RetrogeneDB ID: retro_mdom_1649

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:46052380..46053276(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C14orf79
• Ensembl ID: ENSMODG00000027908
• Aliases: None
• Description: chromosome 14 open reading frame 79 [Source:HGNC Symbol;Acc:20126]

Sequence

>retro_mdom_1649
ATACAGGACCAGCACCTCACAAGAGATCTCTAAGGACAAGAGATTGCCAGTGGAAAGTCCTCCCTCATTGGTCTGGTGGA
TGTGGTAGAAAGGGCTTCTATCAGCAAGATCCTCAAAGGGAATGGTGGAAATTATGCACCTGGCAATAGGGACTGTGACA
AAAGGATAGTGAAAACAGTCTACTATGCTCTGCCATGACTGGAAAGCAAATCAAAAATGCTGCTCTTCCCATTTCTGTAT
TGGATACTGGCATTTCTGACAGCAATGCTTAGGTTCCAAAGAACACAACAGCTCCTGGGGTGACTTTGAAGACTTAAGTG
ATGTTTCTGACAAGTCTGACACTTACAGCACCTGCTATATTCTGGAGCAATGGACAGCACCAGAGCACATGAAAGTAATT
CATATTTAAATGGATGTGTCACAATCTCTTGTGACTATCTACAGTCTGGCAATTTATCCATTATGGTGGAAATTCTGCTT
TTTTCACCTATTAAAGTCAAACTCAGGAATGAAAATATTTTAAGCTTGTTTTCATGAAGTAGTAGTACAACAGATGGCAA
GAGGATATTTACACCATCTTCTATATTTTAGAAAAATATAATGTAAGAAATACTAACCACAAACCTATAGAAAAAACAAT
TTTGCTCTGATTCCTGAAAACTCTGGAGGATTCTATAAGATGAAAGTAGTACATATACTTCAAGATGCCTCTGAAGTAAA
TCTCATTATCAGAAACATTTCTTACTTGTTCTTGGATTAGATACTGCTCAAAAAAAGATCTTTCAGGAGTTAAGAATCAC
ATTCTGGAAGATTCAAACTTGAAAAAGACTGAAGAGTTATTAGAAGTAAGGACATTTAATTTTAATAAGTGTAACATTCT
AATTCAAAACAAACTC

Alignment

ORF - retro_mdom_1649 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.75 %
• Parental protein coverage: 84.7 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  MQDQRPAPRNPRGLEIA-GVALLGDLVEAAENAAVTDPSEGEGENSVAGSRDCDEELVKIDNSALPRLES
          .QDQ....R...G.EIA.G...L..LV...E.A.......G.G.N...G.RDCD...VK....ALP.LES
Retrocopy IQDQH-LTRDL*GQEIASGKSSLIGLVDVVERASISKILKGNGGNYAPGNRDCDKRIVKTVYYALP*LES

Parental  KGR-NAAGPTAAGEAGVSDGG-CSCSVEHNSSWGDFEGFSETSDKSDTFSTLEMLERWAAPG-TRESDAD
          K...NAA.P......G.SD...C..S.EHNSSWGDFE..S..SDKSDT.ST...LE.W.AP....ES...
Retrocopy KSK<NAALPISVLDTGISDSN<CLGSKEHNSSWGDFEDLSDVSDKSDTYSTCYILEQWTAPE<AHESNSY

Parental  LNACGSNSCGCLQADSLTRMSETAAVSPNQASLSYENI-FKLVFQ-EVPVQQMT-EDICTLRHFLEKHNE
          LN.C...SC..LQ...L..M.E....SP....L..ENI.FKLVF..EV.VQQM..EDI.T....LEK.N.
Retrocopy LNGCVTISCDYLQSGNLSIMVEILLFSPIKVKLRNENI<FKLVFM<EVVVQQMA>EDIYTIFYILEKYNV

Parental  ENTSCKSV-KKQLCSESQKLWRILQDEDSTSTSRCLWSKSHCQ-DNFLLVLGID-AAQKDLSGDKNHVLE
          .NT..K...KKQ.CS.S.KLWRIL.DE.ST.TSRCL.SKSH.Q...FL....I.....KDLSG.KNH.LE
Retrocopy RNTNHKPI>KKQFCSDS*KLWRIL*DESSTYTSRCL*SKSHYQ<ETFLTCSWIRYCSKKDLSGVKNHILE

Parental  DSNLKETEELTEVNGFNLNNCKALIQTKL
          DSNLK.TEEL.EV..FN.N.C..LIQ.KL
Retrocopy DSNLKKTEELLEVRTFNFNKCNILIQNKL

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	131.24 RPM
SRP007412_cerebellum	0.00 RPM	87.82 RPM
SRP007412_heart	0.00 RPM	87.12 RPM
SRP007412_kidney	0.00 RPM	196.21 RPM
SRP007412_liver	0.00 RPM	11.08 RPM
SRP007412_testis	0.00 RPM	643.32 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1649 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1649 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000027908	1 retrocopy	retro_mdom_1649 ,