RetrogeneDB ID: retro_mdom_1279

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:252815547..252816366(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000024074
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: C15orf41
• Ensembl ID: ENSMODG00000001293
• Aliases: None
• Description: chromosome 15 open reading frame 41 [Source:HGNC Symbol;Acc:26929]

Sequence

>retro_mdom_1279
ATGATATTGACCAAGGCCCAGTACGAGGAGATAGCTCAGTTCCTCGTGGCTGTGCCACCTACCAGGCAGAGCCTGAGGAA
GCTGAAGCAGAGGTTCCCCAGTCAATCGCAGTCCACTCTGCTGAGCATCTTCTCCCAGGAGTACCAGAAACATATAAAAA
GGACGCATGCTAAACATCATACTGTGGAGGCTATCGAAACTTATTACCAGAGGTACCTGAGTGGAGTGGTGAAAGATGGA
ACAGCCCCTGTGCTTTTGGAGCTGGCCAATGAGGTGGACTATGCACCTTCATTGATGGCTCGAATTATATTGGAAAGGTT
CCTACAAGACCAAGAAGAATCTCCACCCTCCAAGTCCGTTATAAATAGTATGCTGCGGGACCCTTCTCAGATTCCAGATG
GAGTTCTAGCAAATCAGGTCTATCAGTGTATCGTGAATGACTGCTGTTATGGACCACTGGTGGGCTGCATCAAACATGCC
ATTGGGCATGAACATGAAGTCCTGCTGAGAGACTTGCTTCTAGAGAGAAATCTGTCCTTCTTAGATGAAGATCAACTCCG
TGCAAAGGGTTATGACAAAACACCAGATTTTATTTTAGAAGTACCAGTTGCTCTGGAAGGGCACATAATTCACTGGATTG
AAAGCAAAGCCTCATTTGGTGATGAATGTAGCCACCAGGCCTACCTGCACGACCAATTCTGGAGCTACTGGAACAGATTT
GGTCCTGGATTAGTGATCTATTGGTATGGATTCATCAAGGAGCTCAATTGTAACCGAGAAAGGGGCATCTTACTCAAAGA
CTGCTTTCCTACTGACCTT

Alignment

ORF - retro_mdom_1279 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.63 %
• Parental protein coverage: 87.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MILTKAQYEEIAQFLVAVPPTRQSLRKLKQRFPSQSQSTLLSIFSQEYQKHIKRTHAKHHTVEAIETYYQ
          MILTKAQYEEIAQFLVAVPPTRQSLRKLKQRFPSQSQSTLLSIFSQEYQKHIKRTHAKHHTVEAIETYYQ
Retrocopy MILTKAQYEEIAQFLVAVPPTRQSLRKLKQRFPSQSQSTLLSIFSQEYQKHIKRTHAKHHTVEAIETYYQ

Parental  RYLSGVVKDGTAPVLLELANEVDYAPSLMARIILERFLQDQEESPPSKSVINSMLRDPSQIPDGVLANQV
          RYLSGVVKDGTAPVLLELANEVDYAPSLMARIILERFLQDQEESPPSKSVINSMLRDPSQIPDGVLANQV
Retrocopy RYLSGVVKDGTAPVLLELANEVDYAPSLMARIILERFLQDQEESPPSKSVINSMLRDPSQIPDGVLANQV

Parental  YQCIVNDCCYGPLVGCIKHAIGHEHEVLLRDLLLERNLSFLDEDQLRAKGYDKTPDFILEVPVALEGHII
          YQCIVNDCCYGPLVGCIKHAIGHEHEVLLRDLLLERNLSFLDEDQLRAKGYDKTPDFILEVPVALEGHII
Retrocopy YQCIVNDCCYGPLVGCIKHAIGHEHEVLLRDLLLERNLSFLDEDQLRAKGYDKTPDFILEVPVALEGHII

Parental  HWIESKASFGDECSHQAYLHDQFWSYWNRFGPGLVIYWYGFIKELDCNRERGILLKDCFPTDL
          HWIESKASFGDECSHQAYLHDQFWSYWNRFGPGLVIYWYGFIKEL.CNRERGILLKDCFPTDL
Retrocopy HWIESKASFGDECSHQAYLHDQFWSYWNRFGPGLVIYWYGFIKELNCNRERGILLKDCFPTDL

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	2.86 RPM
SRP007412_cerebellum	0.00 RPM	2.94 RPM
SRP007412_heart	0.00 RPM	3.79 RPM
SRP007412_kidney	0.00 RPM	7.90 RPM
SRP007412_liver	0.00 RPM	1.01 RPM
SRP007412_testis	0.00 RPM	0.59 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1279 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1279 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.

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000014422	1 retrocopy	retro_dnov_2681,
Monodelphis domestica	ENSMODG00000001293	1 retrocopy	retro_mdom_1279 ,
Oryctolagus cuniculus	ENSOCUG00000016099	1 retrocopy	retro_ocun_1574,
Otolemur garnettii	ENSOGAG00000006789	1 retrocopy	retro_ogar_3224,