RetrogeneDB ID: retro_mdom_889

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:329938505..329941149(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000018482
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000011768
• Aliases: None
• Description: None

Sequence

>retro_mdom_889
TTGAATATTTTAGATTGGAAGAGTAAACAAAACAATGTTGAAGTGCCCTTTCTCCCTGCCCGTGTTCTCCTTCAAGATTT
TACTGGGATACCAGCAATGGTGGATTTTGCTGCTATGAGAGAAGCAATGAAAACTCTTGGTGGAGATTCCAAGAATGTCC
ATCCTGCCAGCCCTACAGATCTCACTGTTGACCACTCTTTGAAAATTGATCAGTAAATGTGCAATACAGAATGCTCCAAA
TCCTAGAGGTGGTGGCCTACAGAAAACCACAAGCAAACTTTCTCCACTTAAAGTGCAGCCTCGAAAAGTCTCCTGCAGAG
GCCAGACTACCTGTGGAGGGCCATGTGATACTGGAGAACTGGGAGGCAACTCAGGAAAATTTTCTGCACAGATTGAGAAC
ACACCAATCCTATGTCCTTTTCATTTACAACCTGTGCCTGAGCCTGAAACAGTGTTAAAAAACCAAGAGGTAGAATTTGG
CAGAAATAGAGAAAGACTACAGTTTTTCAAATGGAGTTCAAAAGTTTTTAAGAATGTGACTCTAATTCCCCCTGGAACTG
GAATGGCCCATCAAGTCAATTTGGAGTATTTGTCAAGAGTGGTTTTTGAAGGAGAGGACCTCTTCTTTCCAGACAGTGTG
GTTGGAACAGACTCTCATATAACTATGGTGAATGGCTTGGGCATCCTAGGATGGGGAGTTGGGGGCATGGAGACAGAAGC
AGTTATGCTTGGTCTTCCAGTCTCTCTTACTTTGCCTGAGGTGGTTGGGTGTGAATTGATTGGATCATCAAGTTCTTTGG
CTACATCCATAGACATGGTTCTTGGTTTTACAAAGCACCTCAGACAAGTAGGAGTGGCTGGAAAATTTGTCAAATTCTTT
GGAAGTGGAGTTCCTCAACTCTCTGTGACTGATCAAACCACAATTGCAAACATGTGTCCTTAATATGGTGCTATTCTGAG
CTTTTTCCCTGTTGATAATGTGACTTTAAAGCACTTAAAGCATACAGGTTTTGACAAAGAGAAACTTACATTAATGGAAG
CATACCTTAAAGCTGTGAAGTTGTTTAGAAGTGACCAGAGTTCTTCAACAGAGCCTGAGTATTCCCAGATAATACAGATT
AATCTGAACTCTATAATTCCATCTGTCAGTGGTCCAAAGAGGCCCCAGGATCGAGTGGCTGTGAGTGATATGAAAAGTGA
TTTCTAAGCTTGCCTAAATGAAAAGATTGGATTTAAAGGCTTTCAAATTGCCATAGAAAAACAAAATGATATCGTGCCTA
TTCAGTATGAAGGAATTGAGTATAAACTGTCTCATGGTTCTGTTGTCATTGCTGCGGTGATCAGTTGTACCAATAACTGT
AATCCTTCTGTCATGCTTGCTGCAGGTCTGTTGGCAAAAAAAGCTGTTGAAGCTGGCCTCCGGGTTAAACCTTACATCAG
AACAAGCTTATCTCCTGGCAGTGGGATGGTTACACATTACCTCAGTTCAAGTGGAGTGTTACCATACCTTAGTAAACTTG
GATTTGAAGTAGTGGGTTATGGATGTTCAACCTGTGTTGGAAATACAGCTCCCTTACCAGAAGCTGTTCTGAATGCAATA
AAAGAGGGTGACTTAGTTGCGTGTGGGGTGCTATCTGTCAACAAGAATTTTGAAGGTCTTCTCTGTGACTGTGTCCGTGC
CAACTACCTTGCCTCCCCACCTCTAGTAGTAGCTTATGCCATTGCAGGAACAGTGAACATAGATTTCCAGACTGAGCCTT
TAGGTACTGATCCTCAAGGCAGAAACATCTACCTACGAGACATTTGGCCTAATCGAGAGGAGCTCCATAAAGTCGAGGAA
GAGCATGTGATATTCTCTAAGTTTAAATAATTAAAGGAAAAAATGGAGAAGGGAAATAAGCGGTGGAATTCCTTAGATGC
CCCAGATTCTGTTTTGTTCCCATGGGATTCAAAATCTACTTATATCAGATGTCCATCTTTTTTTGATAAACTTGCCAAAC
AGCCAGTTTCCCTGCAACCTATTGAAAATGCCCATGTCTTGCTCTATTTGGGAGACTGTGTCACAACAGACCATATATCC
CCTGCTGGAAGCATCGCCAGGAGTAGTGCTGCTGCCAAGTATCTGACAAATAGAGGCCTTACACCTCGTGAATTCAATTC
TTATGGAGCCCGAAGAGGCAATGATGCTGTGATGACAAGGGGCACTTTTGAAAATATCGAGCTTCAAAATAAGTTTATTG
GAAAACCTGTCCCCAAAACACTTCATTTTCCATCAGGACAGACACTGGATGTATTTGAGGCTGCTGAATTATACCAGAAA
GAAGGTATTCCATTGATTATTTTAGCAGGAAAGAAATATGGCTCTGGAAATTCAAGAGACTGGGCTGCCAAAGGACCATA
TTTGATGGGTGTGAAAGCTGTTATAGCTGAAAGTTATGAAAAGATTCACAAAGACCATTTGATTGGAATTGGTATCGCTC
CACTGCAGTTTCTTCCAGGAGAAAGTGCCAGTTCCTTGGGCCTCTCTGTCAGAGAGCAGTTTTCTTTGTCATTCCCTGAA
GACCTATCACCAGGAGTCACCTTAAATGTAAACACAAGCACTGGAAAAGTATTCAGCGTGATTGCTTCATTTGAAAATGA
TGTG

