General information for g8748.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Prominin-like protein.
Parent gene
- The parent gene g8748 is located on chr_2: 32787855..32792993 (+ 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_2 | g8748 | g8748.t1 | isoform | g8748.t1 | 32779023 | 32788426 |
| chr_2 | g8748 | g8748.t1 | exon | g8748.t1.exon1 | 32779023 | 32779545 |
| chr_2 | g8748 | g8748.t1 | cds | g8748.t1.CDS1 | 32779023 | 32779545 |
| chr_2 | g8748 | g8748.t1 | exon | g8748.t1.exon2 | 32782256 | 32782529 |
| chr_2 | g8748 | g8748.t1 | cds | g8748.t1.CDS2 | 32782256 | 32782529 |
| chr_2 | g8748 | g8748.t1 | exon | g8748.t1.exon3 | 32782795 | 32783147 |
| chr_2 | g8748 | g8748.t1 | cds | g8748.t1.CDS3 | 32782795 | 32783147 |
| chr_2 | g8748 | g8748.t1 | exon | g8748.t1.exon4 | 32783209 | 32783333 |
| chr_2 | g8748 | g8748.t1 | cds | g8748.t1.CDS4 | 32783209 | 32783333 |
| chr_2 | g8748 | g8748.t1 | exon | g8748.t1.exon5 | 32784373 | 32784396 |
| chr_2 | g8748 | g8748.t1 | cds | g8748.t1.CDS5 | 32784373 | 32784396 |
| chr_2 | g8748 | g8748.t1 | exon | g8748.t1.exon6 | 32785354 | 32785799 |
| chr_2 | g8748 | g8748.t1 | cds | g8748.t1.CDS6 | 32785354 | 32785799 |
| chr_2 | g8748 | g8748.t1 | exon | g8748.t1.exon7 | 32785859 | 32786828 |
| chr_2 | g8748 | g8748.t1 | cds | g8748.t1.CDS7 | 32785859 | 32786828 |
| chr_2 | g8748 | g8748.t1 | exon | g8748.t1.exon8 | 32787258 | 32787379 |
| chr_2 | g8748 | g8748.t1 | cds | g8748.t1.CDS8 | 32787258 | 32787379 |
| chr_2 | g8748 | g8748.t1 | exon | g8748.t1.exon9 | 32787669 | 32787719 |
| chr_2 | g8748 | g8748.t1 | cds | g8748.t1.CDS9 | 32787669 | 32787719 |
| chr_2 | g8748 | g8748.t1 | exon | g8748.t1.exon10 | 32787855 | 32788001 |
| chr_2 | g8748 | g8748.t1 | cds | g8748.t1.CDS10 | 32787855 | 32788001 |
| chr_2 | g8748 | g8748.t1 | exon | g8748.t1.exon11 | 32788239 | 32788325 |
| chr_2 | g8748 | g8748.t1 | cds | g8748.t1.CDS11 | 32788239 | 32788325 |
| chr_2 | g8748 | g8748.t1 | exon | g8748.t1.exon12 | 32788384 | 32788426 |
| chr_2 | g8748 | g8748.t1 | cds | g8748.t1.CDS12 | 32788384 | 32788426 |
| chr_2 | g8748 | g8748.t1 | TTS | g8748.t1 | 32788697 | 32788697 |
| chr_2 | g8748 | g8748.t1 | TSS | g8748.t1 | NA | NA |
Sequences
>g8748.t1 Gene=g8748 Length=3165
ATGGGTGTGCCATCATTTCACCATAAACACGCGACCAATCGATATGATTTCAAAAAATTA
GGTTTAACAGCCGCTGTTTTGGCGGCATTTATCGTGATAGTAAATGTAGGCAATGTCAAT
GCATCTGATAGTTGGGCAAATGAACAGCATTTATTTCATAAAGAATATGAGCGACTGCAT
AAGCAAATAAAACCACAAACTTACTCCTTGCAAGATCAGATAGCTAGCAATCAACAGTAT
AATCGTCGTGCTCCAGTCTATCAGCCACCACAATTTAATGCTAATGTACCAAACAGAGGA
GACCATCATTTTGGTGTACAACATCAAGAACAACGACAAGAGCAAACACATCATCAACAG
CAGAGAACACTCGAAATTGAAAATACAAAATATTCAATTTGGTCACAAAACATGACTTAC
ATGAGCTCAACTGGTTACAATCCACTGGGCATGACTCCACTTTATAATCTTACCAATAAA
GTCATTGATTTCTTTGTTGACAAAGATGAACCAATTCCACCAGGTTATATCATCATTGAT
GAGATGAAAGTGAGCTTGGGACCGAATGTACAAAAACATCAATATTACGACATACTTAAG
AAATATTGGCTAATTATAATCATCGCCATTGTTACGATTATTACGGCATTGTTGATGCCA
TTAATTGGTCTATGTTTCTGTTGCTGCCGATGCGCTGGAGCATGTGGTGGAAGATCACAA
