RetrogeneDB ID: retro_mdom_1916

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:113931388..113933245(-)
• Located in intron of: ENSMODG00000018283

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000012887
• Aliases: None
• Description: None

Sequence

>retro_mdom_1916
AATAACCTGGTAAAAGAATGGATACGGGAAATCAGTGAAAGCAAGAATCTTCCATAGTCTGTAATTGAAAATGTTGGAGG
AAAAATTTTTACATTTGGATCCTACAGATTAGGAGTTCATACAAAAAGGTGCTGATATTGATGCATTGTGTTTTGCACCA
AGACATGTTGACCGCAGTGACTTTTTCACCTCATTCTATGAAAAATTGAAGTTACAGGAAGAAGGAAAAGATTTGAGAGC
TATTGAAGAGGCATTTGTACCAGTTATCAAGCTATGTTTTGATGGTATTGAGATTGATATTTTGTTTGCAAGATTAGCAC
TGCAGACTATTCCTGAAAATTTGGACCTTCGTGATGACAGTCTACTAAAAAATTTAGATATTAGATGCATAAGAAATCTT
TATGGTTGCAGGGTAACCGATGAAATTTTACATCTAGTATCAAACATTGACAACTTCAGGTTAACTCTGAGAGCTTTCAA
ACTTTGGGCCAAACGCCACAACATCTATTCCAATATATTAGGTTTCCTCAGTGGTGTTCCCTAGTAGCAAGAACTTGCCA
GCTTTATCCAAATGCAATAGCATCAACTCTTGAACATAAATTTTTCTTGGTATTTTCTAAATGGGAATGGCCAAATCCAG
TGCTATTGAAACAACCTGAAGAATGCAATTTTAATTTGCCTGTGTGGGACCCAAGGGTAAACCCCAGTGATAGGTACCAT
CTTATTCCTATAATTACACCAGCATACCCATAACAGAATTCTACATACAATGTGTTCATTTCTACATGGAATGTCATGGT
TGAGGAGTATAATAAACAAGGTCTTGCTATCACAGATGAAATTTTGCTGAGTAAGGCAGAGTGGTCCAAACTTTTTGAAG
CTCCCAACTACTTTCAAAAGTACAAGCATTATATTGTACTTTTAGCAAGTGCACCAACAGAAAAGCAGTGACTAGAATGG
GTGGGCTTGATGGAATCAAAAATCCGAATCCTGGTTGGAAATTTGGAGAAGAATGAATTTATTACACTGGCTCATGTGAA
TCCTCAGTCATTTCCAGCACCGAAAGAAAATCCTGACAAGGAAGAATTTCCTACAATGTGGGTGATTGGATTAGTGTTTG
AAAAAACAGAAAACTCTGAAAACCTCAGTGTTGACCTTACATATGACATTCAGTCTTTTACAGATACAGTTTATAGGCAA
GCAATAAACAGCAAGATGTTTGAGATGGATATGAAAATTGCTGCAATGCATGTAAAAAGAAGACAACTTCATCAACTCCT
ACCTAATCACGTGCTTCAGAAAAAGAAAAAGCATTCATCAGAAGTTCAATTGACAGCTCTAAATGTCAGCAGTCTAGATT
TGTCTATGGATAGTGACAACAGCATGTCTGTGCCTTCTCCTACCAGTGCTATGAAGACCAGTCCATTGAATAGTTCTGGC
AGCTCGCAGGGCAGAAACAATCCTGCTCCAGCTGTAACAGCAGCATCTTTGACCAACATCCAGGCAACTGAGGTTTCTGT
GCCACAAGTAAATTCCAGTGAAAGCTCAAGGGGTACTTCAAGTGAAAGCATTCCTCAAACTGCCACTCAGCCAGCCATTT
CTCCACCACCAAAGCCTACAGTCTCCAGAGTTGTTTCCTCAACATGTCTGGTAAACCAACCACCAAGACCTTCAGGAAAC
ACAGCAACAAAAGTTCCTAATCCTATAGTAGGAGTCAAAAGGACGTCTTCACCTCATAAAGAAGAGAGTCCCAAGAAAAC
CAAAACAGAGGAGGATGAGACAAGTGAAGATGTCAACTGTCTTGATTTGATTGAACATGATAAACGGGAAACTAAGAAAA
AACATCCAGTACAGACC

Alignment

ORF - retro_mdom_1916 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.31 %
• Parental protein coverage: 84.15 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NNLVKEWIREISESKNLPQSVIENVGGKIFTFGSYRLGVHTK-GADIDALCVAPRHVDRSDFFTSFYEKL
          NNLVKEWIREISESKNLP.SVIENVGGKIFTFGSYRLGVHTK.GADIDALC.APRHVDRSDFFTSFYEKL
Retrocopy NNLVKEWIREISESKNLP*SVIENVGGKIFTFGSYRLGVHTK>GADIDALCFAPRHVDRSDFFTSFYEKL

Parental  KLQEEVKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNGCRVT
          KLQEE.KDLRA.EEAFVPVIKLCFDGIEIDILFARLALQTIPE.LDLRDDSLLKNLDIRCIR.L.GCRVT
Retrocopy KLQEEGKDLRAIEEAFVPVIKLCFDGIEIDILFARLALQTIPENLDLRDDSLLKNLDIRCIRNLYGCRVT

Parental  DEILHLVPNIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVS-WAMLVARTCQLYPNAIASTLVHKFFLVF
          DEILHLV.NIDNFRLTLRA.KLWAKRHNIYSNI...LG..S.W..LVARTCQLYPNAIASTL.HKFFLVF
Retrocopy DEILHLVSNIDNFRLTLRAFKLWAKRHNIYSNI---LGFLS<WCSLVARTCQLYPNAIASTLEHKFFLVF

