General information for g8354.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Dystroglycan.
Parent gene
- The parent gene g8354 is located on chr_2: 29934050..29941632 (+ 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 | g8354 | g8354.t1 | TSS | g8354.t1 | 29908049 | 29908049 |
| chr_2 | g8354 | g8354.t1 | isoform | g8354.t1 | 29933605 | 29941632 |
| chr_2 | g8354 | g8354.t1 | exon | g8354.t1.exon1 | 29933605 | 29933712 |
| chr_2 | g8354 | g8354.t1 | cds | g8354.t1.CDS1 | 29933605 | 29933712 |
| chr_2 | g8354 | g8354.t1 | exon | g8354.t1.exon2 | 29933792 | 29933992 |
| chr_2 | g8354 | g8354.t1 | cds | g8354.t1.CDS2 | 29933792 | 29933992 |
| chr_2 | g8354 | g8354.t1 | TTS | g8354.t1 | 29933936 | 29933936 |
| chr_2 | g8354 | g8354.t1 | exon | g8354.t1.exon3 | 29934050 | 29934438 |
| chr_2 | g8354 | g8354.t1 | cds | g8354.t1.CDS3 | 29934050 | 29934438 |
| chr_2 | g8354 | g8354.t1 | exon | g8354.t1.exon4 | 29934787 | 29934850 |
| chr_2 | g8354 | g8354.t1 | cds | g8354.t1.CDS4 | 29934787 | 29934850 |
| chr_2 | g8354 | g8354.t1 | exon | g8354.t1.exon5 | 29935845 | 29936681 |
| chr_2 | g8354 | g8354.t1 | cds | g8354.t1.CDS5 | 29935845 | 29936681 |
| chr_2 | g8354 | g8354.t1 | exon | g8354.t1.exon6 | 29938314 | 29938586 |
| chr_2 | g8354 | g8354.t1 | cds | g8354.t1.CDS6 | 29938314 | 29938586 |
| chr_2 | g8354 | g8354.t1 | exon | g8354.t1.exon7 | 29939167 | 29939265 |
| chr_2 | g8354 | g8354.t1 | cds | g8354.t1.CDS7 | 29939167 | 29939265 |
| chr_2 | g8354 | g8354.t1 | exon | g8354.t1.exon8 | 29939323 | 29940997 |
| chr_2 | g8354 | g8354.t1 | cds | g8354.t1.CDS8 | 29939323 | 29940997 |
| chr_2 | g8354 | g8354.t1 | exon | g8354.t1.exon9 | 29941062 | 29941427 |
| chr_2 | g8354 | g8354.t1 | cds | g8354.t1.CDS9 | 29941062 | 29941427 |
| chr_2 | g8354 | g8354.t1 | exon | g8354.t1.exon10 | 29941499 | 29941632 |
| chr_2 | g8354 | g8354.t1 | cds | g8354.t1.CDS10 | 29941499 | 29941632 |
Sequences
>g8354.t1 Gene=g8354 Length=4146
ATGATTTTTAAACGACGATTCAGTGCGATTTTTCTAGTTCTGTTATTTAGCACATTTGTA
GCAACAGAACACAGCGAAGACTTTAAATTTGATAGTGATGATTTACAGGTCGTGTATTCA
GATCCTGCGGAAATTGCCATTAAGACACCGTCACGCTACTCTTATACAAAAGAAATCGCA
CAATGTCCATCTGGGGAGAGCAAAATGATGTTGACACTTTTGCTGCAATCACTTAGATGG
AAAGACGTGGGTGAAAAAAAGAAAGAAAAGGCCATTAAAAAGATGTCACGTTTCTTCCTT
GTTCCAGTGAAATATATCAAACTCGATGACATTCATACAACTGAAATGCTCGAAATGCTT
AAGCATTCAATCAATAAAAGTAATAATTTACTCAATACCAAAGATGCTGTCGGACGAATT
GAATTTATGATCGGATGTGGTGACAAGTTGTTTGCGAGCACAAAAACATTAGCGCATAAA
ATTAATGAATATGTGAAATCAGGAAAACTACAGGAACTTTCTGGATTGCCAATCAACTGG
TGGAACATTTGGTCTAAACATGTCAAGAGTCGTGTACAGAGAACAAGGCGTGATACTCTT
CTTGAAGGATCGGGCAATGCTGAGGAACAAGACTATTATGATGAGGAAGATGAAGAATTC
TCTGAAACAGAAGGCAATGAAGATGAAGATGAAGAAATCAATAACGAAGAAGAATCTCAC
AAGTCATTCTCAGAGCAAGTCAATCACCAAAATACTAATCAGCGAAAGAAGCAGCAGTAT
