RetrogeneDB ID: retro_mdom_557

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:296025420..296026493(-)
• Located in intron of: ENSMODG00000014690

Retrocopy information

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

Parental gene information

• Parental gene symbol: PEX12
• Ensembl ID: ENSMODG00000019129
• Aliases: None
• Description: peroxisomal biogenesis factor 12 [Source:HGNC Symbol;Acc:8854]

Sequence

>retro_mdom_557
ATGGCCGAGCATGGAGCTCACATCATAGTCGCCTCTGGTGCTGATAAATGGCCCTCCATCTTCGAAGTGGTTGCTCAGGA
CAGTCTGATGATGGCTGTGAGGCCTGCCCTTCAGCATGTGGCCAAGGTTCTTGCAGAATCCAACCCTGCCCATTATGGCT
TCCTCTGGAGATGGTTTGACGAAACCTTCACTTTTCTGAATCTTTTGCTACAGCAGCACTACTTGTCTAAAGCTAGTGCC
TTGTTCTCTGAAAACTTTTATGGCTTAAAGAGAATCATGATGGGAGACCCTCAAGGGGTCCAGAGATTGGCCAGTGTTGG
CCTCCCAAAGAAGCAGCTTTGGAAGTCCCTCTTATTCCTGGTCCTCCTTCCCTGCTTGAAAGTGTTGGAGAAGTTGGTCT
CCAGCCTAAGAGAAGAGGATGAATATTCCATCCATCCCCCCTCTTCCTGTTGGAAGCGTTTTTACTGAGCTTTCCTGACA
GCTTATCCATTTGTGACTATGACCTGGGAAGGCTGGTTCCTCATATAGCAGTTATGTTACATCCTGGGGAAGGCTCAGCA
TCATTCACCATTGCTGAGCTAGCTGGAGTTCGCCTAGGTCGACTCTCAGCTGAAGATAGCAGAGCACTGGAAAAGACACT
AGCTCAAGCTAGTAGGATGCCACAACCAGCTACAAGTATTTGAGAGAAGGTGCAATCAGCTGTCAAGAAAGCTATAGGAG
GCCTTGCCTTGTCTGTCTCTACTGGCCTTTCTGTAGGTGTTTTCTTCCTGCAATTCATAGATTGGTGGTACTCCTCAGAG
AATCAAGAAACCATCAAATCTCTGACTGCCCTGCCTACCCCACCACCCTCTGTCCACCTGGACTACAACTCTGATTCTTC
TCTGTTGTCAAAGCTGAAGGCTGTGTGTTCCTTATGTTGAAAAATCTGGGTAAATGACACAGCACTTGCCACCTCTGGCT
ACATGTTTTGTTACCGATGTGTGTATAACTATGTGAAGAGTCACCAAACCTGCCCCATCACAGGCTATGCAACAGAAGTC
CAGCACTTGGTTAAATTATACTCCCCCGAAAAC

Alignment

ORF - retro_mdom_557 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.67 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAEHGAHITAASGADDRPSIFEVVAQDSLMTAVRPALQHVAKVLAESNPAHYGFLWRWFDEIFTFLDLLL
          MAEHGAHI..ASGAD..PSIFEVVAQDSLM.AVRPALQHVAKVLAESNPAHYGFLWRWFDE.FTFL.LLL
Retrocopy MAEHGAHIIVASGADKWPSIFEVVAQDSLMMAVRPALQHVAKVLAESNPAHYGFLWRWFDETFTFLNLLL

Parental  QQHYLSKASASFSENFYGLKRIVTGDPQGVQRLASVGLPKKQLWKSLLFLVLLPYLKVKLEKLVSSLREE
          QQHYLSKASA.FSENFYGLKRI..GDPQGVQRLASVGLPKKQLWKSLLFLVLLP.LKV.LEKLVSSLREE
Retrocopy QQHYLSKASALFSENFYGLKRIMMGDPQGVQRLASVGLPKKQLWKSLLFLVLLPCLKV-LEKLVSSLREE

Parental  DEYSIHPPSSCWKRFYRAFLAAYPFVTMAWEGWFLIQQLRYILGKAQHHSPLLS-LAGVRLGRLSAEDIR
          DEYSIHPPSSCWKRFY.AFL.AYPFVTM.WEGWFLI.QL.YILGKAQHHSPLLS.LAGVRLGRLSAED.R
Retrocopy DEYSIHPPSSCWKRFY*AFLTAYPFVTMTWEGWFLI*QLCYILGKAQHHSPLLS<LAGVRLGRLSAEDSR

Parental  ALEKTLAQASGMPQPATSIQEKVQSAVKKAIGGLALSISTGLSVGVFFLQFLDWWYSSENQETIKSLTAL
          ALEKTLAQAS.MPQPATSI.EKVQSAVKKAIGGLALS.STGLSVGVFFLQF.DWWYSSENQETIKSLTAL
Retrocopy ALEKTLAQASRMPQPATSI*EKVQSAVKKAIGGLALSVSTGLSVGVFFLQFIDWWYSSENQETIKSLTAL

Parental  PTPPPPVHLDYNSDSSLLPKLKTVCPLCRKIRVNDTALATSGYVFCYRCVYNYVKSHQTCPITGYATEVQ
          PTPPP.VHLDYNSDSSLL.KLK.VC.LC.KI.VNDTALATSGY.FCYRCVYNYVKSHQTCPITGYATEVQ
Retrocopy PTPPPSVHLDYNSDSSLLSKLKAVCSLC*KIWVNDTALATSGYMFCYRCVYNYVKSHQTCPITGYATEVQ

Parental  HLVKLYSPEN
          HLVKLYSPEN
Retrocopy HLVKLYSPEN

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	0.24 RPM	0.00 RPM
SRP007412_cerebellum	0.98 RPM	0.00 RPM
SRP007412_heart	0.20 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.50 RPM	0.00 RPM
SRP007412_testis	0.20 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_557 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_557 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000003330	1 retrocopy	retro_ggor_957,
Macaca mulatta	ENSMMUG00000006047	1 retrocopy	retro_mmul_749,
Monodelphis domestica	ENSMODG00000019129	1 retrocopy	retro_mdom_557 ,
Nomascus leucogenys	ENSNLEG00000013933	1 retrocopy	retro_nleu_697,
Pan troglodytes	ENSPTRG00000009020	1 retrocopy	retro_ptro_839,