General information for g1987.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as ABC transporter G family member 23.
Parent gene
- The parent gene g1987 is located on chr_3: 14228767..14229943 (+ 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 | g1987 | g1987.t1 | TSS | g1987.t1 | 14226195 | 14226195 |
| chr_3 | g1987 | g1987.t1 | isoform | g1987.t1 | 14226352 | 14229943 |
| chr_3 | g1987 | g1987.t1 | exon | g1987.t1.exon1 | 14226352 | 14226550 |
| chr_3 | g1987 | g1987.t1 | cds | g1987.t1.CDS1 | 14226352 | 14226550 |
| chr_3 | g1987 | g1987.t1 | exon | g1987.t1.exon2 | 14227497 | 14227695 |
| chr_3 | g1987 | g1987.t1 | cds | g1987.t1.CDS2 | 14227497 | 14227695 |
| chr_3 | g1987 | g1987.t1 | exon | g1987.t1.exon3 | 14227762 | 14228133 |
| chr_3 | g1987 | g1987.t1 | cds | g1987.t1.CDS3 | 14227762 | 14228133 |
| chr_3 | g1987 | g1987.t1 | exon | g1987.t1.exon4 | 14228203 | 14228589 |
| chr_3 | g1987 | g1987.t1 | cds | g1987.t1.CDS4 | 14228203 | 14228589 |
| chr_3 | g1987 | g1987.t1 | exon | g1987.t1.exon5 | 14228646 | 14229242 |
| chr_3 | g1987 | g1987.t1 | cds | g1987.t1.CDS5 | 14228646 | 14229242 |
| chr_3 | g1987 | g1987.t1 | exon | g1987.t1.exon6 | 14229305 | 14229657 |
| chr_3 | g1987 | g1987.t1 | cds | g1987.t1.CDS6 | 14229305 | 14229657 |
| chr_3 | g1987 | g1987.t1 | exon | g1987.t1.exon7 | 14229720 | 14229943 |
| chr_3 | g1987 | g1987.t1 | cds | g1987.t1.CDS7 | 14229720 | 14229943 |
| chr_3 | g1987 | g1987.t1 | TTS | g1987.t1 | NA | NA |
Sequences
>g1987.t1 Gene=g1987 Length=2331
ATGGATCAATTGTTGAAGATTTATGAGCCAGCCCGTGCTTTTTCAAAAGATTCAATCAGA
CTAATCAAGAGATGTACAAAACCTGATCGTCGTGAGTTCCAGAAGATTGCTATTGCAACA
GCTATTGGTTTCTGTATTATGGGATTCATTGGATTCTTTGTGAAACTCATTCACATACCA
ATCAATAATATTATTGTTGAATTAATTCATAAAATCAGTCTTGAATTAGCGCTCAGTATG
GATAGCAGCACAGAGCTTCAGCTAGAAAAAATTAATAACGGCGTCGTGTCGTGTGATTAT
GCAGTAAAAATTCGGAATGCATACAAGTGTTTTCAACAAAGGAATGAGAAGGTCGAAATT
CTTAAAAGATTAAATATGTCGATAAAAAAGAAATCAATATATGCACTGATGGGTTGTAGT
GGTGTAGGAAAAACAACTTTATTACGTTCTATAATTGCAATTGATACACTACAAAGTGGG
AAAATTGAAATTTTTGGTGAACCAGTAGTTCAAAATGATCCTAGAATCGGTTTTATGCCT
CAGGAAATTTCACTCATCGAAAATTTTACAGTGAAAGAAATGGTCGATTTTTTCAGTGTA
TTATACAAATTGAGAACTGAGAAAATCAATGCACGATTTAAATTTTTAAGTGAATTACTT
GAACTTCCCGATGATAATAAATTTATTAAAGAATGCAGTCTCGGTGAAAAAAGGCGAATT
TCGTTTGCATGTGCTTTAGTTCATGAGCCAAAAATTTTAATTTTAGATGAACCAACAGTT
GGTATTGACGCAGTGCTACGTAAAAAGATTTGGGATTTTCTAATAGAACTTGTAGCTACT
TCTGACACTACTGTAATAATTTCAACACATTATATTCAAGAATCAATGAATTCCACGTGT
GTAGGATTAATGAGAAATGGAAAAATTTTAATTGAAGATAAACCACAAGACATTATTCAA
AGATATAACACAAAGAATTTAGAGGAAGCATTTTTGATACTGAGCGATGAACAAGATAAG
AGTCTTAGTGTTTCAGAAACAAATGAAGAAGAATTTGATTTTCTTTATCATGTGCCGAAG
CAATCGTTCAATTTTTCAATGAAACGGTTAATGGCGCTTTTAACAAAAAATTTTATTCAT
CAGAAAAGAAGCAAGACAATGTTTATGTTTCTTTGTGTTTTTCCGCTAATCGTACTCATG
AGTATTGCTACATTTGGAAGAGATCCACAGGGATTAAAGATAGGCATAGTTGATGATGAA
GTTGATAACCTTGAACAATGCTACAATTCATCACTCATCACCACATTTTTGAATGAAACC
ACATGTTATATCAAAGATATCTCTTGTCGTTTTGTTAATCAACTGAAGGACGATGTAGCT
ATAAAAATATTTTATAACAATCTCGACTCAGCTGTTCATGACGTAAAAAATGGAAAAATT
GTTGGCTTGATTCATTTCAGTAAAGAATTTACAAACATACTACAGCAAAAATTTAATCGA
