RetrogeneDB ID: retro_mdom_77

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:28605484..28606840(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000025155
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000025630
• Aliases: None
• Description: None

Sequence

>retro_mdom_77
GGGACCCCTCCCTGGGGCTCCCCACGGGCCTGGCTGAGCTCCGCGTGCCCGGAGAAAGCTGCGGTGGCACCAGCAGCCGA
AGAGTGGGGTCCGGATCCCGGCTCGTGGCCCGAGCGGCTAGCGGACCTAGTGACGCCGCTATGGCGACTGGATTACGAGC
AGCAGCTCCGAGTGAAGACGGACGCGCTGCGCGGCCTCCTGCAGTGGCTCGAGGGTCGCCTGCGTCTGCTCGGGAGCCCG
GATGGTGAGGCCGGCGTACTCTGCTCGCGCCTGCAGCCCTTCCGGCCGTCCCCCGTCCTCCACGGCTATCGGAACAAGTG
TAATTTCGCCGTCCGACAGGGCCCCGACGGCCGACCCCGGACAGTGGGCTACGTGCTAGGCTCCGGCGGCGAGCAGCAGC
CGGTGTGCGTGCGGCCCGGACACCTGAAGCACATACCCGACGCGCACCAGCGCGTGGCCCGCTGCTACCAGGATTTTCTT
GAGCAGACCCCTCTCGACCCCTACCTGGACTCGGATGCCAGCGGACACTGGCACGAACTCACAGTCAGGAGCACCAGCCA
GGGCCACACGATGGCCATCGTCACCTTCCAGCTGCAGGGACTGAGTCCAGAGGAGCTCCAGGAGCCCCAGGAAGAGCTCC
GCGAATTCTTTACCCGAGGGCCCGGGGCCATCTGTGAATTGGCCTCCCTCTACTTCCAAGAAAGGTCAGGCGACCAGCAG
CAGCCTTGCTACCAGCTCCTGGCAGGAAACCCTTACCTTTTTGAGGACCTGCCAGGCTTTAAATTCCGCATTTCTCCAGG
AGCCTTTTTCCAAATTAATTCAGCTGCTGTGGAGGTTCTTTACCGTGTGGTGGGAGAGCTAATCGGAGTGGACCCCAATA
CCCTCCTCCTTGACCTTAGCCAAGGAACCGGAGCCACCAGCCTCTCCCTGGCTCCGCACACATCCCAGGTCCTAAGCACT
GGGCTAGTGGGGCAGGCCGTGGAGGATGCCAAATGGACCACGGCTTTCAATGGAATCACCAACTGGGAATTCCATGCTGA
CCATGTAGAGAATGTAGTGCCCCAGCTTTTAAAGTCGCAGGAGGCCGGTCAATCGCCAGTGGTTATGGTGGACCCATCCC
GGACTGGATTGAACTTCCAAGTGGTTCGGGCCATTCGAAATTGCACAGCCATCAGGACGCTGCTGTATGTTTCCTGCTAC
CCAGAGGGAAAGGCCAAAAGAAACTTCCTTGAGTTGTGCTGCCCCCCAGACCCTGGCAAGGACCTCCTGGGCGAGCCTTT
TGTCCTGAGACAAGCTGTGCCTGTGGACATGTTTCCACATACCCCGCACTATGAGCTGGTGGTGCTGTTCACTAGA

Alignment

ORF - retro_mdom_77 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.71 %
• Parental protein coverage: 88.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EESSQNLDFWRKRLADQMLPLWRLNYEEQLKVKFESLKKNLETLETRLRKIGAGVPEPSAAESKRLCSLL
          EE.......W..RLAD...PLWRL.YE.QL.VK...L...L..LE.RLR....G.P.....E...LCS.L
Retrocopy EEWGPDPGSWPERLADLVTPLWRLDYEQQLRVKTDALRGLLQWLEGRLRLL--GSPD---GEAGVLCSRL

