RetrogeneDB ID: retro_mdom_638

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:622463607..622464396(-)
• Located in intron of: None

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_638
GAAAATTGAATTTCTACAAAGAAAGTTTGGACTTGTGAGCATGAGGAAGTATTTAATATGGCCATAGAAATACCTTGTTG
GACAAATGTTAAAATCGAGATTGACACCAAGGAGCCATTGAATCCCACTAAACAAGATATAAAGAAAGGCAAGCTATGTT
ATGTGGCAAATATCTTCCCTCACAAGGATCATATATGGAATTATGGGGCCCTTCCTCAGACTTGGGGGGACCCTCATCAT
GTAGACTTTTGCACCACTTGCCATGGGAGTATGATCCCCTTGACGTTTGTGAAATAGGCTTCAGGGTTCATGCTCCTGGA
AACATTATCCAGGTGAAGATTCTTGGGATTTTGGCCCTTATTGATGGGGATGAGACAGATTGGAAGTTAATTGCTATTAG
CATGGATGACCCAGAAGCTTCCAGCTTCTATAGTATTGATGATGTGCAGAAGTGTAAATAAAATTACCTAAAGGTGACAG
TTGACTGGTTCTGATTTTACAAAGTGCTAGATGGGAAGCCAGAAAATGTATTTGCTTTTAATGGAGGATTTAAAGACAAG
GATTTCACTCATCAAGTTATTGAATCTACCCACAAATGTTGGAAAACTTTGCTTTATAAAAGAAGTTGATCAAGGAGGTA
TAAAATGTGTTAATGTGGAGATAAGAGATAGCCCTTTCTGTTGCAGTGAAGAGGAAGCCAGATCCATAGTGCAGAAGGTA
TCAGCTTCTGTGGGCAAAGATTTTGATTCCAAAGATGAAGATATCAACAAGTGGCATTTTATTAAGAAA

Alignment

ORF - retro_mdom_638 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.32 %
• Parental protein coverage: 72.73 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EKGIPTKKARTSEHEEVFNMVVEIPRWTNAKMEIDTKEPLNPIKQDIKKGKLRYVANIFPHKGFIWNYGA
          E..I.TKK..T.EHEEVFNM..EIP.WTN.K.EIDTKEPLNP.KQDIKKGKL.YVANIFPHK..IWNYGA
Retrocopy EN*ISTKKVWTCEHEEVFNMAIEIPCWTNVKIEIDTKEPLNPTKQDIKKGKLCYVANIFPHKDHIWNYGA

Parental  LPQTWEDPCHIDSITKCHG-DNDPLDVCEIGSKVHAPGDIIQVKILGILALIDGDETDWKLIAISIDDPE
          LPQTW.DP.H.D..T.CHG...DPLDVCEIG..VHAPG.IIQVKILGILALIDGDETDWKLIAIS.DDPE
Retrocopy LPQTWGDPHHVDFCTTCHG<EYDPLDVCEIGFRVHAPGNIIQVKILGILALIDGDETDWKLIAISMDDPE

Parental  ASNFHSIDDVRKYKPNYLEATVDWFRFYKVPDGKPENTFGFNGEFKDKDFAHEVIESTHKCWKALLH-KE
          AS.F.SIDDV.K.K.NYL..TVDWF.FYKV.DGKPEN.F.FNG.FKDKDF.H.VIESTHKCWK.LL..KE
Retrocopy ASSFYSIDDVQKCK*NYLKVTVDWF*FYKVLDGKPENVFAFNGGFKDKDFTHQVIESTHKCWKTLLY>KE

Parental  IDQGGIKCVNVKINDSPYCCSEEEARSIVEKASASVDKDFVSQEDEDINKWHFIKK
          .DQGGIKCVNV.I.DSP.CCSEEEARSIV.K.SASV.KDF.S..DEDINKWHFIKK
Retrocopy VDQGGIKCVNVEIRDSPFCCSEEEARSIVQKVSASVGKDFDS-KDEDINKWHFIKK

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_638 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_638 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,