RetrogeneDB ID: retro_mdom_1156

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:270634634..270635135(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000005175
• Aliases: None
• Description: None

Sequence

>retro_mdom_1156
GTTGCTATGAAGTCCGTTTTTGTCACCTTGGGCACCACCAGTTTCTACGAGCTCGTAGTCTGTGTGTCCTCCAGGGCTAT
GCTCCAGAACCTCAGGAGACTTGGATATCGCAAGCTTGTCCTACAGATTGGAAAAGGAAGAGTGGTGCCAGACTCCTTTG
CTTCTACAACTTTTTCCTTGATTGTTTACAAGTACAAGAATTCCTTGAAAGAGGACATTAAGAGAGCAGATCTCATCATT
AGCCATGCAGGTGCGGGGAGCTGCTTGGAGGCCCTGGAAGAAGGGAAACCTTTGGTGGTAGTTGTAAATGAAAAGCTGAT
GGACAATCACCAGTTAGAGCTCGCCAGACAGCTACACAAAGAAGGTTATCTTTTCTATTGCTCATGCAGCACCCTTCTTG
AGCTGTTAAGTTCAGTGGACTTATCATCATTGAGGCTCTTTCCTCCTGGCAAGCCAGAGATGTTCTCTGAGGTTTTGGAT
AAAGTTGTGGGGTTTGAAAAA

Alignment

ORF - retro_mdom_1156 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.61 %
• Parental protein coverage: 93.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VAMKSVFVTVGTTSFDELVACVSSRATLQILRRLGYRKLVLQIGKGRVVPDSFASTTFSLIVYRYKNSLK
          VAMKSVFVT.GTTSF.ELV.CVSSRA.LQ.LRRLGYRKLVLQIGKGRVVPDSFASTTFSLIVY.YKNSLK
Retrocopy VAMKSVFVTLGTTSFYELVVCVSSRAMLQNLRRLGYRKLVLQIGKGRVVPDSFASTTFSLIVYKYKNSLK

Parental  EDIKRADLIISHAGAGSCLEALEEGKPLVVVVNEKLMDNHQLELARQLHKEGYLFYCSCSTLLELLRSVD
          EDIKRADLIISHAGAGSCLEALEEGKPLVVVVNEKLMDNHQLELARQLHKEGYLFYCSCSTLLELL.SVD
Retrocopy EDIKRADLIISHAGAGSCLEALEEGKPLVVVVNEKLMDNHQLELARQLHKEGYLFYCSCSTLLELLSSVD

Parental  LSSLRRFPPGKPEMFSEFLDKVVGFEK
          LSSLR.FPPGKPEMFSE.LDKVVGFEK
Retrocopy LSSLRLFPPGKPEMFSEVLDKVVGFEK

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_1156 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1156 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000005613	1 retrocopy	retro_etel_1023,
Monodelphis domestica	ENSMODG00000005175	1 retrocopy	retro_mdom_1156 ,
Mus musculus	ENSMUSG00000041718	1 retrocopy	retro_mmus_256,
Oryctolagus cuniculus	ENSOCUG00000000232	2 retrocopies	retro_ocun_1459, retro_ocun_477,
Otolemur garnettii	ENSOGAG00000031713	2 retrocopies	retro_ogar_2864, retro_ogar_3363,
Tupaia belangeri	ENSTBEG00000010726	2 retrocopies	retro_tbel_117, retro_tbel_6,