RetrogeneDB ID: retro_mdom_1640

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:8898378..8899643(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000007512
• Aliases: None
• Description: None

Sequence

>retro_mdom_1640
GCCAGTGGGATCCTTATGGAATAACAAGATGGTGATAAAAGCAACTGTGAGGATTACCTTATGATTTCCTTGGATGATGC
TGGGAAGACAGAACATAATGACTCTTTTGAAATTACCATGAATACTGAATCTGAATTTGAATTTATAAAGTACCTGGTAG
TCACTCTGAAATCAACAAAGTTATATTTTTAAGGCTGATCCTGGATAGGATTATTTCGGTGGGACAGTGTATATTGTGGA
GAGTGAACTTGAGAATGATCCTGGAGTTGGACCACTTAATCAGAATAACAGTATTTGTACTTCAAGAGAAAACATGGTTT
AAATGACTGTAAAAGACTCTCAGCAAGAAGATAAAGATTCAAATATTGTGAAAATCACTGATGGAGTTTATATGAAAATG
ATTACTGGTAAGGAAGACATAATAGTGGCACCTGAACAACAAATTGATGATATTGAAATAAAAACTTTCAAGCCAATAAC
TTGGGCAGTAGCCTATGGTAACAATACTGATAGAACTGAAAACCAGACTGGCACTTCAAGTTCCCCTTTGCATATAGATG
AGTCTTCTGAACTTGGCAGACTGGAAAAAGAAAAAACAAAGTAGAGAAGACCTGATTTTAGGCAGTACCAAACAGCAATA
ATTATTGACCCTTTTGGACAACCATTGAATGCCTGTCTTTGTAGGTTTTGTGGGAAGAAGTTTAAAATCAGAGAAGATTT
ATAGGAAAAACTATTCACAGTACCTTACGAGAAAAAAAAATTATTGATGCATAGGTTGTGATTACTCTACTAATAAAAAA
GATACATTACACAACCATCTGGAAAGCCACACATTGACCAACAAAACCAAAAATGTAATTGAATATGATGAATGTGGGAA
ACATTTCTCTCATGCTGAAATCTTGTTCACTCACAACACTATGTATAAGGAAAAAGAAGTCAACAAAATGCATATGTGCA
AATTCTGCCATTCTGAAGCTGCTGAAGAAAGGTTATTGAACTGCCATCTTCTGGCAGTCCACAGCAAAGACTTTCCTTAT
ATTTGTGTGAAAAATTGCAAAAGTTTCCATCTTCCCTCAGAGCTCAAGAAATACAGGTGTATCCTTACAAATGAGAAGCT
ACACCAATGTCAATACTGAGAATATAGATCCACTGATTCTTCTAATTTGAAAACTTATGTAAAGACTAAACATAGAAAAG
AGATGGCATTCAAGTGTAAGATTTGTCTTCTGACTTTCTCAGATATCAAAAAGGGGGTTGAACAT

Alignment

ORF - retro_mdom_1640 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.57 %
• Parental protein coverage: 53.53 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ANGIPVEQQDDDKSNCEDYLMISLDDAGKIEHDGSSEITMDAESEIDPCK-VDGTCPEVIKV-YIFKADP
          A.GI..E.QD.DKSNCEDYLMISLDDAGK.EH..S.EITM..ESE....K.V.G...E..KV.YIFKADP
Retrocopy ASGILME*QDGDKSNCEDYLMISLDDAGKTEHNDSFEITMNTESEFEFIK<VPGSHSEINKV<YIFKADP

Parental  GEDDLGGTVDIVESEPENDHGVGLLDQSSSIRVPREKMVYMTVNDSQQEDEDLNVAEIADEVYMEVIVGE
          G.D..GGTV.IVESE.END.GVG.L.Q..SI...RE.MV.MTV.DSQQED.D.N...I.D.VYM..I.G.
Retrocopy G*DYFGGTVYIVESELENDPGVGPLNQNNSICTSRENMV*MTVKDSQQEDKDSNIVKITDGVYMKMITGK

Parental  EDAAVAHEQQIDDTEIKTFMPIAWAAAYGNNTDGIENRNGTASALLHIDESAGLGRLAKQKPKKRRRPDS
          ED..VA.EQQIDD.EIKTF.PI.WA.AYGNNTD..EN..GT.S..LHIDES..LGRL.K.K.K.RR.PD.
Retrocopy EDIIVAPEQQIDDIEIKTFKPITWAVAYGNNTDRTENQTGTSSSPLHIDESSELGRLEKEKTK*RR-PDF

Parental  RQYQTAIIIGPDGHPLTVYPCMIC-GKKFKSRGFLKRHMKNHPEHLTKKK-YRCTDCDYTTNKKISLHNH
          RQYQTAIII.P.G.PL....C..C.G...KS....K...KN....LT....Y.C..CDY.TNKK..LHNH
Retrocopy RQYQTAIIIDPFGQPLNACLCRFC>GRSLKSE---KIYRKNYSQYLTXXXXY*CIGCDYSTNKKDTLHNH

Parental  LESHKLTNKTEKAIECDECGKHFSHAGALFTHKMVHKEKGANKMHKCKFCDYETAEQGLLNRHLLAVHSK
          LESH.LTNKT...IE.DECGKHFSHA..LFTH....KEK..NKMH.CKFC..E.AE..LLN.HLLAVHSK
Retrocopy LESHTLTNKTKNVIEYDECGKHFSHAEILFTHNTMYKEKEVNKMHMCKFCHSEAAEERLLNCHLLAVHSK

Parental  NFPHICVECGKGFRHPSELKKHMRIHTGEKPYQCQYCEYRSADSSNLKTHVKTKHSKEMPFKCEICLLTF
          .FP.ICV...K.F..PSELKK...I.T.EK..QCQY.EYRS.DSSNLKT.VKTKH.KEM.FKC.ICLLTF
Retrocopy DFPYICVKNCKSFHLPSELKKYRCILTNEKLHQCQY*EYRSTDSSNLKTYVKTKHRKEMAFKCKICLLTF

Parental  SDTKEVQQH
          SD.K....H
Retrocopy SDIKKGVEH

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_1640 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1640 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	ENSMODG00000007512	1 retrocopy	retro_mdom_1640 ,
Mus musculus	ENSMUSG00000079509	1 retrocopy	retro_mmus_644,