Parental  HPFIPSPVIDGYRNKSSFCINRGPDGNSETVGYYLKSWGGSNIFCVQPSHLKDIPEKHNQIAQCFELFLQ
          .PF.PSPV..GYRNK..F....GPDG...TVGY.L.S.G.....CV.P.HLK.IP..H...A.C...FL.
Retrocopy QPFRPSPVLHGYRNKCNFAVRQGPDGRPRTVGYVLGSGGEQQPVCVRPGHLKHIPDAHQRVARCYQDFLE

Parental  QSKLSSYIDSQKGGLWHELIVRTTFLGHTMVIIIFNPQELSQEEFCVQKEEIKEFFSTGPGSVCDLTSLY
          Q..L..Y.DS...G.WHEL.VR.T..GHTM.I..F..Q.LS.EE.....EE..EFF..GPG..C.L.SLY
Retrocopy QTPLDPYLDSDASGHWHELTVRSTSQGHTMAIVTFQLQGLSPEELQEPQEELREFFTRGPGAICELASLY

Parental  VKERTPRHQELTPFQLLAGEPYLFEEILGLKFRISPGAFFQLNTSAAEVLYRTVGELGRVDSNTVILDFS
          ..ER....Q.....QLLAG.PYLFE...G.KFRISPGAFFQ.N..A.EVLYR.VGEL..VD.NT..LD.S
Retrocopy FQERSGDQQQPC-YQLLAGNPYLFEDLPGFKFRISPGAFFQINSAAVEVLYRVVGELIGVDPNTLLLDLS

Parental  HGTGATGLSLARQTSKVFRMGLVGEALEDAKWTAAFNGITNWEFCPGNVNEIMSQILESQEDGCSFMALV
          .GTGAT.LSLA..TS.V...GLVG.A.EDAKWT.AFNGITNWEF....V.....Q.L.SQE.G.S....V
Retrocopy QGTGATSLSLAPHTSQVLSTGLVGQAVEDAKWTTAFNGITNWEFHADHVENVVPQLLKSQEAGQSPVVMV

Parental  DPSQCGLSNRVVQDIRNCKAIQTLVFVSCRPYGKSMENIIELCRPPDPERNLLGEPFVLRQAVPVDMFPH
          DPS..GL...VV..IRNC.AI.TL..VSC.P.GK...N..ELC.PPDP...LLGEPFVLRQAVPVDMFPH
Retrocopy DPSRTGLNFQVVRAIRNCTAIRTLLYVSCYPEGKAKRNFLELCCPPDPGKDLLGEPFVLRQAVPVDMFPH

Parental  SLQCELVFLFTR
          ....ELV.LFTR
Retrocopy TPHYELVVLFTR

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	16.57 RPM	0.00 RPM
SRP007412_cerebellum	13.38 RPM	0.00 RPM
SRP007412_heart	25.32 RPM	0.00 RPM
SRP007412_kidney	9.22 RPM	0.00 RPM
SRP007412_liver	47.33 RPM	0.00 RPM
SRP007412_testis	5.11 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_77 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_77 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 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004570	1 retrocopy	retro_cjac_1676,
Homo sapiens	ENSG00000188917	1 retrocopy	retro_hsap_272,
Gorilla gorilla	ENSGGOG00000023759	1 retrocopy	retro_ggor_319,
Macropus eugenii	ENSMEUG00000006532	2 retrocopies	retro_meug_1325, retro_meug_74,
Macaca mulatta	ENSMMUG00000010394	1 retrocopy	retro_mmul_567,
Monodelphis domestica	ENSMODG00000025630	1 retrocopy	retro_mdom_77 ,
Nomascus leucogenys	ENSNLEG00000007522	1 retrocopy	retro_nleu_1485,
Pongo abelii	ENSPPYG00000020545	1 retrocopy	retro_pabe_397,
Pan troglodytes	ENSPTRG00000023413	1 retrocopy	retro_ptro_228,