CCTTTCGATAAGAAACATGACACGTGCAGACGATTTCTTCTCGGTTTCATGCTGCTGATT
GTTGTATCTTCTATGGTCTTTGGTGTCATTGTTGCATACGTAACAAATATAACACTTCAG
CATGGTGTAGAAAATGCAACTTTGTCAGCACGAATTGCAGTTGATGATACGAGGACTTAT
CTAAAGTCGACATCATATCAAGTCAATCATCTTCTCGTGACAAATTATGGCGAATTAAGA
GAGCATTTGTTCCATACTCTTGATAAAACAGCAGATACGGTTGTTGCAAACTTGGATAAA
GCATCAAATGCTGTTTCACTTGATACACTACATGACATTGTAGAATCGCTGCCGGAAATT
CAAGAGAATTTGATTGAAATGGGTAAAATTACAAAAGACATGCAACAGAAAGCATCGCAG
TTGAATGATGGATTGAGAGGAGTTAAACGTGAATTATTGAGTGCTTTGCAAAGGTGCAAT
ACGAACGAATGCAAACAGGTACAAAAGGATTATGAAATTGGACGTTTAGATGAGAGCAAT
ATTCATTACGATAAGGAGATAGACAGATATTATCCAAGGCTTCCTGATCAAACTGAAATC
ATCACAAATGTTCAATCTTTATTGGATGGAACACTTCAACAAACTGTTGCATCAAGCGAG
AAAAAGGTGCGCGATATCCGAAATGAGATTGAGAACATCATAAAATCTAATGTGCCGGAA
GTTAAGATGTCGATTAACAAAGTTGGTCAGGCTCTTCATGAAATCTCAAATTCAGTGACG
CGCCAAATTGATGGCATTTCTGACATTGTTGGCAATAACACGTTCACACATTTTGACACT
GCCGAACATTATATTGCTCAGTATAGCATTTACCGATATTATGGTGGTCTAATTGTGAGC
TCTGTGCTGCTCATTGTGCTTGTGTTTACCACTTTTGGTCTTCTATGTGGCATATGTGGA
AAAAGACCTGATGGCTATGGCGATGATTGTTGTACTAAAGGTGCTGGCTCAAGATTTCTC
ATGTGTGGCGTGGCAATTATCTTCCTCACAATCTCTGCTTTGCTCATTATTTGTCTTGGA
CTCTTCCTTGCTGGTCTTGTTATGCGTCGTGGCGCTTGTGATCCACTTAAAAATCCACAA
CATGATCAAATTTTCAGTGATTATATTGACAAGTTTGTTGACATTAATAAATTTGTTTTT
AAAAATCAAAAAAATCCTTTACAACAACCAGAACAAAATGAAGAGCGAACAATTGAACCA
TTGAGAATTTCACAAGTCATTGCTGACTGTCATCGAAATAAATCCATTTTTGAAGTTTTC
CGAGTTGAAAATCGCATAAATATTAGTCAAATTGAAGATTTTCCTCGACGTTATGGCATC
GATTCAAAGCTAACTGAATTGGCCGATAATGTTGTGATAAATTCACAAATCAAAATTTTA
TCAGATGATGCTCGAAGAGAAATTCGTGTGCTTGCCAAGTCAGAACTCAATAATTTTGAA
GCATACAAGTACATTGATAATCTCACTCACAATATTACACACTTTAATCTCATTAGTTTG
GCTGATCGATTGAAGGTCGCTTCAACACGGCTCTCACCAGGCACTGAGACAAGGACAAAA
ATTGAAGTTCAGGAACTGCATTTACGAACTTACCAGAAGAATCTTGTTGATCCTTTAGTC
AATGGCACAAATCGTTTGCTATCGTTGTCAAAAACATTGTATGACAAATTGAATTTCAAG
CAGATGAGTTTTGAGAAGGCAATCATCAAATTGACACAAGAGATTGACGAAGCAGAAAGA
TTTTTGAATGAAGAGGGAAGTTCTTATGTACAAAAAGTCTCTCATCAATTGCTTGACAAC
TTTAGCCGCAATATCAAAGCTTATTTGAGCCTTGTTATTAATGCAACAACAGGCGATGTT
GGACGTTGTGAGCCAATCAGTAATGTTTACAATTCTACTATTGTAGCTGTCTGCAACCGT
GTTGTTGATCCATTCAATGGCTTTTGGGCAGGCGTAATCTTTTGTGTTCTTTTGTTCTTC
CCAACCATTGTACTTAGTGCAAAGCTATCGACATTATATCAAAAATCAGATCCCTATCCT
GGACCACTTGTGGAAGCTGAATATTTGTATGATGCATATAGTGAACGGGATAACATACCA
TTGGCAAACGTTCCAAAGAACAAAAGACGTCGTAAGAATGATAGACGTAGTCAGGGTAGA
GACAGACGTGGAGAGTATTATGAAGAAGCAAGTCCCGCACCATCCTCGAGCCATCCACAT
TCTCGTGATGCTCGCTACAACGATATGGCACCAAAGAATTGGGACAATGCACCACCACGA
TATCAAAATGCAGTAGCACCACCATCATCTGAATATGAAAGACCACCGCCATACTATTAT
AGTGGTTTTGGAACTGGAACTTCAGCACCAAGCGAAACAGACTAA
>g8748.t1 Gene=g8748 Length=1054
MGVPSFHHKHATNRYDFKKLGLTAAVLAAFIVIVNVGNVNASDSWANEQHLFHKEYERLH
KQIKPQTYSLQDQIASNQQYNRRAPVYQPPQFNANVPNRGDHHFGVQHQEQRQEQTHHQQ
QRTLEIENTKYSIWSQNMTYMSSTGYNPLGMTPLYNLTNKVIDFFVDKDEPIPPGYIIID
EMKVSLGPNVQKHQYYDILKKYWLIIIIAIVTIITALLMPLIGLCFCCCRCAGACGGRSQ
PFDKKHDTCRRFLLGFMLLIVVSSMVFGVIVAYVTNITLQHGVENATLSARIAVDDTRTY
LKSTSYQVNHLLVTNYGELREHLFHTLDKTADTVVANLDKASNAVSLDTLHDIVESLPEI
QENLIEMGKITKDMQQKASQLNDGLRGVKRELLSALQRCNTNECKQVQKDYEIGRLDESN
IHYDKEIDRYYPRLPDQTEIITNVQSLLDGTLQQTVASSEKKVRDIRNEIENIIKSNVPE
VKMSINKVGQALHEISNSVTRQIDGISDIVGNNTFTHFDTAEHYIAQYSIYRYYGGLIVS
