RetrogeneDB ID: retro_mdom_538

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:216927484..216928298(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CNPPD1
• Ensembl ID: ENSMODG00000015328
• Aliases: None
• Description: cyclin Pas1/PHO80 domain containing 1 [Source:HGNC Symbol;Acc:25220]

Sequence

>retro_mdom_538
ATCACGTCCAGAATGATGGCCAGTAAGAGCCCGTATGATGAAGGAGAAGAGGAGGAGGTCTTCAGTGGTAAATAGGGGAC
TCCTGGGAGTCTGGCTGTGACTATCCTTAACACACTAGAGAGAGGCTTCTTGAGTGCTACAAATTCAAGCCTCTCCATTG
CCTCCCAGGGGATATTTGAGATTCTGAATTGGCTGGAAGGCTGTGTAGCTGAGCAGCAGGATTGTTGCCATGGCTCATCC
ACCTACATAGGATTGTATATGCTATTGAATCAGCAAACCTAGCAGTTGACTTTGGCCTCATTATACCAGTGTCTGCCCAA
GGTGGACTGGCCTGCTAGCCTTGGCTTACATGAATAGTAGGATTGTGGCTGTGGCTCTCATGTCCCAGGTCTTGGAGTTG
CATGACACTCTCCTCCCAGGTTCTGGTGATCTTGGTTGTTCAGCTATCAAATGCCCAATGGAACCCTGATCTCTGTCTTC
AATTTCCATTCTACAGTTTCCATCTCATTTTGACAAGATTTATCACAATCTAGTGGGGTGATGAGGCTGAAATCCCTGTG
ACAGAGCCTTCTGGATACTTTGTCTCCTCCATTACTTCCACCACTTTTATAAGATATTCTTACTTCTTTCCAATCCTGCG
CCCTTTGTTTGGAGCTCCAGATAGACTCCCCAACACACCATGACTATCAGCAGATAAACTATACAACCACAAAACATCTC
AGTCTCTGTTATTGACCTAGGCTAGCTCTTCTCTAGCCCTGGAGTCCTGTCATCTCTGCTCTCCCCTAGCTACAATAGTC
CCTGTCTGGTGTTG

Alignment

ORF - retro_mdom_538 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.54 %
• Parental protein coverage: 66.83 %
• Number of stop codons detected: 9
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LISMMVASKYLYDEGEEEEVFNDEWGAAGGVAVPTLNALERGFLNAMDWSLYTDPREIFEVLSWLEGCVA
          ..S.M.ASK..YDEGEEEEVF....G..G..AV..LN.LERGFL.A...SL......IFE.L.WLEGCVA
Retrocopy ITSRMMASKSPYDEGEEEEVFSGK*GTPGSLAVTILNTLERGFLSATNSSLSIASQGIFEILNWLEGCVA

Parental  EQQGRRRGWYTYTDLCVLLEQRTWQLALGSLCQRLAKL-ACLLALAYVSSVTVAVASVTILHQTLGLRGT
          EQQ....G..TY..L..LL.Q.T.QL.L.SL.Q.L.K....LLALAY..S..VAVA......Q.L.L..T
Retrocopy EQQDCCHGSSTYIGLYMLLNQQT*QLTLASLYQCLPKV>TGLLALAYMNSRIVAVA---LMSQVLELHDT

Parental  PPPGPPDLGCFAPKCPLEPCSLSSASGPQLLNSSANTSQNLVGEIG-LHSLWGSLLATLTP---PPLLPG
          ..PG..DLGC.A.KCP.EP.SLSS.S..Q..........NLVG..G.L.SL..SLL.TL.P...PPLL..
Retrocopy LLPGSGDLGCSAIKCPMEP*SLSSISILQFPSHFDKIYHNLVG**G<LKSL*QSLLDTLSPPLLPPLL*D

Parental  TPPS-QPCPLCRQLQIDSPAHHACQNTNYSTTTRPLNPWYPPPGQVPPWSWSPMAPVL-PQPSAPCLVL
          ...S.Q.C.LC..LQIDSP.HH..Q..NY.TT........P......PW..SP....L.P....PCLVL
Retrocopy ILTSFQSCALCLELQIDSPTHHDYQQINYTTTKHLSLCY*PRLALL*PW--SPVISAL>PSYNSPCLVL

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_538 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_538 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000015328	1 retrocopy	retro_mdom_538 ,
Pteropus vampyrus	ENSPVAG00000010786	1 retrocopy	retro_pvam_857,
Rattus norvegicus	ENSRNOG00000018325	1 retrocopy	retro_rnor_2150,