g4002 g4002.t4 exon g4002.t4.exon4 29449097 29449445
chr_3 g4002 g4002.t4 cds g4002.t4.CDS4 29449097 29449445
chr_3 g4002 g4002.t4 TTS g4002.t4 NA NA

Sequences

>g4002.t4 Gene=g4002 Length=948
ATGGGTAAAACAAAAATTTACTGCGCGAAATGCCAGAAAAAGTGTTCAGGTGAAGTGCTG
CGAGTTACTGACAAATATTTTCACAAAGCGTGCTTTCAGTGTGTTAAATGCAGCAAATCA
TTAGCAGCAGGCGGCTTTTTTGCAAAAGATAATAGCTACTACTGTGTAGTCGATTATCAG
AAGTTATTTGGCACAAAGTGTGCTGTATGTCAGCAATATGTTGAAGGCGAAGTTGTGTCA
ACAATGGGCAATACATACCATCAAAAGTGTTTCACATGCACTCGCTGTAGTCTGCCTTTT
GAATCTGGTAGTAAGGTCACAAATACCGGAAAAGAAATTTTATGTGAGAAATGTGTTGAG
GGTAAACCAGTTGTGGCTAAACCAATTGTCCAACAACAACAGCAGCATCAGCAACAACAA
AAGCAGCTGCATTCTAGTCCAACAAAAGCTACAGCTCAGCAGCAGCATCACGAAACTCTA
CAGAAACCAATGAGTCCAAAGGATATTGATCCAAACAATTGTGCCGGTTGTAATGCAGAA
TTAAAGGAGGGTCAGGCACTCATCGCTTTAGATAGGCAGTGGCATATTTGGTGCTTCCGT
TGTATGGTGTGTGGACAAGTATTAAGTGGCGAATACATGGGTAAAGACGGACAACCGTAT
TGCGAAAAAGATTACCAGAAATCATTTGGTGTCAAGTGCGCTTATTGCGAACGCTACATA
AGTGGAAAAGTTCTGCAAGCGGGTGATAATCATCATTTTCATCCTACCTGTGCTCGTTGC
TCTAAATGTGGTGATCCTTTCGGTGATGGCGAAGAAATGTACTTGCAGGGAACTGCAATT
TGGCATCCTCGTTGTGGACCTCATCCATCAGAAAATAATGGCACAATTTTCAATGGAACT
TCGGCTGCTGAAGTTGATAGAATAAGTAATAGCGCGAGCGAAATACAA

>g4002.t4 Gene=g4002 Length=316
MGKTKIYCAKCQKKCSGEVLRVTDKYFHKACFQCVKCSKSLAAGGFFAKDNSYYCVVDYQ
KLFGTKCAVCQQYVEGEVVSTMGNTYHQKCFTCTRCSLPFESGSKVTNTGKEILCEKCVE
GKPVVAKPIVQQQQQHQQQQKQLHSSPTKATAQQQHHETLQKPMSPKDIDPNNCAGCNAE
LKEGQALIALDRQWHIWCFRCMVCGQVLSGEYMGKDGQPYCEKDYQKSFGVKCAYCERYI
SGKVLQAGDNHHFHPTCARCSKCGDPFGDGEEMYLQGTAIWHPRCGPHPSENNGTIFNGT
SAAEVDRISNSASEIQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g4002.t4 CDD cd09327 LIM1_abLIM 8 59 3.37332E-21
17 g4002.t4 CDD cd09329 LIM3_abLIM 174 225 6.69871E-26
12 g4002.t4 Gene3D G3DSA:2.10.110.10 Cysteine Rich Protein 1 59 8.0E-15
15 g4002.t4 Gene3D G3DSA:2.10.110.10 Cysteine Rich Protein 60 124 7.2E-20
13 g4002.t4 Gene3D G3DSA:2.10.110.10 Cysteine Rich Protein 157 230 8.6E-24
14 g4002.t4 Gene3D G3DSA:2.10.110.10 Cysteine Rich Protein 231 295 3.2E-16
25 g4002.t4 MobiDBLite mobidb-lite consensus disorder prediction 136 165 -
26 g4002.t4 MobiDBLite mobidb-lite consensus disorder prediction 136 160 -
5 g4002.t4 PANTHER PTHR24213 ACTIN-BINDING LIM PROTEIN 3 292 3.7E-116
4 g4002.t4 Pfam PF00412 LIM domain 8 62 2.6E-12
3 g4002.t4 Pfam PF00412 LIM domain 67 119 6.6E-11
2 g4002.t4 Pfam PF00412 LIM domain 174 229 2.7E-15
1 g4002.t4 Pfam PF00412 LIM domain 233 275 2.7E-7
20 g4002.t4 ProSitePatterns PS00478 LIM zinc-binding domain signature. 8 41 -
18 g4002.t4 ProSitePatterns PS00478 LIM zinc-binding domain signature. 67 100 -
19 g4002.t4 ProSitePatterns PS00478 LIM zinc-binding domain signature. 233 267 -
30 g4002.t4 ProSiteProfiles PS50023 LIM domain profile. 6 65 13.355
29 g4002.t4 ProSiteProfiles PS50023 LIM domain profile. 66 125 9.197
28 g4002.t4 ProSiteProfiles PS50023 LIM domain profile. 172 231 14.157
27 g4002.t4 ProSiteProfiles PS50023 LIM domain profile. 232 295 6.801
24 g4002.t4 SMART SM00132 lim_4 7 58 6.4E-14
23 g4002.t4 SMART SM00132 lim_4 66 118 9.8E-14
22 g4002.t4 SMART SM00132 lim_4 173 224 3.4E-15
21 g4002.t4 SMART SM00132 lim_4 232 285 2.3E-7
8 g4002.t4 SUPERFAMILY SSF57716 Glucocorticoid receptor-like (DNA-binding domain) 5 32 7.14E-5
11 g4002.t4 SUPERFAMILY SSF57716 Glucocorticoid receptor-like (DNA-binding domain) 33 96 1.43E-17
6 g4002.t4 SUPERFAMILY SSF57716 Glucocorticoid receptor-like (DNA-binding domain) 91 121 2.9E-6
9 g4002.t4 SUPERFAMILY SSF57716 Glucocorticoid receptor-like (DNA-binding domain) 169 199 5.08E-8
10 g4002.t4 SUPERFAMILY SSF57716 Glucocorticoid receptor-like (DNA-binding domain) 200 263 2.54E-14
7 g4002.t4 SUPERFAMILY SSF57716 Glucocorticoid receptor-like (DNA-binding domain) 260 289 2.36E-11

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

There are no GO annotations for this transcript.

KEGG

Orthology

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.

Raw TPM values