ATCGAAGTGGAAAAAATTAGCTCATTAAATGCTGATTATGGAACGATAAATATTTATTTA
GATCAATCAAGTATGGCAGTGACAGAATTTCTAAGACGAAGGCTAGTTGAAACTTATCAA
CAATACTCAGAAAGTCTTATGGAAAGCTGTGGAATTTCTAAAAAGTATGGAAATATTCCA
ATCAATGTTCAAGCATTATTTGGCACATTGCAAGATGAATTTCAAAAATACATGTGTGTT
GGTGTCGCAGTTCTCTGCTACTTTTTTCAAGCATCATCTCTTACTAGCACAGCTTTAATT
GGCGATCGAGTTGATGGAATTTGGAATAGAACACTTGTAGCTGGCACACAGCCATTGGAG
TTAATTCTTTCACATCTTGTACCATGCACTGTACTAATGTTGATCCAATGCACTGAATAT
TTCCTGTTACTTGTTTATTACTTCAGGGACAATCCAAATTCAAACATTTTTCTCTCAGGG
TGCCTTTTTCTACTGCTAGGCATATGTGGATTGATTTATGGAATTTCAGTGTCAGTATAT
GCTGATTCTTATTCCATTGCATTGTTTTTATCAACAGTTATTTTCATTCCAGTTTTAGGC
GTTGCTGGAATATTATGGCCAATTGAAGCAGTACCAATTTATTTACGTTATATAGGATAT
TCGATGCCATTCACTATACCAATTATTGCTATAAGAGGCCTCTTTTTCAAAGGACTAACA
TTCTGCGATCATATTGTTTATTTGTCATTCATCATTGCGATTTTGTGGACAATTTTCTCA
TTTATTTTGTGTTATTTTGGATTGAAAATTCGAAAATATCACAAAAGATGA
>g1987.t1 Gene=g1987 Length=776
MDQLLKIYEPARAFSKDSIRLIKRCTKPDRREFQKIAIATAIGFCIMGFIGFFVKLIHIP
INNIIVELIHKISLELALSMDSSTELQLEKINNGVVSCDYAVKIRNAYKCFQQRNEKVEI
LKRLNMSIKKKSIYALMGCSGVGKTTLLRSIIAIDTLQSGKIEIFGEPVVQNDPRIGFMP
QEISLIENFTVKEMVDFFSVLYKLRTEKINARFKFLSELLELPDDNKFIKECSLGEKRRI
SFACALVHEPKILILDEPTVGIDAVLRKKIWDFLIELVATSDTTVIISTHYIQESMNSTC
VGLMRNGKILIEDKPQDIIQRYNTKNLEEAFLILSDEQDKSLSVSETNEEEFDFLYHVPK
QSFNFSMKRLMALLTKNFIHQKRSKTMFMFLCVFPLIVLMSIATFGRDPQGLKIGIVDDE
VDNLEQCYNSSLITTFLNETTCYIKDISCRFVNQLKDDVAIKIFYNNLDSAVHDVKNGKI
VGLIHFSKEFTNILQQKFNRIEVEKISSLNADYGTINIYLDQSSMAVTEFLRRRLVETYQ
QYSESLMESCGISKKYGNIPINVQALFGTLQDEFQKYMCVGVAVLCYFFQASSLTSTALI
GDRVDGIWNRTLVAGTQPLELILSHLVPCTVLMLIQCTEYFLLLVYYFRDNPNSNIFLSG
CLFLLLGICGLIYGISVSVYADSYSIALFLSTVIFIPVLGVAGILWPIEAVPIYLRYIGY
SMPFTIPIIAIRGLFFKGLTFCDHIVYLSFIIAILWTIFSFILCYFGLKIRKYHKR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 30 | g1987.t1 | CDD | cd03230 | ABC_DR_subfamily_A | 102 | 309 | 2.33067E-48 |
| 12 | g1987.t1 | Gene3D | G3DSA:1.20.5.820 | Preprotein translocase SecE subunit | 8 | 67 | 4.0E-32 |
| 11 | g1987.t1 | Gene3D | G3DSA:3.40.50.300 | - | 98 | 357 | 1.3E-51 |
| 8 | g1987.t1 | Hamap | MF_00422 | Protein translocase subunit SecE [secE]. | 9 | 64 | 12.807115 |
| 4 | g1987.t1 | PANTHER | PTHR43038 | ATP-BINDING CASSETTE, SUB-FAMILY H, MEMBER 1 | 101 | 345 | 5.1E-184 |
| 6 | g1987.t1 | PANTHER | PTHR43038:SF2 | RH61964P | 101 | 345 | 5.1E-184 |
| 5 | g1987.t1 | PANTHER | PTHR43038 | ATP-BINDING CASSETTE, SUB-FAMILY H, MEMBER 1 | 360 | 772 | 5.1E-184 |
| 7 | g1987.t1 | PANTHER | PTHR43038:SF2 | RH61964P | 360 | 772 | 5.1E-184 |
| 1 | g1987.t1 | Pfam | PF00584 | SecE/Sec61-gamma subunits of protein translocation complex | 13 | 65 | 8.3E-13 |
| 3 | g1987.t1 | Pfam | PF00005 | ABC transporter | 121 | 259 | 5.1E-23 |
| 2 | g1987.t1 | Pfam | PF12698 | ABC-2 family transporter protein | 386 | 763 | 4.2E-26 |
| 17 | g1987.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 35 | - |
| 24 | g1987.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 36 | 54 | - |
| 21 | g1987.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 55 | 386 | - |
| 25 | g1987.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 387 | 406 | - |
