General information for g5204.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as ER degradation-enhancing alpha-mannosidase-like protein 3.
Parent gene
- The parent gene g5204 is located on chr_2: 7640557..7641534 (- 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 | g5204 | g5204.t1 | TTS | g5204.t1 | 7636897 | 7636897 |
| chr_2 | g5204 | g5204.t1 | isoform | g5204.t1 | 7637175 | 7641534 |
| chr_2 | g5204 | g5204.t1 | exon | g5204.t1.exon1 | 7637175 | 7637267 |
| chr_2 | g5204 | g5204.t1 | cds | g5204.t1.CDS1 | 7637175 | 7637267 |
| chr_2 | g5204 | g5204.t1 | exon | g5204.t1.exon2 | 7637324 | 7637725 |
| chr_2 | g5204 | g5204.t1 | cds | g5204.t1.CDS2 | 7637324 | 7637725 |
| chr_2 | g5204 | g5204.t1 | exon | g5204.t1.exon3 | 7637785 | 7637880 |
| chr_2 | g5204 | g5204.t1 | cds | g5204.t1.CDS3 | 7637785 | 7637880 |
| chr_2 | g5204 | g5204.t1 | exon | g5204.t1.exon4 | 7637939 | 7638210 |
| chr_2 | g5204 | g5204.t1 | cds | g5204.t1.CDS4 | 7637939 | 7638210 |
| chr_2 | g5204 | g5204.t1 | exon | g5204.t1.exon5 | 7638274 | 7639487 |
| chr_2 | g5204 | g5204.t1 | cds | g5204.t1.CDS5 | 7638274 | 7639487 |
| chr_2 | g5204 | g5204.t1 | exon | g5204.t1.exon6 | 7641061 | 7641200 |
| chr_2 | g5204 | g5204.t1 | cds | g5204.t1.CDS6 | 7641061 | 7641200 |
| chr_2 | g5204 | g5204.t1 | exon | g5204.t1.exon7 | 7641295 | 7641301 |
| chr_2 | g5204 | g5204.t1 | cds | g5204.t1.CDS7 | 7641295 | 7641301 |
| chr_2 | g5204 | g5204.t1 | exon | g5204.t1.exon8 | 7641398 | 7641534 |
| chr_2 | g5204 | g5204.t1 | cds | g5204.t1.CDS8 | 7641398 | 7641534 |
| chr_2 | g5204 | g5204.t1 | TSS | g5204.t1 | 7641630 | 7641630 |
Sequences
>g5204.t1 Gene=g5204 Length=2361
ATGAATTTCGTGCATAAGAATGATGCACGGGTGCATCAGATCATAAGTTTAGTGGTAGTT
TTAGTATTTTTTATTAATTTAGTAAATTCACAAAATTTAAACAATATTTTATCTACGAAG
GAAAAAAATGAGCTCAAGGAAGAGGCTCGGGAAATGTTCTATCATGCTTATAGAGCATAT
ATGGATAATGCTTTTCCTGCGGACGAACTGCAGCCACTTTCTTGTAAAGGAAGAATTCGT
GGTATTTCGAAATCGAGAGGGGATTTGGATGATACATTAGGAAATTTTTCTATGACTTTG
GTAGATACACTCGATACATTAGTGATATTAGGAGATTTTGAAGAATTTGAGTCAGCTGTA
AAGCTTGTGATTAAAAATGTTCAATTTGACAATGATATCATTGTGTCTGTATTTGAGACA
AATATCCGTATGCTTGGCGGCCTCTTGTCAGCTCACGTGCTTGCCGAATATATTCAGAAA
GAAGCTCACATAATGATGTGGTATCGAGGAGAATTACTCGAAATGGCAAAAGATCTTGGC
TATCGATTGCTTCCTGCGTTCAATACATCCACTGGTATTCCACATGCACGAATCAATTTA
AAATATGGAATGAAATCGGAAGCACTGAAACATTCACGTGAAACTTGTACAGCATGTGCT
GGTACAATTCTTTTAGAGTTTGCTGCTCTTTCTCGTCTTAGTGGTGAACCAATATTCGAA
GCTAAAGCACATCAAGCTATGGACGCTTTATGGAAAATCAGAAATCGTTCTTCTAATTTG
ATGGGAACTGTAGTCAACGTTCATTCGGGTGATTGGATCAGACGAGATTCTGGTGTTGGT
