Gene loci information

Transcript annotation

  • This transcript has been annotated as Lipoma-preferred partner-like protein.

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_1 g12528 g12528.t1 TSS g12528.t1 24262846 24262846
chr_1 g12528 g12528.t1 isoform g12528.t1 24263137 24264828
chr_1 g12528 g12528.t1 exon g12528.t1.exon1 24263137 24263257
chr_1 g12528 g12528.t1 cds g12528.t1.CDS1 24263137 24263257
chr_1 g12528 g12528.t1 exon g12528.t1.exon2 24263320 24263342
chr_1 g12528 g12528.t1 cds g12528.t1.CDS2 24263320 24263342
chr_1 g12528 g12528.t1 exon g12528.t1.exon3 24263402 24264655
chr_1 g12528 g12528.t1 cds g12528.t1.CDS3 24263402 24264655
chr_1 g12528 g12528.t1 exon g12528.t1.exon4 24264709 24264828
chr_1 g12528 g12528.t1 cds g12528.t1.CDS4 24264709 24264828
chr_1 g12528 g12528.t1 TTS g12528.t1 24265227 24265227

Sequences

>g12528.t1 Gene=g12528 Length=1518
ATGGATGAATTGGCTGAAAATTTACAAAAATTGAATATGATCAAAGCTAAATTTGATCAA
ACAAAAGATCATGGCACAAATTCACCGACTTACAGTAAACCGGGGACAAAGAAAGCACCA
ATCGTGCCACCAAAACCAAAAAAAAACGATGATGTCACCTCAATACCACTTGTACCGAGA
AGTACATTGAGCAATAAAATTTGTAAGCCATCATATGTGACTCCTTTAGTTGGTGGAGTT
GCATCTGATGATCCACACATTTATGCCAATGCAAATAAAACACTCGATGATGCGATTGAG
TTGCAGTTAAAAAAAGAAGCACTCGAACATAGGAAGAAAATTTTAGAATATAATAAAAAT
ATTTATGCAAATAGTCAGAAAGCACAATTTTATGAAAATATCAATAATCAAGGTGATAAA
TTGATTTATTCAAATTTAATGCATCCACCACCACCACCACCACCGCTTGATGTGAACACA
GTGGCTGAACATGATGAAGAATTTCCAGGTCCTCCATCACCAGTGTCTTCATCATATTCT
GAATTAAGACGTGCAACTGACACAAATTGTTATGCAACAACAATCTTGCCAGCACCAATT
AATCATCAATATCGAATTGGAAATGTTGTAGCTAATCAGCATCAAATAAAAAATAATACT
TATTCGAATGATTATGGAATTTATGGTGGTCCACTTTCTCAAAATTCAACAACTTATGAA
TCAATTTATGAACCAATTAATCCACGTCCACAATCACAAATGTCTTCGCGCTCAAATTAC
TCACTTTATGCTCCATATGTTGACGGACTGTGCAGTAGCAGTAGCTCAATGAATCGCTTG
CCAGTTATTACACAAGAGACAGAAGTTGATGCGCTCACTGATTTATTAGTCCAATCAATT
CATCAAGCAAATCCCGATCCTGATAATTATGGAACTTGTTGTAAATGCAATGGTATTGTC
ACTGAAGCATCCGGTTGTACTGCTATGGAAAAAATTTATCACATTGCTTGTTTCACGTGT
CATCAATGTCAAACGAGCTTGCAAGGTAAACCGTTTTATGGACTCGATGGTAAACCATTT
TGTGAAGAAGATTATTTGAATACACTCGAGAAATGTTGTGTTTGCTTGCAACCAATTACT
GAACGCATTTTAAGAGCAACAGGAAAACCTTATCATCCACAATGCTTTAAATGTATTGTT
TGTGGTGAAAGTTTAGATGGCATTCCTTTCACTGTTGATGCTACAAATAAAATTCATTGC
ATTGAAGATTTTCATAAACGCTTTGCACCACGTTGTTCTGTTTGCAAGAAGCCCATTATG
CCGGAACCAGGAAAAGAAGAAACTATTCGGGTTGTGGCACTTGACCGTAGTTTTCATATC
AATTGTTATAAATGCGAGGATTGTGGACTATTGCTATCATCAGAGGCAGAAGGAAGAGGT
TGCTTCCCGCTTGATGATCATGTATTGTGTAAAAATTGCAATGCCAAACGAGTTCAAGCT
TTGACGAGTATGATTTAA

