RetrogeneDB ID: retro_mdom_1124

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:166728868..166729117(-)
• Located in intron of: ENSMODG00000007376

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHCHD7
• Ensembl ID: ENSMODG00000024930
• Aliases: None
• Description: coiled-coil-helix-coiled-coil-helix domain containing 7 [Source:HGNC Symbol;Acc:28314]

Sequence

>retro_mdom_1124
ATTGTTACCAAGAGACTTAGAGACCCTGATGTAAATCCTTGTTTATTGGAGTCAGATGCTTCTACCAGATGTATGGATGA
AAATAATTATATCAGAGAAATGTGCACCACTTGCTTCTTGAAGTATAAAAACTGCAGGAAATTTTGGAATGCCATTATGA
TTGAAAGACGACGAAATGAAGTTAAACCACATATGCCCACAGCTGCAGAAAGAGAAAAAATCTTGGGAGAAATGGGAAAG
ATGCCCTAT

Alignment

ORF - retro_mdom_1124 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.18 %
• Parental protein coverage: 86.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IVTKRLRDPDVNPCLSESDASTRCMDENNYDREMCTTCFLKYKNCRKFWNAIMIERRRNGVKPHMPTAAE
          IVTKRLRDPDVNPCL.ESDASTRCMDENNY.REMCTTCFLKYKNCRKFWNAIMIERRRN.VKPHMPTAAE
Retrocopy IVTKRLRDPDVNPCLLESDASTRCMDENNYIREMCTTCFLKYKNCRKFWNAIMIERRRNEVKPHMPTAAE

Parental  REKILGAMGKMPY
          REKILG.MGKMPY
Retrocopy REKILGEMGKMPY

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_1124 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1124 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000007055	1 retrocopy	retro_cfam_1197,
Echinops telfairi	ENSETEG00000020301	2 retrocopies	retro_etel_1330, retro_etel_888,
Monodelphis domestica	ENSMODG00000024930	1 retrocopy	retro_mdom_1124 ,
Ictidomys tridecemlineatus	ENSSTOG00000002724	1 retrocopy	retro_itri_278,