GCAGGCATAGATTCTTACTACGAATATTGTTTAAAATCTTACATATTACTTGGGGATGAA
CGATATTTATCGAGATTTAATCGTCATTATAATGCTGTCATGAAATACGTTAAACAAGGG
CCTATGTTTCTAGATGTGCATATGCATCGACCACACACAAAGAGTAAAAACTTTATGGAC
GCATTGCTTGCTTTTTGGCCTGGATTGCAAGTTTTAAGCGGTGACTTAAAACCAGCCGTA
CAAACACACGAAATGCTATATCAAGTAATGCAAATTCATAAATTCATTCCTGAAGCTTTT
ACATACGATTTTCAAATTCACTGGGGTCAATATCATTTAAGACCGGAATTTATTGAATCT
ACATACTTTTTGTACAAAGCAACTGGAGATCATTATTATTTACAAGTGGGTAAGACAGCG
CTCAAAACAATCCAAAAATATGCCAAAGTCCCTTGTGGATATGCCGCAGTAAACGATATC
AGAACTGGCAAACACGAAGACCGAATGGACTCATTCATGCTTTCTGAAACAATCAAATAC
CTTTATCTTCTATTTGCTGAAGAAGAAGATCTTCCTTTAAATATTGATGACTTTATTTTT
ACTACAGAAGCACATTTACTTCCACTTAGTCTTGGAAAACTAACAAATAACACAGGAACT
ACAATTAAAGATGATGATGATAGTCACGTTATGGATTTAGATTTCATGCGTTCATGTCCA
TCGCCAAACAAGTTATTTCCTGAATCAGTTCGTCGACCACTCCGAGATTTGGTCACAGCT
TCCTGTCCACGTGTCAGCAATGCAAACAGATTACGAGCTTCTGAATTTCAAGCAAGTAAT
GCAGACCATCTTCGGACACTTTTCGACATGGGTGTTACCATGGTATCACTCGGTAATGGA
AAAGTTCAACTACTTCATAGCTTCTACAATGCAAAATCAGTAGAAGAAGCAGAACGTGGT
CTTTTATTCATGCAAGAAATGGTTGAATTATCTAAATCAAATCAAATTCCAACAGCAGAT
TTACATAGTGTGACATTTAAACATCCAACAACAGGAGAACTCGTGAATTTATCAGCAGGA
CCTTCGCATTTTAGTCCTGAATTTTTACAACCAATAACAAACCAAATTGTCTTCGTAGAA
CCATTCCATTTATGCTCAGAAATAGAAAATAAGCAATTAGTAAATGGAAAAATTGCTATG
GTCCAACGAGGTGATTGTACATTTGTTGATAAAGCGAGACGAGCAATGAAAGCAGGCGCA
AAAGCAGTTATCATTATAGACAATATGGCTGATACTTCGATCCATAATCAACCTCCATTT
GCTATGTCAGGCGATGGTAAAGACGACGTAACAATTCCAACTTGCTTCCTTTTTACACTC
GAAGCAAAAACCTTAAAAGATGCCTTAAAAATTAAGAGTGATTTAGAGGTAACTATCACG
TCAATCAATAATAATAATGAGAAAAATGTTGAAAATGAAAACGAGCAACTAAGCAATAAG
AACCAGAAAGCAGGAGATTAA
>g5204.t1 Gene=g5204 Length=786
MNFVHKNDARVHQIISLVVVLVFFINLVNSQNLNNILSTKEKNELKEEAREMFYHAYRAY
MDNAFPADELQPLSCKGRIRGISKSRGDLDDTLGNFSMTLVDTLDTLVILGDFEEFESAV
KLVIKNVQFDNDIIVSVFETNIRMLGGLLSAHVLAEYIQKEAHIMMWYRGELLEMAKDLG
YRLLPAFNTSTGIPHARINLKYGMKSEALKHSRETCTACAGTILLEFAALSRLSGEPIFE
AKAHQAMDALWKIRNRSSNLMGTVVNVHSGDWIRRDSGVGAGIDSYYEYCLKSYILLGDE
RYLSRFNRHYNAVMKYVKQGPMFLDVHMHRPHTKSKNFMDALLAFWPGLQVLSGDLKPAV
QTHEMLYQVMQIHKFIPEAFTYDFQIHWGQYHLRPEFIESTYFLYKATGDHYYLQVGKTA
LKTIQKYAKVPCGYAAVNDIRTGKHEDRMDSFMLSETIKYLYLLFAEEEDLPLNIDDFIF
TTEAHLLPLSLGKLTNNTGTTIKDDDDSHVMDLDFMRSCPSPNKLFPESVRRPLRDLVTA
SCPRVSNANRLRASEFQASNADHLRTLFDMGVTMVSLGNGKVQLLHSFYNAKSVEEAERG
LLFMQEMVELSKSNQIPTADLHSVTFKHPTTGELVNLSAGPSHFSPEFLQPITNQIVFVE
PFHLCSEIENKQLVNGKIAMVQRGDCTFVDKARRAMKAGAKAVIIIDNMADTSIHNQPPF
AMSGDGKDDVTIPTCFLFTLEAKTLKDALKIKSDLEVTITSINNNNEKNVENENEQLSNK
NQKAGD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 17 | g5204.t1 | Coils | Coil | Coil | 763 | 786 | - |