GCAAAGAAGATGCCAAATGTTGAAATCTCAGAGCCACAATCAAAAATCCACGATGATCCG
CCAAATGGTGCGGCAGAAATTGAGAATAATGAGCGAAACGAGAATGAAGATAATATCAAT
AATGGAGAAAAGCAAGAGAGCACGGATTATCAGATATCACCTGAAGAGCCATTAGCACCA
ATTGAGAATGTCGATGATTCAATTAAGGAGGATATTGTCGAGGAAGTCACACAACGTTTA
AATGTTATCGATGTCGAAGTCAATAGTCCAACGCCTATTGGCACAAATGAGATAATTAAG
TTAGAAAAAGAAGTCGATAAAACAATTGAAAATGCCAATAATGTCGATGATGTTCCTTTC
CCATCAAAGCAACAGGATGACAAGATTTTAGAAGAGTTTGTAAATAGTATGATTTCAAAT
GCACCAATTCAAGAGCTAACAACAGACAGTGAAATTTTTACAATTTTAACATCACCTACA
GTATCAAGTGAAACAACTTCATCACACCATCATCATTTACATCATCATCATGAAATGTCA
GAGACAGTGACAAGTGAAACTGTTGAAATTCATCCCGAAAGTCCATCATCAACAGCAGTC
GTTGTTACCGAAGAAATGATAAATGAATCAACAACCACATCAACCACGATAGTGCATGCT
CTCGAAGCGGAAACAATTTTCACTCCTATAAATAACGATACACACAATGAGCACATTAAT
ATTGATGAAAAATTTCCAATTGTTACGACATCATTGACTTTAGATTTAACGACAATATCG
GAAACGACCAATATGGCAATTGAAAAAGAATCAATACTGATTGAGGAAAATATCACGGAT
CAAATGCCATCTTTATCATCACAACTATCATCAACACCATTAATAATTTCATCAACCTCA
TATGATCATGAAACGACTACTTATAATTATCCCATATCGACAAATCCAACAATTTTAACA
ACAACAACAGCTGAAATAACAACAATCATAACCAATAATATAACTACTTCTACTGAGCCA
TCCATAACAGAAACATCAACAACCCTTAAAAATGTAGTAGATGCGACTATTGCATTTGTC
GCTGTGGATAAGGATATGTCATCCACTGATAAAGCAATTGAGGAGAAAAAATCTGATGAG
GAGTCTAATTATGATGATGAATATGATGACGATGAAGAGAACTTTGTTGAACCAAGTAAA
AAGTCATCGAGTGTTGCCACAACTGCTTCATCACCAACAACAATAAAAGAAGATCGTAGA
ACGCCACTTCCTTTAATTCCAACTTCACCAGATGAAGATGATGACGAAGATAATGAAGAA
GAAGAAACAGATGAGTCAGTTTTATTAGGATTGCCTTCAACTACATTACCACCACCAACT
ACAACAACAATACCTTCAACTACTACAATTCAAACGACCACAGTACAAATAACTTCAACA
TCAACTGAATCAGCACCAACAACAAGCGAATCTGTTGAAGTTACAAGTGAAAATTCTGAT
TATAGTGAAGAAAATCAAGCACCAACAGTTGTAAAAAGAATCAAGAAAATTCAAGCTACT
TCAGGCAAGGCCTTTAGTTATAAACTTGAGGAAGCAATTTTCGATGATGATGAAGGAGCA
GATAGTTTGCGTCTTGAATTGTTGGATAAAAACGATCAACCATTGCCATCATCTTCATGG
ATTCGTTTTGACGCAAAGAAACAAGAAATTTATGGATTACCACTTGAGAATGATGTCAGC
CGACACGAATTTAAATTGCGTGCAACCGACAGCAGTGGTGAATATGTAGATGAGAATGTC
GATGTAACTGTACAACAACATAAAGGCTACAGAAGTGTAAATCATGAGATATTTATTCAA
GTAACCTTGGATAAGCAATATGACTCAGATATCGATTGGAAAATTCGTTTAATACGTGGA
ATTGTTGAAGCTTTAGAAGATGATTCAATTGGCAGTATTATAGTTCGTGATGTCAAACCA
CACAAATATGAACCAAAACATTACACATTCTCATACACGAATGACACATTACCAAAGGAT
CATTGCCCTAAGGAAGAGTTAGAGCAATTGACACAGAGATTAACAAAGAAAGCATTAAAT
GATGTCATGCGTAGAGAAATAACTGTTCGTAATGTTGAGAAAGAATTAATAAATGCATGT
GCTGAAGTAAAAACTCCTATCCCGCAGCCACCATTACAACCAAATAACAAACAGAATTAC
CCACCAACTGTTCGTAATCATGTGGATAGAGTTGGCGCTGTTGTTGGTCAATTGTTGGTA
TTTAAAGTGCCTTCTGACACTTTTTACGATCCAGAAGATTTAAATGATCTTAAATTATCA
CTTCTCAATGAAAATCGTTCGCCATTGGATCCTACAAATTGGTTACAATTTGATGCTAAG
AATCATGAATTTTATGGCGTTCCAACCATTCACGACAAAACACAAACATATGTTCTCGTT
GCTGAAGATAAAAATGGTCTTTCTACAAACGATGCACTAGTTGTTGAAATTAATAATTTG
CACTCAAAACGTGATTATGGTGCAACATTCGAATATCAGCTTGAAATTGGCATTGATCAA
TTCCAAAATGCTGCAACAAAACGTAAATTTATTGAACGAATTCAACAATTCTTTGGTGAT
GGTGATACTAGTGCAATTGTCATTAAATCAATCAAGAAAGTTCAATATTCAGGACGTACA
GCTGTGGTTGTACAAAATACTACATTAAGTGGTCGTGGTTGTCCTGTAGATGAAATCAAA
