RetrogeneDB ID: retro_mdom_535

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:200406890..200407685(-)
• Located in intron of: ENSMODG00000017868

Retrocopy information

• Ensembl ID: ENSMODG00000017870
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000013918
• Aliases: None
• Description: None

Sequence

>retro_mdom_535
CTCTTTGTTGGCAACCTCGATTGTAAAGTGACAGAGGAGCTGCTCTTCGAGCTTTTCCATCAGGCAGGTCCTGTAATAAA
AGTTAAAATTCCAAAGGATAAAGATGGTAAACCAAAGCAGTTTGCGTTTGTGAATTTCAAACATGAAGAATCCGTTCCTT
ATGGAATGAATCTACTTAATGGAATAAAACTTTTTGGAAGGCCCATCAAAATTCAGTTCAGATCAGGAAGTAGTCATGCT
TCTCAGGAGGTTAGTTCATCATATTCCCAGCATAATCTTGGGAATGCAAGTCCATCTAGCATGCCACAATCCACTTCAGC
TTCTAGCAGATATGAAAGGAATATGGATAACTTGTCATCTGGATATAATGCTTCACAAATGATACAGAGGTCTTTCTCAT
CTCCAGATAATCTTCAAAGACAGGCTGTGATGATCAATGTTCTGTGGCAGCAGCAGGGATCATTCAGTGGAAAGTTTGTA
CCTCAGCATTTGGATCAGCCTAGTTTTACACCCTCAGGGCAGCAGCATGGTCATTCATTTAACCTCTCTTCAAGCTCCCA
GTGGTGCCCGGATACACCAGTGTCGCAAAGGAAAACCAGGCAGAACTCCCATCCCTACCAATCAGATAGGCTTTATAGTT
GCGAGCAGCGTTATGGGGATCATGGATCTGACCATCATTATAGAGGAAACAGAGATGATTCCTACTATGAAGATAGGATC
CATGACGGTTGGAGCCATGACTATGATAGCAGAAGAGAAAACAGTAGGGATGGAAAATGGCGCCCATCCCGGCAC

Alignment

ORF - retro_mdom_535 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.74 %
• Parental protein coverage: 96.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LFVGNLDCKVTEELLFELFHQAGPVIKVKIPKDKDGKPKQFAFVNFKHEESVPYGMNLLNGIKLFGRPIK
          LFVGNLDCKVTEELLFELFHQAGPVIKVKIPKDKDGKPKQFAFVNFKHEESVPYGMNLLNGIKLFGRPIK
Retrocopy LFVGNLDCKVTEELLFELFHQAGPVIKVKIPKDKDGKPKQFAFVNFKHEESVPYGMNLLNGIKLFGRPIK

Parental  IQFRSGSSHASQEVSSSYSQHNLGNASPSSIPQSTSASSSRYERNMDNLTSGYNASQMIQRSFSSPDNLQ
          IQFRSGSSHASQEVSSSYSQHNLGNASPSS.PQSTSASS.RYERNMDNL.SGYNASQMIQRSFSSPDNLQ
Retrocopy IQFRSGSSHASQEVSSSYSQHNLGNASPSSMPQSTSASS-RYERNMDNLSSGYNASQMIQRSFSSPDNLQ

Parental  RQAVMNNVLWQQQGSFSGKFVPQHLDQPSFTPSGQQHGHSFNLSSSSQWCQDTPVSQRKTRQNSHPYQSD
          RQAVM.NVLWQQQGSFSGKFVPQHLDQPSFTPSGQQHGHSFNLSSSSQWC.DTPVSQRKTRQNSHPYQSD
Retrocopy RQAVMINVLWQQQGSFSGKFVPQHLDQPSFTPSGQQHGHSFNLSSSSQWCPDTPVSQRKTRQNSHPYQSD

Parental  RLYSREQRYGDHGSDHHYRGNRDDSYYEDRIHDGWSHDYDSRRENSRDGKWRPSRH
          RLYS.EQRYGDHGSDHHYRGNRDDSYYEDRIHDGWSHDYDSRRENSRDGKWRPSRH
Retrocopy RLYSCEQRYGDHGSDHHYRGNRDDSYYEDRIHDGWSHDYDSRRENSRDGKWRPSRH

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	0.12 RPM	0.00 RPM
SRP007412_cerebellum	0.33 RPM	0.00 RPM
SRP007412_heart	0.40 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.50 RPM	0.00 RPM
SRP007412_testis	1.38 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_535 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_535 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 16 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013514	1 retrocopy	retro_cfam_1021,
Choloepus hoffmanni	ENSCHOG00000012747	1 retrocopy	retro_chof_570,
Homo sapiens	ENSG00000076053	1 retrocopy	retro_hsap_2283,
Gorilla gorilla	ENSGGOG00000009941	1 retrocopy	retro_ggor_1696,
Loxodonta africana	ENSLAFG00000012444	1 retrocopy	retro_lafr_892,
Myotis lucifugus	ENSMLUG00000023234	2 retrocopies	retro_mluc_1555, retro_mluc_587,
Monodelphis domestica	ENSMODG00000013918	1 retrocopy	retro_mdom_535 ,
Mus musculus	ENSMUSG00000042396	1 retrocopy	retro_mmus_2436,
Nomascus leucogenys	ENSNLEG00000007323	1 retrocopy	retro_nleu_409,
Oryctolagus cuniculus	ENSOCUG00000003342	1 retrocopy	retro_ocun_924,
Otolemur garnettii	ENSOGAG00000016857	1 retrocopy	retro_ogar_3103,
Pongo abelii	ENSPPYG00000003894	1 retrocopy	retro_pabe_1669,
Pan troglodytes	ENSPTRG00000004305	1 retrocopy	retro_ptro_1617,
Ictidomys tridecemlineatus	ENSSTOG00000012459	1 retrocopy	retro_itri_889,
Tursiops truncatus	ENSTTRG00000001515	3 retrocopies	retro_ttru_1316, retro_ttru_1441, retro_ttru_478,
Vicugna pacos	ENSVPAG00000006300	1 retrocopy	retro_vpac_311,