SVLLIVLVFTTFGLLCGICGKRPDGYGDDCCTKGAGSRFLMCGVAIIFLTISALLIICLG
LFLAGLVMRRGACDPLKNPQHDQIFSDYIDKFVDINKFVFKNQKNPLQQPEQNEERTIEP
LRISQVIADCHRNKSIFEVFRVENRINISQIEDFPRRYGIDSKLTELADNVVINSQIKIL
SDDARREIRVLAKSELNNFEAYKYIDNLTHNITHFNLISLADRLKVASTRLSPGTETRTK
IEVQELHLRTYQKNLVDPLVNGTNRLLSLSKTLYDKLNFKQMSFEKAIIKLTQEIDEAER
FLNEEGSSYVQKVSHQLLDNFSRNIKAYLSLVINATTGDVGRCEPISNVYNSTIVAVCNR
VVDPFNGFWAGVIFCVLLFFPTIVLSAKLSTLYQKSDPYPGPLVEAEYLYDAYSERDNIP
LANVPKNKRRRKNDRRSQGRDRRGEYYEEASPAPSSSHPHSRDARYNDMAPKNWDNAPPR
YQNAVAPPSSEYERPPPYYYSGFGTGTSAPSETD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g8748.t1 | Coils | Coil | Coil | 456 | 476 | - |
| 10 | g8748.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 960 | 1054 | - |
| 2 | g8748.t1 | PANTHER | PTHR22730:SF1 | PROMININ-LIKE PROTEIN | 119 | 1022 | 3.6E-196 |
| 3 | g8748.t1 | PANTHER | PTHR22730 | PROMININ PROM PROTEIN | 119 | 1022 | 3.6E-196 |
| 1 | g8748.t1 | Pfam | PF05478 | Prominin | 117 | 934 | 1.2E-200 |
| 19 | g8748.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 41 | - |
| 20 | g8748.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 19 | - |
| 21 | g8748.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 20 | 33 | - |
| 27 | g8748.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 34 | 41 | - |
| 16 | g8748.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 42 | 201 | - |
| 22 | g8748.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 202 | 231 | - |
| 15 | g8748.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 232 | 251 | - |
| 26 | g8748.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 252 | 274 | - |
| 17 | g8748.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 275 | 532 | - |
| 23 | g8748.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 533 | 558 | - |
| 14 | g8748.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 559 | 578 | - |
| 25 | g8748.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 579 | 608 | - |
| 18 | g8748.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 609 | 907 | - |
| 24 | g8748.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 908 | 927 | - |
| 13 | g8748.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 928 | 1054 | - |
| 11 | g8748.t1 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 41 | - |
| 6 | g8748.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 20 | 39 | - |
| 9 | g8748.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 202 | 224 | - |
| 7 | g8748.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 252 | 274 | - |
| 8 | g8748.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 533 | 555 | - |
| 5 | g8748.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 585 | 607 | - |
| 4 | g8748.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 905 | 927 | - |
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:0016021 | integral component of membrane | CC |
KEGG
Orthology
- This transcript has been annotated with K06532 (prominin 1)
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.
