RetrogeneDB ID: retro_mdom_273

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 7:83604112..83604475(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000025070
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000005770
• Aliases: None
• Description: None

Sequence

>retro_mdom_273
CCCTCCTATCCCGCCGAAACGTTTCCTCTCTCGACTCCGGGGCCAGCCGCCGAAATGTCAACAAGTGGGCCGCCTCCTTC
AGGTGCTGCTTCTGGCAGTAATCGCAGACTTCAGCAGGCACAAAATCAAGTAGATGAGGTGGTGGATATTATGCGAGTCA
ATGTGGACAAAGTTCTGGAGAGAGATCAGAAACTTTCTGAGTTAGATGACCGCGCAGATGCACTGCAAGCAGGGGCTTCC
CAGTTTGAGACAAGTGCAGCCAAATTGAAGAGAAAGTACTGGTGGAAGAATTGCAAGATGTGGGCGATACTAATTACTGT
TGTGGTTGTCATCATCGTCATCATCATTGTGTGGAGTGTTTCT

Alignment

ORF - retro_mdom_273 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100. %
• Parental protein coverage: 99.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  STSGPPPSGAASGSNRRLQQAQNQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAKL
          STSGPPPSGAASGSNRRLQQAQNQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAKL
Retrocopy STSGPPPSGAASGSNRRLQQAQNQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAKL

Parental  KRKYWWKNCKMWAILITVVVVIIVIIIVWSVS
          KRKYWWKNCKMWAILITVVVVIIVIIIVWSVS
Retrocopy KRKYWWKNCKMWAILITVVVVIIVIIIVWSVS

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_273 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_273 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 7 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000000277	2 retrocopies	retro_lafr_1094, retro_lafr_463,
Monodelphis domestica	ENSMODG00000003811	1 retrocopy	retro_mdom_268,
Monodelphis domestica	ENSMODG00000005770	1 retrocopy	retro_mdom_273 ,
Mus musculus	ENSMUSG00000028955	1 retrocopy	retro_mmus_1851,
Otolemur garnettii	ENSOGAG00000009797	1 retrocopy	retro_ogar_2300,
Procavia capensis	ENSPCAG00000004825	1 retrocopy	retro_pcap_389,
Tarsius syrichta	ENSTSYG00000007733	6 retrocopies	retro_tsyr_1027, retro_tsyr_1435, retro_tsyr_1634, retro_tsyr_1757, retro_tsyr_524, retro_tsyr_968,