AAATTAAAAGATCGCCTTGTACGAACGGATGGAAGTCTTCATGATGACGTAAGAGAAGCA
ATTGGAACTGAATTCAATGTGCAGAAAATTAGTATAGTTCCCATTGGAAAATGTGCAAGT
GGTGACACATATCATCATCCTGATGAAACAATTCCTGTTGAACGTCCAGAGGAGCATGAT
GGTCCTCTTATTAATGAAGAAGTACTTATCACATATGTCCTTCCTACAGCCATTATTTTG
TTGATGCTATTAATTGCATTGTTGATCGCATGCCTTTTGTATAAGCGCCGAAATACAGGC
AAAATGGAATTGGGCGATGAAGAAGAGCGAAAATCTTTCCGTTCAAAAGGAATTCCTGTG
ATTTTCCAAGATGAATTAGATGAAAAACCTGAAATTGTTACAAAATCACCTATCATCTTG
AAAGATGAAAAACCACCACTTCTTCCACAATATAATGGTTTAAATCAAGATGGTGAAGAA
GACGTTGATCAATATATTCCACCTCAGCCACTTTTGATGGGTTCACGTGGAGGAGAACGT
GGAAAATCACCAGTATCACAAAACACACCTAGTTATCGCAAACCACCACCATACGTTAGT
CCATAA
>g8354.t1 Gene=g8354 Length=1381
MIFKRRFSAIFLVLLFSTFVATEHSEDFKFDSDDLQVVYSDPAEIAIKTPSRYSYTKEIA
QCPSGESKMMLTLLLQSLRWKDVGEKKKEKAIKKMSRFFLVPVKYIKLDDIHTTEMLEML
KHSINKSNNLLNTKDAVGRIEFMIGCGDKLFASTKTLAHKINEYVKSGKLQELSGLPINW
WNIWSKHVKSRVQRTRRDTLLEGSGNAEEQDYYDEEDEEFSETEGNEDEDEEINNEEESH
KSFSEQVNHQNTNQRKKQQYAKKMPNVEISEPQSKIHDDPPNGAAEIENNERNENEDNIN
NGEKQESTDYQISPEEPLAPIENVDDSIKEDIVEEVTQRLNVIDVEVNSPTPIGTNEIIK
LEKEVDKTIENANNVDDVPFPSKQQDDKILEEFVNSMISNAPIQELTTDSEIFTILTSPT
VSSETTSSHHHHLHHHHEMSETVTSETVEIHPESPSSTAVVVTEEMINESTTTSTTIVHA
LEAETIFTPINNDTHNEHINIDEKFPIVTTSLTLDLTTISETTNMAIEKESILIEENITD
QMPSLSSQLSSTPLIISSTSYDHETTTYNYPISTNPTILTTTTAEITTIITNNITTSTEP
SITETSTTLKNVVDATIAFVAVDKDMSSTDKAIEEKKSDEESNYDDEYDDDEENFVEPSK
KSSSVATTASSPTTIKEDRRTPLPLIPTSPDEDDDEDNEEEETDESVLLGLPSTTLPPPT
TTTIPSTTTIQTTTVQITSTSTESAPTTSESVEVTSENSDYSEENQAPTVVKRIKKIQAT
SGKAFSYKLEEAIFDDDEGADSLRLELLDKNDQPLPSSSWIRFDAKKQEIYGLPLENDVS
RHEFKLRATDSSGEYVDENVDVTVQQHKGYRSVNHEIFIQVTLDKQYDSDIDWKIRLIRG
IVEALEDDSIGSIIVRDVKPHKYEPKHYTFSYTNDTLPKDHCPKEELEQLTQRLTKKALN
DVMRREITVRNVEKELINACAEVKTPIPQPPLQPNNKQNYPPTVRNHVDRVGAVVGQLLV
FKVPSDTFYDPEDLNDLKLSLLNENRSPLDPTNWLQFDAKNHEFYGVPTIHDKTQTYVLV
AEDKNGLSTNDALVVEINNLHSKRDYGATFEYQLEIGIDQFQNAATKRKFIERIQQFFGD
GDTSAIVIKSIKKVQYSGRTAVVVQNTTLSGRGCPVDEIKKLKDRLVRTDGSLHDDVREA
IGTEFNVQKISIVPIGKCASGDTYHHPDETIPVERPEEHDGPLINEEVLITYVLPTAIIL
LMLLIALLIACLLYKRRNTGKMELGDEEERKSFRSKGIPVIFQDELDEKPEIVTKSPIIL
KDEKPPLLPQYNGLNQDGEEDVDQYIPPQPLLMGSRGGERGKSPVSQNTPSYRKPPPYVS
P
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g8354.t1 | Coils | Coil | Coil | 226 | 246 | - |
| 13 | g8354.t1 | Coils | Coil | Coil | 285 | 305 | - |
| 11 | g8354.t1 | Gene3D | G3DSA:3.30.70.1040 | Dystroglycan | 61 | 199 | 7.3E-11 |
| 9 | g8354.t1 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 760 | 870 | 7.9E-13 |
| 10 | g8354.t1 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 995 | 1105 | 7.5E-10 |
| 25 | g8354.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 199 | 263 | - |
| 26 | g8354.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 208 | 235 | - |
| 32 | g8354.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 245 | 260 | - |
