RetrogeneDB ID: retro_mdom_1961

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: Un:34805913..34807104(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000021160
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000012842
• Aliases: None
• Description: None

Sequence

>retro_mdom_1961
AAACATGTTACAAAAGCCAAGATCCAGGACCCTCTAGAATCCAAAGTGGAAAAAACCCAACTGAGTAAGGAGTCCTTGGA
TATAGAGAAATGGATGAAAGATAAGGGAGTGTCTAGCAACTTACAGCCCCAGGAGAGGAAATACATAGCTCCAAATGCCC
ACAAAAGCCCAGCAAGCTGCCTTCTCAGGTGTGGGGAGGCAGAAGTCTACAATAAAGACAGACAGCCCACCTCAACTTTT
GGGTTTAATCTCAACTGTGCCTGGCAGCCACAGAGGAAAAAGAATATAAACATTCCAACTGTAGCTCATGGAGACAAAGG
TCACATTAAAGAGAACTGTGCCAGAACTGATAGTAAAAGCCCCTATTCAGTTCAAAAGCTGCCTAATATGAATGATGGCA
AACCAGAGCAACAACAATCTGGAGCTATGTTGACCAAACGGAAAAATATCTCCATCCATGTGCCATCACACTTAGGAGAT
ATCCCCTTGTCTGCAGAACAAGCAAGTCGTCAGTTTTCATCACTCGGAACAGCGCTCCCCATGAAATTGAAGAAGAAAAC
AGCATCCTACCATGAGGACGAGGGACTCGGATTTATAGGCCGGAGGAGGAATTCCAAGATGCAAGTTTATTCAGGACCTA
AATGTGTTTACCAACCGAAATTAATATCGCTGCACCAGCAATGTATCAAGGTCCTCAATAACAATTTAGATTCCATCTTT
GATATTGGTAGTGTACCTTATACTGTGCTGGAACCGGTCCTGGAGAAATGTACACCTAAACAACTGCAGAGAATTGAGGA
ATATAATCACTTTTTAATTGGGGAGACCAACCAGTTGTGGAAAATTCATTGTAATCGAGATTTCAGATGGGAACAACCAA
GAGAATTTGAGTCCTGGAGGGAGCTATACCTTCGACTCCAGGAAGCTCGAGAGCAGCGGCTGCTGTTCTTGACCGAGAAT
ATTCGATCATCTCATGCCAATAAACCCAAAGGCCGTCAGACAATGATGGCCTTTGTTAATTCTGAGGCGAAACCGCCTCG
GGATATTAGAAAGAGGCAGGAAAAATTTGGCACTGGCAGAATAACTACTCCTGAAATGACCAGGCCTGCCTTATACACCC
CAACCACCCACTATGGTCACAGTGCTGTCCAGCCACATGCTGGCCCAAACACTGGCGGTTTTCAATCAGCA

Alignment

ORF - retro_mdom_1961 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.98 %
• Parental protein coverage: 51.74 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KDAQKSKLEKTKLS-VDSFDVGKWEGEFSPKSKGKGGSNSLKTREGKSKASDSDRKTSGHFPGAGETDVD
          K...K.K......S.V......K.........K.KG.S..L...E.K..A..............GE..V.
Retrocopy KHVTKAKIQDPLESKVEKTQLSKESLDIEKWMKDKGVSSNLQPQERKYIAPNAHKSPASCLLRCGEAEVY

Parental  DDYEQPTMSFESYLSYD-QPQRKKKKVVKTTTGVRTEKSHSKQNGSKADHKNSNSAVQKLPKMNESKAEK
          ....QPT..F...L....QPQRKK.......T.....K.H.K.N....D.K...S.VQKLP.MN..K.E.
Retrocopy NKDRQPTSTFGFNLNCAWQPQRKKN--INIPTVAHGDKGHIKENCARTDSKSPYS-VQKLPNMNDGKPEQ

Parental  QHSGASSAKLKKISPDVTPTLPDIPLPTIQANYRPLPSLELIPSFQPKRKAVSSPHEDEEAGFTGRRMNS
          Q.SGA...K.K.IS..V...L.DIPL...QA..R...SL........K.K..S..HEDE..GF.GRR.NS
Retrocopy QQSGAMLTKRKNISIHVPSHLGDIPLSAEQAS-RQFSSLGTALPMKLKKKTASY-HEDEGLGFIGRRRNS

Parental  KMQVYSGSKCAYLPKMMSLHQQCIRVLNNNIDSIYEVGGVPYSVLEPVLERCTPEQLYRIEECNHVLTEE
          KMQVYSG.KC.Y.PK..SLHQQCI.VLNNN.DSI...G.VPY.VLEPVLE.CTP.QL.RIEE.NH.L..E
Retrocopy KMQVYSGPKCVYQPKLISLHQQCIKVLNNNLDSIFDIGSVPYTVLEPVLEKCTPKQLQRIEEYNHFLIGE

Parental  TDQLWKIHCHRDFKRERPEEFESWREMYLRLQDAREQRLLLLTENIRSAHANKPKGRQAKMAFVNSVAKP
          T.QLWKIHC.RDF..E.P.EFESWRE.YLRLQ.AREQRLL.LTENIRS.HANKPKGRQ..MAFVNS.AKP
Retrocopy TNQLWKIHCNRDFRWEQPREFESWRELYLRLQEAREQRLLFLTENIRSSHANKPKGRQTMMAFVNSEAKP

Parental  PRDVRRRQEKFGTGGAAVPEKIKIKPAPYTSNSSYACSS-SSSVGSVGGSYNSA
          PRD.R.RQEKFGTG....PE.....PA.YT....Y..S......G...G...SA
Retrocopy PRDIRKRQEKFGTGRITTPE--MTRPALYTPTTHYGHSAVQPHAGPNTGGFQSA

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_1961 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1961 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000011241	1 retrocopy	retro_dnov_1854,
Loxodonta africana	ENSLAFG00000017306	1 retrocopy	retro_lafr_424,
Myotis lucifugus	ENSMLUG00000005258	1 retrocopy	retro_mluc_498,
Monodelphis domestica	ENSMODG00000012842	1 retrocopy	retro_mdom_1961 ,
Sarcophilus harrisii	ENSSHAG00000006165	1 retrocopy	retro_shar_665,