RetrogeneDB ID: retro_mdom_1379

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:200682071..200682392(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000010609
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CHRAC1
• Ensembl ID: ENSMODG00000000756
• Aliases: None
• Description: chromatin accessibility complex 1 [Source:HGNC Symbol;Acc:13544]

Sequence

>retro_mdom_1379
ATGGTGGACAGGTTCAGTAGCACAGAGAAATACAGCAACCAGAGGTTGGTCTTGTTGCCCATGTCTCACATTTGGGTGAT
CATGAAAAGCTCACCTGAGATGTCCAGTATCAATCAAAAAGCACTGGCGCTCACAGCCAAGGCTGTGGAACTCTTTGTTC
AGTATATAGCCACCTATTCCTACACACATGCCAGTGGAAAGGAGAAGAAAGCACTTATTTAAAATGATTTATCAAATACT
TCAGAAGAATAGAAAACATTTCAGTTTCTTACAGATATATTTCCAAAGAAGATTTTAACCAGCAAATACCTGAAAATGCT
T

Alignment

ORF - retro_mdom_1379 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.7 %
• Parental protein coverage: 77.54 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADGFGGKEKCSDQRLVSLPLSRIRVIMKSSPEVSSINQEALVLTAKATELFVQYLATYSYKHGSGKEKK
          M.D.F...EK.S.QRLV.LP.S.I.VIMKSSPE.SSINQ.AL.LTAKA.ELFVQY.ATYSY.H.SGKEKK
Retrocopy MVDRFSSTEKYSNQRLVLLPMSHIWVIMKSSPEMSSINQKALALTAKAVELFVQYIATYSYTHASGKEKK

Parental  ALIYSDLSNTAEESETFQFLADILPKKILASKYLKML
          ALI..DLSNT.EE..TFQFL.DI.PKKIL.SKYLKML
Retrocopy ALI*NDLSNTSEE*KTFQFLTDIFPKKILTSKYLKML

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_1379 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1379 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 7 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005017	1 retrocopy	retro_amel_1736,
Cavia porcellus	ENSCPOG00000010427	5 retrocopies	retro_cpor_1545, retro_cpor_721, retro_cpor_722, retro_cpor_723, retro_cpor_724,
Loxodonta africana	ENSLAFG00000001188	1 retrocopy	retro_lafr_932,
Monodelphis domestica	ENSMODG00000000756	2 retrocopies	retro_mdom_1379 , retro_mdom_355,
Ochotona princeps	ENSOPRG00000008780	2 retrocopies	retro_opri_636, retro_opri_726,
Pan troglodytes	ENSPTRG00000020621	1 retrocopy	retro_ptro_2764,
Ictidomys tridecemlineatus	ENSSTOG00000008105	1 retrocopy	retro_itri_358,