General information for g1947.t6
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Protein lin-54-like protein.
Parent gene
- The parent gene g1947 is located on chr_3: 14016138..14023833 (+ 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 | g1947 | g1947.t6 | TSS | g1947.t6 | 14013670 | 14013670 |
| chr_3 | g1947 | g1947.t6 | isoform | g1947.t6 | 14014405 | 14016138 |
| chr_3 | g1947 | g1947.t6 | exon | g1947.t6.exon1 | 14014405 | 14014601 |
| chr_3 | g1947 | g1947.t6 | cds | g1947.t6.CDS1 | 14014553 | 14014601 |
| chr_3 | g1947 | g1947.t6 | exon | g1947.t6.exon2 | 14014677 | 14015469 |
| chr_3 | g1947 | g1947.t6 | cds | g1947.t6.CDS2 | 14014677 | 14015469 |
| chr_3 | g1947 | g1947.t6 | exon | g1947.t6.exon3 | 14015604 | 14015737 |
| chr_3 | g1947 | g1947.t6 | cds | g1947.t6.CDS3 | 14015604 | 14015737 |
| chr_3 | g1947 | g1947.t6 | exon | g1947.t6.exon4 | 14015807 | 14016138 |
| chr_3 | g1947 | g1947.t6 | cds | g1947.t6.CDS4 | 14015807 | 14016138 |
| chr_3 | g1947 | g1947.t6 | TTS | g1947.t6 | 14016363 | 14016363 |
Sequences
>g1947.t6 Gene=g1947 Length=1456
ATGGCATCAAAACAGATTTGTAAGTTTATATGTGAATCCAGTATTAAAAGATTCAATAAT
TGTAAAATTATTTCTCAAAAATGTAGTAAAAGAGGATGGAAGATATGTTATAATCAATCA
GGATGGTCGCTCAATTCCATTGAAAGTGATGAATGTTCAAAAAGAAACTCCAGAGCCTAA
AAAATATGTTGTAAAAACGAGTTCAGGACAAGTGATTTCAGTTTCATCACCAACAGCAGT
CAAAGTTGAAAAGCAAGGTTCAGTAAAAACAATTGGTCCTGCTGGATCAATTACAATCGG
TGGCCAAAGAAAGACAGTCTCAACATCTTCAAATGAACAAGGTTTTAAAATTGTATCTTC
GCCCACTTCACCTTCAACAAGTGGTGTAAAGGTGGTAAGAGTTGTTACTTCAGGAGGAGG
AACAACCCAAAAAGTCATTCAAGTTCAAAAACAATCTGCTCCACGTATTCTCAATCAAAC
ATGGAGTCATACTTCTGAAGTAAAACCTGAACCTGTTCAACCGCGTGCAATCACTGTTGT
TAGAAAATCAGAGACAGGTTTTGAGCCACCAGCTAAAAAGACAAAGTACATTACATTGAC
ATCGTCACAAATAAGTCAAATTGAAGGTGCTACAATAATAAATGATGGGGACAAAAAACG
AGTTATGTTGCCAACAAATTATCGTGAGCAACTTGAAAAGATTTCACCTACCAAAAGTTC
AGGTCAGGTATTTAAAATTGTCCAAGAAGTCAAAAAACCAGCTCTTGAGATTGATCCACT
TGATATGAATAAATCATATCCTGGAATGAAGAAACCAAAGAGACCTTGTAATTGTACAAA
ATCTCAATGTCTCAAATTTTATTGCGATTGTTTTGCTGCTGGAGAATACTGTGTTGGATG
TAATTGCAAGGATTGTTTGAATGAACATGACACTGAAGAGCGTGAAAAAGCTGTTAAATT
ATGTATGGAGAGAAATCCGTTTGCATTCAAATCAAAAGAAGCTAACGAAGAGCAACAACG
TCTGCATCAACGCGGTTGTAATTGTAAAAGATCAGGTTGCTTGAAAAACTATTGCGAGTG
TTACGAAGCAAAAATTTCTTGTTCTGCAAATTGCCGTTGTTTAGGTTGCAAAAACGTTGA
CGATATAGACGAAAAAATGGAAATGGAGTTGCAATATCTAAAGCAATGTGGAAAACGTGG
ACAATTTAGTGAAGAAATTTACGAGAAAAATTTGGCAGCTCTAAAAAAAGTCACTGATTT
GAATGAATTAGTTAAAAAGCCGTACAATTTTATGACTCAGGATGTCATTGAAGCTACTGT
TCAGTGCATGATTGCACAGGCTGAAGAATGTGAAAAAATGAGTGTATCAAAGAAAGAAGG
AGAACGAATGATTCTTGAAGAGTTTAGTCGATGTCTACAAGAGATTATTGAATTCTCAGC
AAAGAATGTTGATTAA
>g1947.t6 Gene=g1947 Length=435
MNVQKETPEPKKYVVKTSSGQVISVSSPTAVKVEKQGSVKTIGPAGSITIGGQRKTVSTS
SNEQGFKIVSSPTSPSTSGVKVVRVVTSGGGTTQKVIQVQKQSAPRILNQTWSHTSEVKP
EPVQPRAITVVRKSETGFEPPAKKTKYITLTSSQISQIEGATIINDGDKKRVMLPTNYRE
QLEKISPTKSSGQVFKIVQEVKKPALEIDPLDMNKSYPGMKKPKRPCNCTKSQCLKFYCD
CFAAGEYCVGCNCKDCLNEHDTEEREKAVKLCMERNPFAFKSKEANEEQQRLHQRGCNCK
RSGCLKNYCECYEAKISCSANCRCLGCKNVDDIDEKMEMELQYLKQCGKRGQFSEEIYEK
NLAALKKVTDLNELVKKPYNFMTQDVIEATVQCMIAQAEECEKMSVSKKEGERMILEEFS
RCLQEIIEFSAKNVD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 3 | g1947.t6 | PANTHER | PTHR12446 | TESMIN/TSO1-RELATED | 173 | 432 | 0.000 |
| 4 | g1947.t6 | PANTHER | PTHR12446:SF36 | PROTEIN LIN-54 HOMOLOG | 173 | 432 | 0.000 |
| 1 | g1947.t6 | Pfam | PF03638 | Tesmin/TSO1-like CXC domain, cysteine-rich domain | 225 | 259 | 0.000 |
| 2 | g1947.t6 | Pfam | PF03638 | Tesmin/TSO1-like CXC domain, cysteine-rich domain | 295 | 329 | 0.000 |
| 7 | g1947.t6 | ProSiteProfiles | PS51634 | CRC domain profile. | 223 | 332 | 30.282 |
| 6 | g1947.t6 | SMART | SM01114 | CXC_2 | 222 | 262 | 0.000 |
| 5 | g1947.t6 | SMART | SM01114 | CXC_2 | 292 | 333 | 0.000 |
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
- This transcript has been annotated with K21776 (protein lin-54)
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.