Alignment

ORF - retro_mdom_889 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.9 %
• Parental protein coverage: 91.4 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNILDWKSKQNNVEVPFLPARVLLQDFTGIPAMVDFAAMREAVKTLGGDPKNVHPACPTDLTVDHSLQID
          .NILDWKSKQNNVEVPFLPARVLLQDFTGIPAMVDFAAMREA.KTLGGD.KNVHPA.PTDLTVDHSL.ID
Retrocopy LNILDWKSKQNNVEVPFLPARVLLQDFTGIPAMVDFAAMREAMKTLGGDSKNVHPASPTDLTVDHSLKID

Parental  FSKCAIQNAPN-PGGGDLQKTTSKLSPLKVQPRKVSCRGQTTCRGPCDTGELGRNSGKFSAQIENTPILC
          ...C.........GGG.LQKTTSKLSPLKVQPRKVSCRGQTTC.GPCDTGELG.NSGKFSAQIENTPILC
Retrocopy Q*MCNTECSKS>RGGG-LQKTTSKLSPLKVQPRKVSCRGQTTCGGPCDTGELGGNSGKFSAQIENTPILC

Parental  PFHLQPVPEPETVLKNQEVEFGRNRERLQFFKWTSKVFKNVTLIPPGTGMAHQVNLEYLSRVVFEEKDLF
          PFHLQPVPEPETVLKNQEVEFGRNRERLQFFKW.SKVFKNVTLIPPGTGMAHQVNLEYLSRVVFE..DLF
Retrocopy PFHLQPVPEPETVLKNQEVEFGRNRERLQFFKWSSKVFKNVTLIPPGTGMAHQVNLEYLSRVVFEGEDLF

Parental  FPDSVVGTDSHITMVNGLGILGWGVGGIETEAVMLGLPVSLTLPEVVGCELIGSSSSLATSIDVVLGITK
          FPDSVVGTDSHITMVNGLGILGWGVGG.ETEAVMLGLPVSLTLPEVVGCELIGSSSSLATSID.VLG.TK
Retrocopy FPDSVVGTDSHITMVNGLGILGWGVGGMETEAVMLGLPVSLTLPEVVGCELIGSSSSLATSIDMVLGFTK

Parental  HLRQVGVAGKFVEFFGSGVPQLSVTDRTTIANMCPEYGAILSFFPVDNVTLKHLEHTGFDKEKLTLMEAY
          HLRQVGVAGKFV.FFGSGVPQLSVTD.TTIANMCP.YGAILSFFPVDNVTLKHL.HTGFDKEKLTLMEAY
Retrocopy HLRQVGVAGKFVKFFGSGVPQLSVTDQTTIANMCP*YGAILSFFPVDNVTLKHLKHTGFDKEKLTLMEAY