>g12528.t1 Gene=g12528 Length=505
MDELAENLQKLNMIKAKFDQTKDHGTNSPTYSKPGTKKAPIVPPKPKKNDDVTSIPLVPR
STLSNKICKPSYVTPLVGGVASDDPHIYANANKTLDDAIELQLKKEALEHRKKILEYNKN
IYANSQKAQFYENINNQGDKLIYSNLMHPPPPPPPLDVNTVAEHDEEFPGPPSPVSSSYS
ELRRATDTNCYATTILPAPINHQYRIGNVVANQHQIKNNTYSNDYGIYGGPLSQNSTTYE
SIYEPINPRPQSQMSSRSNYSLYAPYVDGLCSSSSSMNRLPVITQETEVDALTDLLVQSI
HQANPDPDNYGTCCKCNGIVTEASGCTAMEKIYHIACFTCHQCQTSLQGKPFYGLDGKPF
CEEDYLNTLEKCCVCLQPITERILRATGKPYHPQCFKCIVCGESLDGIPFTVDATNKIHC
IEDFHKRFAPRCSVCKKPIMPEPGKEETIRVVALDRSFHINCYKCEDCGLLLSSEAEGRG
CFPLDDHVLCKNCNAKRVQALTSMI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g12528.t1 CDD cd09354 LIM2_LPP 372 431 1.0938E-35
13 g12528.t1 CDD cd09437 LIM3_LPP 432 499 2.1284E-42
11 g12528.t1 Coils Coil Coil 1 21 -
12 g12528.t1 Coils Coil Coil 91 118 -
10 g12528.t1 Gene3D G3DSA:2.10.110.10 Cysteine Rich Protein 295 368 6.7E-15
9 g12528.t1 Gene3D G3DSA:2.10.110.10 Cysteine Rich Protein 369 427 1.2E-17
8 g12528.t1 Gene3D G3DSA:2.10.110.10 Cysteine Rich Protein 428 504 3.6E-18
18 g12528.t1 MobiDBLite mobidb-lite consensus disorder prediction 15 52 -
4 g12528.t1 PANTHER PTHR24207:SF2 ZYX102 PROTEIN 47 504 2.4E-151
5 g12528.t1 PANTHER PTHR24207 ZYX102 PROTEIN 47 504 2.4E-151
1 g12528.t1 Pfam PF00412 LIM domain 313 367 5.4E-12
2 g12528.t1 Pfam PF00412 LIM domain 372 428 1.5E-9
3 g12528.t1 Pfam PF00412 LIM domain 432 496 6.3E-8
19 g12528.t1 ProSiteProfiles PS50023 LIM domain profile. 311 369 10.375
21 g12528.t1 ProSiteProfiles PS50023 LIM domain profile. 370 430 13.038
20 g12528.t1 ProSiteProfiles PS50023 LIM domain profile. 431 500 10.316
16 g12528.t1 SMART SM00132 lim_4 312 364 5.4E-14
15 g12528.t1 SMART SM00132 lim_4 371 423 1.7E-13
17 g12528.t1 SMART SM00132 lim_4 431 493 1.8E-15
6 g12528.t1 SUPERFAMILY SSF57716 Glucocorticoid receptor-like (DNA-binding domain) 340 398 8.4E-13
7 g12528.t1 SUPERFAMILY SSF57716 Glucocorticoid receptor-like (DNA-binding domain) 397 468 1.08E-12

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