RetrogeneDB ID: retro_mdom_914

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:415928335..415928686(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHCHD1
• Ensembl ID: ENSMODG00000000361
• Aliases: None
• Description: coiled-coil-helix-coiled-coil-helix domain containing 1 [Source:HGNC Symbol;Acc:23518]

Sequence

>retro_mdom_914
GCAGCGCCAAGCCTGCAGGGACGCCCAGCGCACCTGGGCAACGCGAAGCGGCCAATGCTGAAGCCCAACACGCCCCTGGT
ACTGGCCAAAGGGGTGGGGGCAGGGCGTCGTGAGCTTGGGGAGGCCACCTGTACAACAGAGATGTCCCTGATGATGGCTT
GCTGAAAGCAGAATGAATTTAGCCACACGATTTGTGCCAAGGAGATCGAGGACTTCACCAGCCGTGCTTCAAAGGCTGAG
GCAGAGCGGAAACAGAAGGCAAAACAAGAGTATCTGGGCTCCTCTGGGAATTTGACCCCCAAGCAAACAAATAAATTGCT
GAGCAGGTTTCCAAACATATCTTACATTATC

Alignment

ORF - retro_mdom_914 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.91 %
• Parental protein coverage: 99.15 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ATPSLRGRLARLSNGKRPVLKPNKPLVLANRVGAGRRELGEATCITEMSLMMACWKQNEFSDTICAKEIK
          A.PSL.GR.A.L.N.KRP.LKPN.PLVLA..VGAGRRELGEATC.TEMSLMMAC.KQNEFS.TICAKEI.
Retrocopy AAPSLQGRPAHLGNAKRPMLKPNTPLVLAKGVGAGRRELGEATCTTEMSLMMAC*KQNEFSHTICAKEIE

Parental  DFFACASKAEAERKQKAKQEYLGSTGNLTPKQANKLLSRFPNITYII
          DF...ASKAEAERKQKAKQEYLGS.GNLTPKQ.NKLLSRFPNI.YII
Retrocopy DFTSRASKAEAERKQKAKQEYLGSSGNLTPKQTNKLLSRFPNISYII

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	64.84 RPM
SRP007412_cerebellum	0.00 RPM	79.65 RPM
SRP007412_heart	0.00 RPM	194.77 RPM
SRP007412_kidney	0.00 RPM	144.85 RPM
SRP007412_liver	0.00 RPM	115.80 RPM
SRP007412_testis	0.00 RPM	108.82 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_914 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_914 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000015523	1 retrocopy	retro_eeur_341,
Echinops telfairi	ENSETEG00000018904	1 retrocopy	retro_etel_27,
Monodelphis domestica	ENSMODG00000000361	1 retrocopy	retro_mdom_914 ,