Parental  SKWEWPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRMVMVEEF-KQGL
          SKWEWPNPVLLKQPEECN.NLPVWDPRVNPSDRYHL.PIITPAYP.QNSTYNV..ST..VMVEE..KQGL
Retrocopy SKWEWPNPVLLKQPEECNFNLPVWDPRVNPSDRYHLIPIITPAYP*QNSTYNVFISTWNVMVEEYNKQGL

Parental  AITDEILLSKAEWSKLFEAPNFFQKYKHYIVLLASAPTEKQRLEWVGLVESKIRILVGSLEKNEFITLAH
          AITDEILLSKAEWSKLFEAPN.FQKYKHYIVLLASAPTEKQ.LEWVGL.ESKIRILVG.LEKNEFITLAH
Retrocopy AITDEILLSKAEWSKLFEAPNYFQKYKHYIVLLASAPTEKQ*LEWVGLMESKIRILVGNLEKNEFITLAH

Parental  VNPQSFPAPKENPDKEEFRTMWVIGLVFKKTENSENLSVDLTYDIQSFTDTVYRQAINSKMFEMDMKIAA
          VNPQSFPAPKENPDKEEF.TMWVIGLVF.KTENSENLSVDLTYDIQSFTDTVYRQAINSKMFEMDMKIAA
Retrocopy VNPQSFPAPKENPDKEEFPTMWVIGLVFEKTENSENLSVDLTYDIQSFTDTVYRQAINSKMFEMDMKIAA

Parental  MHVKRRQLHQLLPNHVLQKKKKHSSEVRLTALNDSSLDLSMDSDNSMSVPSPTSAMKTSPLNSSGSSQGR
          MHVKRRQLHQLLPNHVLQKKKKHSSEV.LTALN.SSLDLSMDSDNSMSVPSPTSAMKTSPLNSSGSSQGR
Retrocopy MHVKRRQLHQLLPNHVLQKKKKHSSEVQLTALNVSSLDLSMDSDNSMSVPSPTSAMKTSPLNSSGSSQGR

Parental  NSPAPAVTAASVTNIQATEVSVPQVNSSESSGGTSSESIPQTATQPAISPPPKPTVSRVVSSTRLVNQPP
          N.PAPAVTAAS.TNIQATEVSVPQVNSSESS.GTSSESIPQTATQPAISPPPKPTVSRVVSST.LVNQPP
Retrocopy NNPAPAVTAASLTNIQATEVSVPQVNSSESSRGTSSESIPQTATQPAISPPPKPTVSRVVSSTCLVNQPP

Parental  RPSGNTATKVPNPIVGVKRTSSPHKEESPKKTKTEEDETSEDANCLDLIEHDKQETKEQLDTET
          RPSGNTATKVPNPIVGVKRTSSPHKEESPKKTKTEEDETSED.NCLDLIEHDK.ETK......T
Retrocopy RPSGNTATKVPNPIVGVKRTSSPHKEESPKKTKTEEDETSEDVNCLDLIEHDKRETKKKHPVQT

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	209.67 RPM
SRP007412_cerebellum	0.00 RPM	192.93 RPM
SRP007412_heart	0.00 RPM	156.29 RPM
SRP007412_kidney	0.00 RPM	273.90 RPM
SRP007412_liver	0.00 RPM	159.10 RPM
SRP007412_testis	0.00 RPM	460.05 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1916 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1916 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 20 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014142	1 retrocopy	retro_amel_517,
Bos taurus	ENSBTAG00000004054	1 retrocopy	retro_btau_1078,
Canis familiaris	ENSCAFG00000017783	1 retrocopy	retro_cfam_1783,
Callithrix jacchus	ENSCJAG00000006512	2 retrocopies	retro_cjac_1763, retro_cjac_543,
Homo sapiens	ENSG00000090060	1 retrocopy	retro_hsap_30,
Gorilla gorilla	ENSGGOG00000006287	1 retrocopy	retro_ggor_202,
Loxodonta africana	ENSLAFG00000000946	1 retrocopy	retro_lafr_895,
Myotis lucifugus	ENSMLUG00000010922	1 retrocopy	retro_mluc_1396,
Macaca mulatta	ENSMMUG00000018610	1 retrocopy	retro_mmul_1675,
Monodelphis domestica	ENSMODG00000012887	2 retrocopies	retro_mdom_1714, retro_mdom_1916 ,
Mustela putorius furo	ENSMPUG00000003054	1 retrocopy	retro_mputfur_1375,
Mus musculus	ENSMUSG00000021111	1 retrocopy	retro_mmus_37,
Nomascus leucogenys	ENSNLEG00000000625	1 retrocopy	retro_nleu_2771,
Otolemur garnettii	ENSOGAG00000004611	1 retrocopy	retro_ogar_987,
Procavia capensis	ENSPCAG00000004199	1 retrocopy	retro_pcap_91,
Pongo abelii	ENSPPYG00000006128	1 retrocopy	retro_pabe_3113,
Pan troglodytes	ENSPTRG00000006704	1 retrocopy	retro_ptro_2595,
Pteropus vampyrus	ENSPVAG00000013925	1 retrocopy	retro_pvam_360,
Rattus norvegicus	ENSRNOG00000004827	1 retrocopy	retro_rnor_863,
Vicugna pacos	ENSVPAG00000006464	1 retrocopy	retro_vpac_378,