RetrogeneDB ID: retro_mdom_930

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:486177289..486178072(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000004846
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BRCC3
• Ensembl ID: ENSMODG00000016487
• Aliases: None
• Description: BRCA1/BRCA2-containing complex, subunit 3 [Source:HGNC Symbol;Acc:24185]

Sequence

>retro_mdom_930
ATGGCAGTCGTGGCGGTGCACCTGGACTCGGACGCGTTCCTGGTGTGCCTCAACCATGCCCTGAGCACGGAGAAGGAGGA
GGTGATGGGGCTGTGCATCGGCGAGGTGGACACCAGCAAGATCGTGCACATCCACTCGGTGATCATCCTGCGGCGCTCGG
ACAAGCGTAAGGACCGCGTGGAGATCTCCCCAGAGCAGCTGTCCGCTGCGTCCACAGAGGCCGAGCGGCTGGCTGAGCTC
ACGGGCCGGCCCGTGCGGGTGGTGGGCTGGTACCACTCACACCCGCACATCACCGTGTGGCCGTCGCACGTAGACGTGCG
CACGCAGGCCATGTACCAGATGATGGACCAGGGCTTTGTGGGCCTCATCTTCTCGTGCTTCATCGAGGACAAGAACACCA
AGACTGGCAGGCTGCTGTACACGTGCTTCCAGTCAGTGCAGGCGCAGAAGAGCACCGACTATGAGCGCATTGAGATCCCC
ATCCATGTGGTGCCACACGACACCATAGGCAAGGTGTGCCTCGAGTCGGCCATCGAGCTGCCCAAGATCCTGTGCCAGGA
GGAGCAGGATGCCTACCGCCGCATCCACAGCCTCCCACACCTTGACTCCGTCACCATGATCCACAACGGCTCCGTCTTCA
CCAAGAACCTGTGCAGCCAAATGTCGGCCATCAGCGGGCCGCTGCTGCAATGGCTTGAGGACCGACTGGAACAGAATCAG
CAGCGGGTGCGTGAGCTGCAGCGGGAGAAAGAGCGGCTGCTGCAGGAGCTGGCTGCCCTAGAC

Alignment

ORF - retro_mdom_930 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.46 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAVLAVHLQSDAFLVALNHALSTEKEEVMGLCLGEVDTSKIVHILSVIVLRRSDKRKDRVEISPEQLSAA
          MAV.AVHL.SDAFLV.LNHALSTEKEEVMGLC.GEVDTSKIVHI.SVI.LRRSDKRKDRVEISPEQLSAA
Retrocopy MAVVAVHLDSDAFLVCLNHALSTEKEEVMGLCIGEVDTSKIVHIHSVIILRRSDKRKDRVEISPEQLSAA

Parental  SLEAERLAEVTGRPMRVVGWYHSHPHITVWPSHVDIRTQAMYQMMDESFVGLIFSCFVEDKNTKTGRILY
          S.EAERLAE.TGRP.RVVGWYHSHPHITVWPSHVD.RTQAMYQMMD..FVGLIFSCF.EDKNTKTGR.LY
Retrocopy STEAERLAELTGRPVRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDQGFVGLIFSCFIEDKNTKTGRLLY

Parental  TCFQSTQAQKGSEYERVDVPLHVVPQETMGKASLEAAIELPRILCQEEQDAYRKIHSLTHLDAVTKIHNG
          TCFQS.QAQK...YER...P.HVVP..T.GK..LE.AIELP.ILCQEEQDAYR.IHSL.HLD.VT.IHNG
Retrocopy TCFQSVQAQKSTDYERIEIPIHVVPHDTIGKVCLESAIELPKILCQEEQDAYRRIHSLPHLDSVTMIHNG

Parental  SVFTKNLCNQMSAISGPLMQWLEDRRDYNRKLLVELEEEKKALEEELARLE
          SVFTKNLC.QMSAISGPL.QWLEDR...N.....EL..EK..L..ELA.L.
Retrocopy SVFTKNLCSQMSAISGPLLQWLEDRLEQNQQRVRELQREKERLLQELAALD

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_930 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_930 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007817	2 retrocopies	retro_btau_1327, retro_btau_1646,
Cavia porcellus	ENSCPOG00000001882	2 retrocopies	retro_cpor_388, retro_cpor_627,
Homo sapiens	ENSG00000185515	1 retrocopy	retro_hsap_3271,
Gorilla gorilla	ENSGGOG00000027248	1 retrocopy	retro_ggor_2226,
Monodelphis domestica	ENSMODG00000016487	1 retrocopy	retro_mdom_930 ,
Mus musculus	ENSMUSG00000031201	1 retrocopy	retro_mmus_672,
Nomascus leucogenys	ENSNLEG00000014460	1 retrocopy	retro_nleu_2940,
Sarcophilus harrisii	ENSSHAG00000005392	1 retrocopy	retro_shar_51,
Ictidomys tridecemlineatus	ENSSTOG00000019781	2 retrocopies	retro_itri_1271, retro_itri_806,