| 15 | g1987.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 407 | 576 | - |
| 23 | g1987.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 577 | 601 | - |
| 20 | g1987.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 602 | 620 | - |
| 28 | g1987.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 621 | 648 | - |
| 16 | g1987.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 649 | 654 | - |
| 29 | g1987.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 655 | 680 | - |
| 18 | g1987.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 681 | 685 | - |
| 26 | g1987.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 686 | 706 | - |
| 13 | g1987.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 707 | 717 | - |
| 27 | g1987.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 718 | 739 | - |
| 19 | g1987.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 740 | 744 | - |
| 22 | g1987.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 745 | 768 | - |
| 14 | g1987.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 769 | 776 | - |
| 41 | g1987.t1 | ProSitePatterns | PS01067 | Protein secE/sec61-gamma signature. | 14 | 42 | - |
| 40 | g1987.t1 | ProSitePatterns | PS00211 | ABC transporters family signature. | 232 | 246 | - |
| 43 | g1987.t1 | ProSiteProfiles | PS50893 | ATP-binding cassette, ABC transporter-type domain profile. | 102 | 331 | 18.181 |
| 39 | g1987.t1 | SMART | SM00382 | AAA_5 | 130 | 315 | 7.8E-7 |
| 9 | g1987.t1 | SUPERFAMILY | SSF103456 | Preprotein translocase SecE subunit | 6 | 65 | 1.16E-11 |
| 10 | g1987.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 101 | 323 | 1.84E-47 |
| 42 | g1987.t1 | TIGRFAM | TIGR00327 | secE_euk_arch: protein translocase SEC61 complex gamma subunit, archaeal and eukaryotic | 12 | 66 | 4.4E-14 |
| 36 | g1987.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 36 | 58 | - |
| 35 | g1987.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 386 | 405 | - |
| 38 | g1987.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 579 | 601 | - |
| 31 | g1987.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 621 | 643 | - |
| 34 | g1987.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 656 | 675 | - |
| 33 | g1987.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 685 | 707 | - |
| 37 | g1987.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 714 | 736 | - |
| 32 | g1987.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 746 | 768 | - |
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:0016020 | membrane | CC |
| GO:0006886 | intracellular protein transport | BP |
| GO:0006605 | protein targeting | BP |
| GO:0005524 | ATP binding | MF |
| GO:0015450 | protein-transporting ATPase activity | MF |
| GO:0015031 | protein transport | BP |
| GO:0016887 | ATP hydrolysis activity | MF |
KEGG
Orthology
- This transcript has been annotated with K07342 (protein transport protein SEC61 subunit gamma and related proteins)
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.