| 15 | g5204.t1 | Gene3D | G3DSA:1.50.10.10 | - | 34 | 499 | 4.7E-150 |
| 16 | g5204.t1 | Gene3D | G3DSA:3.50.30.30 | - | 620 | 764 | 6.8E-25 |
| 3 | g5204.t1 | PANTHER | PTHR45679:SF2 | ER DEGRADATION-ENHANCING ALPHA-MANNOSIDASE-LIKE PROTEIN 3 | 35 | 766 | 0.0 |
| 4 | g5204.t1 | PANTHER | PTHR45679 | ER DEGRADATION-ENHANCING ALPHA-MANNOSIDASE-LIKE PROTEIN 2 | 35 | 766 | 0.0 |
| 6 | g5204.t1 | PRINTS | PR00747 | Glycosyl hydrolase family 47 signature | 52 | 72 | 6.4E-61 |
| 9 | g5204.t1 | PRINTS | PR00747 | Glycosyl hydrolase family 47 signature | 97 | 111 | 6.4E-61 |
| 10 | g5204.t1 | PRINTS | PR00747 | Glycosyl hydrolase family 47 signature | 134 | 152 | 6.4E-61 |
| 11 | g5204.t1 | PRINTS | PR00747 | Glycosyl hydrolase family 47 signature | 185 | 204 | 6.4E-61 |
| 5 | g5204.t1 | PRINTS | PR00747 | Glycosyl hydrolase family 47 signature | 280 | 297 | 6.4E-61 |
| 7 | g5204.t1 | PRINTS | PR00747 | Glycosyl hydrolase family 47 signature | 338 | 354 | 6.4E-61 |
| 8 | g5204.t1 | PRINTS | PR00747 | Glycosyl hydrolase family 47 signature | 392 | 416 | 6.4E-61 |
| 12 | g5204.t1 | PRINTS | PR00747 | Glycosyl hydrolase family 47 signature | 451 | 471 | 6.4E-61 |
| 1 | g5204.t1 | Pfam | PF01532 | Glycosyl hydrolase family 47 | 52 | 488 | 1.2E-117 |
| 2 | g5204.t1 | Pfam | PF02225 | PA domain | 665 | 744 | 2.1E-13 |
| 19 | g5204.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 30 | - |
| 20 | g5204.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 13 | - |
| 21 | g5204.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 14 | 25 | - |
| 22 | g5204.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 26 | 30 | - |
| 18 | g5204.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 31 | 786 | - |
| 13 | g5204.t1 | SUPERFAMILY | SSF48225 | Seven-hairpin glycosidases | 43 | 489 | 2.75E-149 |
| 14 | g5204.t1 | SUPERFAMILY | SSF52025 | PA domain | 673 | 716 | 1.07E-10 |
| 23 | g5204.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 13 | 30 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5204/g5204.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5204.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0016020 | membrane | CC |
| GO:0005509 | calcium ion binding | MF |
| GO:0004571 | mannosyl-oligosaccharide 1,2-alpha-mannosidase activity | MF |
| GO:0005975 | carbohydrate metabolic process | BP |
KEGG
Orthology
- This transcript has been annotated with K10086 (ER degradation enhancer, mannosidase alpha-like 3)
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.
