RetrogeneDB ID: retro_mdom_824

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:96857361..96858262(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: COPS4
• Ensembl ID: ENSMODG00000019311
• Aliases: None
• Description: COP9 signalosome subunit 4 [Source:HGNC Symbol;Acc:16702]

Sequence

>retro_mdom_824
TCTGGGTCTGTGCTTCAGAATTTGGGCCAGCTCATGAACTCCAACAGGTCTCATAAGGCCCTGGTGAACAAGTACCGGGC
AGATATTGGAAAAAGCCATTCAGTTGCCTAGGGCAGAGCAATTTGAGGTTTTAAAAGCCTTTGTGGAAGAAATGGTAAAT
GAGAATGTCAGTCTAATGATCTCTTGGCAATTTCTCACTGATTTCTGCATATACCTACCTAATCTACCTGACAGTCCCAC
CAAAGAAATCTATCATTTCACCTTGGAAAAGATCCAGCCCAGAGTCATTTCATTTGAGGAGCTTCAATTGAAGGTTGCTT
CAATAAGGCGGAATCTTGCATCAATATATGAGAAAGAAGAAGACTAGAGAAATGATGCACAAGTATTGGTGGGAATTCCC
TTGGACCGGAACAAAAAACAGCATAATGTGGATTATAAAATGGAGACTTATTTGAAAATTGTCAGGCTTTATCTGGAAGA
TGATGACCCTGTCCAAGCAAAGGCTTACATCAACCAAGATTCCCTACTCCAGAATGAATCGACCAATGAACAATTGCAGA
TCCATCACAAGGTGTGCTATGCTCATGTTCTTGATTATAGAAGGAAATTCATTGAAGCTGCCCAAAGATACAATGAGCTC
TCATATAAGATGACAGTCCATGAAAGTGAGTGACTAGAGGCCTTAAAACATGCTTTGCACTGTACCATCTTAGCATCAGC
AGGACAACAGTGCTCTTGAATGCTAGCCATTCTTTTTAAGGATGAAAGGAGTCAACAGCTTGCAGCCTATAGAATCTGAG
AGAAAATGTATCTAGATAGAATTATCAGAGGAAATCAGCTTGAAGAATTTGCTACCATGTTTATGTCTCTCCAAAAAGCA
ACTGCAGCTGATATGTCTTCA

Alignment

ORF - retro_mdom_824 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.73 %
• Parental protein coverage: 73.15 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AAAVRQDLGQLMNSSGSHKDLAGKYR-QILEKAIQLPGAEQLEALKAFVEAMVNENVSLVISRQLLTDFC
          ...V.Q.LGQLMNS..SHK.L..KYR.QILEKAIQLP.AEQ.E.LKAFVE.MVNENVSL.IS.Q.LTDFC
Retrocopy SGSVLQNLGQLMNSNRSHKALVNKYR>QILEKAIQLPRAEQFEVLKAFVEEMVNENVSLMISWQFLTDFC

Parental  THLPNLPDSTAKEIYHFTLEKIQPRVISFEE---QVASIRQHLASIYEKEEDWRNAAQVLVGIPLETGQK
          ..LPNLPDS..KEIYHFTLEKIQPRVISFEE....VASIR..LASIYEKEED.RN.AQVLVGIPL....K
Retrocopy IYLPNLPDSPTKEIYHFTLEKIQPRVISFEELQLKVASIRRNLASIYEKEED*RNDAQVLVGIPLDRNKK

Parental  QYNVDYKLETYLKIARLYLEDDDPVQAEAYINRASLLQNESTNEQLQIHYKVCYARVLDYRRKFIEAAQR
          Q.NVDYK.ETYLKI.RLYLEDDDPVQA.AYIN..SLLQNESTNEQLQIH.KVCYA.VLDYRRKFIEAAQR
Retrocopy QHNVDYKMETYLKIVRLYLEDDDPVQAKAYINQDSLLQNESTNEQLQIHHKVCYAHVLDYRRKFIEAAQR

Parental  YNELSYKTIVHESERLEALKHALHCTILASAGQQRSRMLATLFKDERCQQLAAYGILEKMYLDRIIRGNQ
          YNELSYK..VHESE.LEALKHALHCTILASAGQQ.S.MLA.LFKDER.QQLAAY.I.EKMYLDRIIRGNQ
Retrocopy YNELSYKMTVHESE*LEALKHALHCTILASAGQQCS*MLAILFKDERSQQLAAYRI*EKMYLDRIIRGNQ

Parental  LQEFAAMLMPHQKATTADGSS
          L.EFA.M.M..QKAT.AD.SS
Retrocopy LEEFATMFMSLQKATAADMSS

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_824 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_824 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005067	2 retrocopies	retro_cjac_2148, retro_cjac_2345,
Equus caballus	ENSECAG00000015209	2 retrocopies	retro_ecab_315, retro_ecab_600,
Monodelphis domestica	ENSMODG00000019311	1 retrocopy	retro_mdom_824 ,
Mustela putorius furo	ENSMPUG00000014708	1 retrocopy	retro_mputfur_1010,
Otolemur garnettii	ENSOGAG00000027198	1 retrocopy	retro_ogar_3514,
Tupaia belangeri	ENSTBEG00000017599	2 retrocopies	retro_tbel_2134, retro_tbel_53,