RetrogeneDB ID: retro_mdom_946

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:532254851..532255433(-)
• Located in intron of: ENSMODG00000023114

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPA2
• Ensembl ID: ENSMODG00000020635
• Aliases: None
• Description: pyrophosphatase (inorganic) 2 [Source:HGNC Symbol;Acc:28883]

Sequence

>retro_mdom_946
AAACAATCGGGAAGCCCATACTCCCACCAATACCGCCTCTATGTCAAGAATATAACTGGTTACTACATCTCCCACTTACA
TGACGTTCCTCTGAAGCCTGAATCTAAAGAGGAAAATCTCATTCCTACAAAGAAAGCTTGGACCAGTGAGCATTAGGAAG
TATTTAATATGGTGATAGAAATACCTTGTTGGACAAATACTAAAATGGAGATTGACACCAAGGAGCCATTGAACCCCATT
AAACAAGATATAAAGAGAGGCAAGCTAAGTTATGTGGCAAATATCTCCCTTCACAAGGGTTATATATGGAATTATGAAGC
TCTTCCTCTGACTTGGGAAAACCCTCATCATGTACACTCCTGCACCTATTGCCATGGCCATAATGGCCCCCTCGACGTTT
GTGAAATAGGCTCCAAGGTTCATGCTCCTGGTGACATCCAGGTAAATATTCTTGGAATTCGGGCCTTTATTGATGTGGAT
GAGGCAGATTAGACATTAATTGCTATTAGAATGGATGACCCAGAATCTTCCAACATCCATAGTGTTGATGATGTGTGGAA
GGATAAACCAAATTACCTCAAG

Alignment

ORF - retro_mdom_946 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.36 %
• Parental protein coverage: 53.72 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EERGSPHSPQYRLYFKNVAGHYISPFHDIPLKPESKEEKGIPTKKARTSEHEEVFNMVVEIPRWTNAKME
          ...GSP.S.QYRLY.KN..G.YIS..HD.PLKPESKEE..IPTKKA.TSEH.EVFNMV.EIP.WTN.KME
Retrocopy KQSGSPYSHQYRLYVKNITGYYISHLHDVPLKPESKEENLIPTKKAWTSEH*EVFNMVIEIPCWTNTKME

Parental  IDTKEPLNPIKQDIKKGKLRYVANIFPHKGFIWNYGALPQTWEDPCHIDSITKCHGDNDPLDVCEIGSKV
          IDTKEPLNPIKQDIK.GKL.YVANI..HKG.IWNY.ALP.TWE.P.H..S.T.CHG.N.PLDVCEIGSKV
Retrocopy IDTKEPLNPIKQDIKRGKLSYVANISLHKGYIWNYEALPLTWENPHHVHSCTYCHGHNGPLDVCEIGSKV

Parental  HAPGDIIQVKILGILALIDGDETDWKLIAISIDDPEASNFHSIDDVRKYKPNYLE
          HAPGD.IQV.ILGI.A.ID.DE.D..LIAI..DDPE.SN.HS.DDV.K.KPNYL.
Retrocopy HAPGD-IQVNILGIRAFIDVDEAD*TLIAIRMDDPESSNIHSVDDVWKDKPNYLK

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_946 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_946 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 9 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010887	1 retrocopy	retro_cfam_405,
Choloepus hoffmanni	ENSCHOG00000008731	3 retrocopies	retro_chof_1052, retro_chof_430, retro_chof_769,
Echinops telfairi	ENSETEG00000014816	1 retrocopy	retro_etel_1959,
Macaca mulatta	ENSMMUG00000017004	1 retrocopy	retro_mmul_1278,
Monodelphis domestica	ENSMODG00000020635	5 retrocopies	retro_mdom_638, retro_mdom_795, retro_mdom_945, retro_mdom_946 , retro_mdom_947,
Oryctolagus cuniculus	ENSOCUG00000005941	2 retrocopies	retro_ocun_1338, retro_ocun_1470,
Ochotona princeps	ENSOPRG00000007086	1 retrocopy	retro_opri_847,
Sus scrofa	ENSSSCG00000022365	1 retrocopy	retro_sscr_557,
Tursiops truncatus	ENSTTRG00000003141	2 retrocopies	retro_ttru_1307, retro_ttru_606,