RetrogeneDB ID: retro_mdom_968

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:55129456..55129738(+)
• Located in intron of: ENSMODG00000015662

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000007194
• Aliases: None
• Description: None

Sequence

>retro_mdom_968
CAAGAAGTTCTGAAAAATTCTCTAATAAACACTAAGAGTCAGACTGTTAAGAATGGAGGAGGCAGCATTGTCCTGAAGGT
GCTCACCTCTTTTAAATCTCAGAATATTGAAAAGTCAGTTCAGTCTCTTGACAAGAATGATATGGATCTTCTAAAACATG
TATATATTCTTGTGGGCTTTGGAAATCCCTCTGAAAATAGCAGTACTATGTTATTGCAGGGGCATGAAATGGCACTTGCT
GCTGAAGGAATCCTTCATGTCTTAATCACCAGGAAAATGGTT

Alignment

ORF - retro_mdom_968 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.89 %
• Parental protein coverage: 59.63 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QAALKNPPINTKSQAVKDRAGSIVLKVLISFKANDIEKAVQSLDKNGVDLLMK-YIYKGFESPSDNSSAV
          Q..LKN..INTKSQ.VK...GSIVLKVL.SFK...IEK.VQSLDKN..DLL...YI..GF..PS.NSS..
Retrocopy QEVLKNSLINTKSQTVKNGGGSIVLKVLTSFKSQNIEKSVQSLDKNDMDLLKHVYILVGFGNPSENSSTM

Parental  LLQWHEKALAAGGVGSIVRVLTARKTV
          LLQ.HE.ALAA.G...I..VL..RK.V
Retrocopy LLQGHEMALAAEG---ILHVLITRKMV

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_968 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_968 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 8 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000560	2 retrocopies	retro_chof_1502, retro_chof_783,
Dasypus novemcinctus	ENSDNOG00000010375	3 retrocopies	retro_dnov_1277, retro_dnov_199, retro_dnov_2495,
Equus caballus	ENSECAG00000019128	1 retrocopy	retro_ecab_1104,
Echinops telfairi	ENSETEG00000014969	1 retrocopy	retro_etel_1922,
Monodelphis domestica	ENSMODG00000007194	1 retrocopy	retro_mdom_968 ,
Mus musculus	ENSMUSG00000008475	1 retrocopy	retro_mmus_281,
Rattus norvegicus	ENSRNOG00000028062	1 retrocopy	retro_rnor_1873,
Tupaia belangeri	ENSTBEG00000006295	8 retrocopies	retro_tbel_1822, retro_tbel_1933, retro_tbel_1962, retro_tbel_2504, retro_tbel_3191, retro_tbel_3192, retro_tbel_3197, retro_tbel_3806,