| 31 | g8354.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 288 | 303 | - |
| 35 | g8354.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 288 | 311 | - |
| 33 | g8354.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 423 | 459 | - |
| 34 | g8354.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 445 | 459 | - |
| 29 | g8354.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 627 | 764 | - |
| 30 | g8354.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 659 | 677 | - |
| 28 | g8354.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 689 | 706 | - |
| 36 | g8354.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 708 | 764 | - |
| 27 | g8354.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1329 | 1381 | - |
| 4 | g8354.t1 | PANTHER | PTHR21559 | DYSTROGLYCAN-RELATED | 35 | 990 | 2.0E-159 |
| 3 | g8354.t1 | PANTHER | PTHR21559 | DYSTROGLYCAN-RELATED | 986 | 1381 | 2.0E-159 |
| 1 | g8354.t1 | Pfam | PF05345 | Putative Ig domain | 768 | 864 | 1.8E-5 |
| 2 | g8354.t1 | Pfam | PF05454 | Dystroglycan (Dystrophin-associated glycoprotein 1) | 1110 | 1381 | 7.9E-55 |
| 16 | g8354.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 25 | - |
| 17 | g8354.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 8 | - |
| 18 | g8354.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 9 | 20 | - |
| 20 | g8354.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 21 | 25 | - |
| 15 | g8354.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 26 | 1251 | - |
| 19 | g8354.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 1252 | 1274 | - |
| 14 | g8354.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1275 | 1381 | - |
| 38 | g8354.t1 | ProSiteProfiles | PS51699 | DG-type SEA domain profile. | 872 | 979 | 26.727 |
| 37 | g8354.t1 | ProSiteProfiles | PS51699 | DG-type SEA domain profile. | 1101 | 1217 | 24.155 |
| 24 | g8354.t1 | SMART | SM00736 | cadg_13 | 769 | 871 | 5.3E-14 |
| 23 | g8354.t1 | SMART | SM00736 | cadg_13 | 1003 | 1104 | 2.5E-17 |
| 6 | g8354.t1 | SUPERFAMILY | SSF49313 | Cadherin-like | 767 | 868 | 1.57E-15 |
| 5 | g8354.t1 | SUPERFAMILY | SSF49313 | Cadherin-like | 1001 | 1099 | 3.14E-15 |
| 8 | g8354.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 22 | - |
| 21 | g8354.t1 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM | 1 | 21 | - |
| 7 | g8354.t1 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 25 | - |
| 22 | g8354.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 1252 | 1274 | - |
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:0005509 | calcium ion binding | MF |
| GO:0016010 | dystrophin-associated glycoprotein complex | CC |
KEGG
Orthology
- This transcript has been annotated with K06265 (dystroglycan 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.
