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 symbol: SF3A1
• Ensembl ID: ENSMODG00000009270
• Aliases: None
• Description: splicing factor 3a, subunit 1, 120kDa [Source:HGNC Symbol;Acc:10765]

Sequence

>retro_mdom_1115
CAGGAGCAGGAGAGGAAGAGAAAGAGAAGGAGCGGGTGGCCTACGCACAGACTGGCACAATTTTGTGGTGGTAGAAACGG
TGGACTTCCAGTCCCTTGAACAAGGGTATTTCCCACTGCCTACCACCCCGGAGGAGCTGGGTGCCCGAATCCTGATCCAG
GAGCTTTATGAGAAGTTTGGGGAGAGTGAGGAAATGGACATGGAGGTGGAATCAGATGATGAGGATGAGAAGCAAGAGAA
GACCAAGGAACCTTCGTCCCAGCTGGACCAGGACACCCAAGTGCAGGACATGGATCAGGGTTCTGAAGATGAAGAGAAGA
GCCAGAAAGTTCCCCCTCCTCCAGAAACACCCATGCCTCCACCACTGCCACCCACCCCCCATCAGGTCATCCTCTGCAAA
GACTATGACCCCAAAGCTTCCAAGCCTCTGCCCCGAGCTCCAACTCCAGATGGGTATCTCGTATCCCCCATCACCAGGGA
GAAGATTCCAGCCAGCAAGATGCAGGAACACATGCGTATCAACCTGCTGGACCTGAGCAGGCTAGAGCAATGGGATCACT
CAATCCGGGAGAAGCAGAATGATGAGATCTATGCCCCAGGGCTGGATATCCAGAGCTACCTGAAGCAGCTGGCAGAGAGG
TGAACCGATATCTTTGGGGTGGGGGAGACGGCTATTGGCAAAAAGATCGGTGAAGAGGAGATCCAGAAGCCTGAAGAGAA
GGTGACCTGGGATGGCCACACTGGCAGCATGGCCAGAATCCAGCAGGTAGCCCAGGTCAACATCACTCTCCAGGAGCAGA
TGGAAGCCATCCACAAGGCCAAGAGGCTGGTGCAAGAAAACAACAGCATGGAAAATATTGACCCCAGCAAGCCCAATGAG
ATCCCACAGCTGTCCCCTCTGTCCCTTGGCCCCCAACATCCCTACCTCAGCCCTGCCCATCACATCCATGCCCTGTCGGC
CCTTGATGCCTCCTCCAGTCTGAACCACAGTTGTCTCTGCCCTGCCGGTCACTCCACGGCCCTCCATGGCCTCCATGGTA
CCCCTGCCTCCTGACTCCGTGATAGCCCCTATGCCTCCCATCATCCATGCTCCCAGCATCAATGTGATGCCCATGCCACC
CTCTGATCCACCCATCATGGCACCCTGTCCACCTCCAATGATTGTGCCAACAGCATTTGTACCAGCCCCTCCTGTA

Alignment

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

Expression

RNA-Seq

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

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1115 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1115 was not experimentally validated.

Homology

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.

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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	retro_ogar_1641,