Parental  LKAVKLFRSDQSSSTEPEYSQIIQINLNSIIPSVSGPKRPQDRVAVSDMKSDFQACLNEKVGFKGFQIAT
          LKAVKLFRSDQSSSTEPEYSQIIQINLNSIIPSVSGPKRPQDRVAVSDMKSDF.ACLNEK.GFKGFQIA.
Retrocopy LKAVKLFRSDQSSSTEPEYSQIIQINLNSIIPSVSGPKRPQDRVAVSDMKSDF*ACLNEKIGFKGFQIAI

Parental  EKQNDIVPIQYEGIEYKLSHGSVVIAAVISCTNNCNPSVMLAAGLLAKKAVEAGLRVKPYIRTSLSPGSG
          EKQNDIVPIQYEGIEYKLSHGSVVIAAVISCTNNCNPSVMLAAGLLAKKAVEAGLRVKPYIRTSLSPGSG
Retrocopy EKQNDIVPIQYEGIEYKLSHGSVVIAAVISCTNNCNPSVMLAAGLLAKKAVEAGLRVKPYIRTSLSPGSG

Parental  MVTHYLSSSGVLPYLSKLGFEVVGYGCSTCVGNTAPLPEAVLNAIKEGDLVACGVLSGNKNFEGRLCDCV
          MVTHYLSSSGVLPYLSKLGFEVVGYGCSTCVGNTAPLPEAVLNAIKEGDLVACGVLS.NKNFEG.LCDCV
Retrocopy MVTHYLSSSGVLPYLSKLGFEVVGYGCSTCVGNTAPLPEAVLNAIKEGDLVACGVLSVNKNFEGLLCDCV

Parental  RANYLASPPLVVAYAIAGTVNIDFQTEPLGTDPQGRNIYLQDIWPNREELHKVEEEHVIFSMFKELKEKM
          RANYLASPPLVVAYAIAGTVNIDFQTEPLGTDPQGRNIYL.DIWPNREELHKVEEEHVIFS.FK.LKEKM
Retrocopy RANYLASPPLVVAYAIAGTVNIDFQTEPLGTDPQGRNIYLRDIWPNREELHKVEEEHVIFSKFK*LKEKM

Parental  EKGNKRWNSLDAPDSVLFPWDSKSTYIRCPSFFDKLAKQPVPLQPIENAHVLLYLGDCVTTDHISPAGSI
          EKGNKRWNSLDAPDSVLFPWDSKSTYIRCPSFFDKLAKQPV.LQPIENAHVLLYLGDCVTTDHISPAGSI
Retrocopy EKGNKRWNSLDAPDSVLFPWDSKSTYIRCPSFFDKLAKQPVSLQPIENAHVLLYLGDCVTTDHISPAGSI

Parental  ARSSAAAKYLTNRGLTPREFNSYGARRGNDAVMTRGTFANIKLLNKFIGKPAPKTLHFPSGQTLDVFEAA
          ARSSAAAKYLTNRGLTPREFNSYGARRGNDAVMTRGTF.NI.L.NKFIGKP.PKTLHFPSGQTLDVFEAA
Retrocopy ARSSAAAKYLTNRGLTPREFNSYGARRGNDAVMTRGTFENIELQNKFIGKPVPKTLHFPSGQTLDVFEAA

Parental  ELYQKEGIPLIILAGKKYGSGNSRDWAAKGPYLMGVKAVIAESYEKIHKDHLIGIGIAPLQFLPGESASS
          ELYQKEGIPLIILAGKKYGSGNSRDWAAKGPYLMGVKAVIAESYEKIHKDHLIGIGIAPLQFLPGESASS
Retrocopy ELYQKEGIPLIILAGKKYGSGNSRDWAAKGPYLMGVKAVIAESYEKIHKDHLIGIGIAPLQFLPGESASS

Parental  LGLSGREQFSLSFPEDLSPGVTLNVKTSTGKVFSVIASFENDV
          LGLS.REQFSLSFPEDLSPGVTLNV.TSTGKVFSVIASFENDV
Retrocopy LGLSVREQFSLSFPEDLSPGVTLNVNTSTGKVFSVIASFENDV

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	108.47 RPM
SRP007412_cerebellum	0.00 RPM	112.63 RPM
SRP007412_heart	0.00 RPM	65.39 RPM
SRP007412_kidney	0.00 RPM	167.24 RPM
SRP007412_liver	0.00 RPM	199.89 RPM
SRP007412_testis	0.00 RPM	117.86 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_889 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_889 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	ENSMODG00000011768	1 retrocopy	retro_mdom_889 ,
Sarcophilus harrisii	ENSSHAG00000017480	1 retrocopy	retro_shar_215,