RetrogeneDB ID: | retro_mdom_1115 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 3:144676164..144677360(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMODG00000025023 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SF3A1 | ||
| Ensembl ID: | ENSMODG00000009270 | ||
| Aliases: | None | ||
| Description: | splicing factor 3a, subunit 1, 120kDa [Source:HGNC Symbol;Acc:10765] |
Retrocopy-Parental alignment summary:
>retro_mdom_1115
CAGGAGCAGGAGAGGAAGAGAAAGAGAAGGAGCGGGTGGCCTACGCACAGACTGGCACAATTTTGTGGTGGTAGAAACGG
TGGACTTCCAGTCCCTTGAACAAGGGTATTTCCCACTGCCTACCACCCCGGAGGAGCTGGGTGCCCGAATCCTGATCCAG
GAGCTTTATGAGAAGTTTGGGGAGAGTGAGGAAATGGACATGGAGGTGGAATCAGATGATGAGGATGAGAAGCAAGAGAA
GACCAAGGAACCTTCGTCCCAGCTGGACCAGGACACCCAAGTGCAGGACATGGATCAGGGTTCTGAAGATGAAGAGAAGA
GCCAGAAAGTTCCCCCTCCTCCAGAAACACCCATGCCTCCACCACTGCCACCCACCCCCCATCAGGTCATCCTCTGCAAA
GACTATGACCCCAAAGCTTCCAAGCCTCTGCCCCGAGCTCCAACTCCAGATGGGTATCTCGTATCCCCCATCACCAGGGA
GAAGATTCCAGCCAGCAAGATGCAGGAACACATGCGTATCAACCTGCTGGACCTGAGCAGGCTAGAGCAATGGGATCACT
CAATCCGGGAGAAGCAGAATGATGAGATCTATGCCCCAGGGCTGGATATCCAGAGCTACCTGAAGCAGCTGGCAGAGAGG
TGAACCGATATCTTTGGGGTGGGGGAGACGGCTATTGGCAAAAAGATCGGTGAAGAGGAGATCCAGAAGCCTGAAGAGAA
GGTGACCTGGGATGGCCACACTGGCAGCATGGCCAGAATCCAGCAGGTAGCCCAGGTCAACATCACTCTCCAGGAGCAGA
TGGAAGCCATCCACAAGGCCAAGAGGCTGGTGCAAGAAAACAACAGCATGGAAAATATTGACCCCAGCAAGCCCAATGAG
ATCCCACAGCTGTCCCCTCTGTCCCTTGGCCCCCAACATCCCTACCTCAGCCCTGCCCATCACATCCATGCCCTGTCGGC
CCTTGATGCCTCCTCCAGTCTGAACCACAGTTGTCTCTGCCCTGCCGGTCACTCCACGGCCCTCCATGGCCTCCATGGTA
CCCCTGCCTCCTGACTCCGTGATAGCCCCTATGCCTCCCATCATCCATGCTCCCAGCATCAATGTGATGCCCATGCCACC
CTCTGATCCACCCATCATGGCACCCTGTCCACCTCCAATGATTGTGCCAACAGCATTTGTACCAGCCCCTCCTGTA
ORF - retro_mdom_1115 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 80.55 % |
| Parental protein coverage: | 50.44 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | KEEEEKEKERVAYA-QIDWHDFVVVETVDFQPNEQGNFPPPTTPEELGARILIQERYEKFGESEEVEMEV |
| .E.E.K.K.R.......DWH.FVVVETVDFQ..EQG.FP.PTTPEELGARILIQE.YEKFGESEE..MEV | |
| Retrocopy | QEQERKRKRRSGWP>RTDWHNFVVVETVDFQSLEQGYFPLPTTPEELGARILIQELYEKFGESEEMDMEV |
| Parental | ESDDEDEKQEKTEEPPSQLDQDTQVQDMDEGSDDEEESQKVPPPPETPMPPPLPPTPDQVIVRKDYDPKA |
| ESDDEDEKQEKT.EP.SQLDQDTQVQDMD.GS.DEE.SQKVPPPPETPMPPPLPPTP.QVI..KDYDPKA | |
| Retrocopy | ESDDEDEKQEKTKEPSSQLDQDTQVQDMDQGSEDEEKSQKVPPPPETPMPPPLPPTPHQVILCKDYDPKA |
| Parental | SKPLPPAPAPDEYLVSPITGEKIPASKMQEHMRIGLLDPRWLEQRDRSIREKQSDDEVYAPGLDIESSLK |
| SKPLP.AP.PD.YLVSPIT.EKIPASKMQEHMRI.LLD...LEQ.D.SIREKQ..DE.YAPGLDI.S.LK | |
| Retrocopy | SKPLPRAPTPDGYLVSPITREKIPASKMQEHMRINLLDLSRLEQWDHSIREKQ-NDEIYAPGLDIQSYLK |
| Parental | QLAERRTDIFGVEETAIGKKIGEEEIQKPEEKVTWDGHSGSMARTQQAAQANITLQEQIEAIHKAKGLVP |
| QLAER.TDIFGV.ETAIGKKIGEEEIQKPEEKVTWDGH.GSMAR.QQ.AQ.NITLQEQ.EAIHKAK.LV. | |
| Retrocopy | QLAER*TDIFGVGETAIGKKIGEEEIQKPEEKVTWDGHTGSMARIQQVAQVNITLQEQMEAIHKAKRLVQ |
| Parental | EDDSKEKIGPSKPNEIPQPPPPS-SAPNIPTSAPPITSVPRPPSMPPPVRTTVVSAVPVMPRPPMASVVR |
| E..S.E.I.PSKPNEIPQ..P.S..APNIPTSA.PITS.P..P.MPPPV.TTVVSA.PV.PRP.MAS.V. | |
| Retrocopy | ENNSMENIDPSKPNEIPQLSPLS>LAPNIPTSALPITSMPCRPLMPPPV*TTVVSALPVTPRPSMASMVP |
| Parental | LPPGSVIAPMPPIIHAPRINVVPMPPSAPPIMAPRPPPMIVPTAFVPAPPV |
| LPP.SVIAPMPPIIHAP.INV.PMPPS.PPIMAP.PPPMIVPTAFVPAPPV | |
| Retrocopy | LPPDSVIAPMPPIIHAPSINVMPMPPSDPPIMAPCPPPMIVPTAFVPAPPV |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
Expression validation based on RNA-Seq data:
| Library | Retrocopy expression | Parental gene expression |
|---|---|---|
| SRP007412_brain | 0 .00 RPM | 0 .00 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 0 .00 RPM |
| SRP007412_heart | 0 .00 RPM | 0 .00 RPM |
| SRP007412_kidney | 0 .00 RPM | 0 .00 RPM |
| SRP007412_liver | 0 .00 RPM | 0 .00 RPM |
| SRP007412_testis | 0 .00 RPM | 0 .00 RPM |
Monodelphis domestica was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mdom_1115 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1115 was not experimentally validated.
Retrocopy orthology:
Monodelphis domestica does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Monodelphis domestica | ENSMODG00000009270 | 1 retrocopy |
retro_mdom_1115 ,
|
| Otolemur garnettii | ENSOGAG00000012931 | 1 retrocopy |