RetrogeneDB ID: retro_mdom_285

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:601333440..601334187(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000006101
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000005737
• Aliases: None
• Description: None

Sequence

>retro_mdom_285
GTCAGAATGGCAGCTCCCGGACCTGTTCTCTGCCTCTTCGATATCGACGGCACCCTCACCGCTCCGCGACAGAAAATCAC
CAAAGAAATGGATGCCTTTTTACAAAAATTGAGGCAGAAGTTAAAAATTGGAGTAGTAGGAGGCTCAGACTTTGAGAAGG
TGCGGGAGCAGCTGGGAGATGATGTGCTTGAAAAATATGATTACGTCTTTCCAGAAAATGGTTTGGTAGCATACAAAGAT
GGCAAATTTCTGTGTAAGCAGAATATTCAGGGTCATCTGGGTGAAGAACTAATCCAAGATTTAATCAACTATTGTCTGAG
TTACATTGCCAAGATTAAGCTGCCAAAGAAAAGGGGCACTTTCATTGAGTTCCGAAATGGGATGTTAAATGTGTCTCCTA
TCGGAAGAAGCTGCAGCCAGGAAGAACGACTTGAATTTTATGAACTAGATAAAAAAGAAAATATAAGACAGAAATTTGTG
ACTGATCTGCAGAAAACTTTTGAAGGAAAGGGCCTTACATTTTCTATAGGAGGCCAAATAAGCCTGGATGTATTTCCTAA
TGGATGGGATAAGAGGTACTGTCTGAAACTTGTTGAAAATGATAGCTATAAGACAATCTATTTCTTTGGAGACAAAACCA
TGCCAGGTGGAAATGACTATGAAATCTACACAGATTCCCGAACAGTAGGATATGCAGTGACCAGCCCAAAGGACACGCAA
CGAATCTGTGAGGAGCTTTTCTTATAA

Alignment

ORF - retro_mdom_285 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 98.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VRMAAPGPVLCLFDIDGTLTAPRQKITKEMDAFLQKLRQKLKIGVVGGSDFEKVREQLGDDVLEKYDYVF
          VRMAAPGPVLCLFDIDGTLTAPRQKITKEMDAFLQKLRQKLKIGVVGGSDFEKVREQLGDDVLEKYDYVF
Retrocopy VRMAAPGPVLCLFDIDGTLTAPRQKITKEMDAFLQKLRQKLKIGVVGGSDFEKVREQLGDDVLEKYDYVF

Parental  PENGLVAYKDGKFLCKQNIQGHLGEELIQDLINYCLSYIAKIKLPKKRGTFIEFRNGMLNVSPIGRSCSQ
          PENGLVAYKDGKFLCKQNIQGHLGEELIQDLINYCLSYIAKIKLPKKRGTFIEFRNGMLNVSPIGRSCSQ
Retrocopy PENGLVAYKDGKFLCKQNIQGHLGEELIQDLINYCLSYIAKIKLPKKRGTFIEFRNGMLNVSPIGRSCSQ

Parental  EERLEFYELDKKENIRQKFVTDLQKTFEGKGLTFSIGGQISLDVFPNGWDKRYCLKLVENDSYKTIYFFG
          EERLEFYELDKKENIRQKFVTDLQKTFEGKGLTFSIGGQISLDVFPNGWDKRYCLKLVENDSYKTIYFFG
Retrocopy EERLEFYELDKKENIRQKFVTDLQKTFEGKGLTFSIGGQISLDVFPNGWDKRYCLKLVENDSYKTIYFFG

Parental  DKTMPGGNDYEIYTDSRTVGYAVTSPKDTQRICEELFL
          DKTMPGGNDYEIYTDSRTVGYAVTSPKDTQRICEELFL
Retrocopy DKTMPGGNDYEIYTDSRTVGYAVTSPKDTQRICEELFL

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	0.36 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	0.50 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_285 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_285 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 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001440	2 retrocopies	retro_btau_1188, retro_btau_307,
Cavia porcellus	ENSCPOG00000000235	1 retrocopy	retro_cpor_810,
Homo sapiens	ENSG00000140650	2 retrocopies	retro_hsap_1869, retro_hsap_1913,
Gorilla gorilla	ENSGGOG00000010124	1 retrocopy	retro_ggor_1399,
Monodelphis domestica	ENSMODG00000005737	1 retrocopy	retro_mdom_285 ,
Nomascus leucogenys	ENSNLEG00000010062	1 retrocopy	retro_nleu_3062,
Otolemur garnettii	ENSOGAG00000016560	1 retrocopy	retro_ogar_1095,
Pongo abelii	ENSPPYG00000007084	2 retrocopies	retro_pabe_1583, retro_pabe_1584,
Pan troglodytes	ENSPTRG00000007748	2 retrocopies	retro_ptro_1249, retro_ptro_1279,
Sus scrofa	ENSSSCG00000021236	1 retrocopy	retro_sscr_329,
Tursiops truncatus	ENSTTRG00000014827	2 retrocopies	retro_ttru_1894, retro_ttru_977,