RetrogeneDB ID: retro_mdom_1191

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:417402100..417402425(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GINS1
• Ensembl ID: ENSMODG00000006443
• Aliases: None
• Description: GINS complex subunit 1 (Psf1 homolog) [Source:HGNC Symbol;Acc:28980]

Sequence

>retro_mdom_1191
GAACATAACCAGTACTATAAAAATGATGCTAAGTGAGACAGACAAAGTAACTTGATTCTGACAATCAAATGTTGGCACTG
TTCTTTGCTGAGAAATCAAAGCTGTATTGTTAGAGTATTTATGTGACCGATTGCTCTAGATTCCAGTTCTCAGGTGGGAA
TACAGCAATGTCTTGCCAAATGCTCTGCAATTCTGCACATCAATTGAAGAAAGGGAATAGTTCAATCATTATAAAAAGTC
TCTTGCTACATACATGAGATGTTTGGGTAGAGATGAAGGATTAGACAGTATACAGGCCATGAAATCCTGTAAAAGCCTAT
ATATT

Alignment

ORF - retro_mdom_1191 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.06 %
• Parental protein coverage: 55.1 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EQNQSDVNETKSDGRSDLIPTIKFRHSSLLRNRRCIVA-YLYDRLLRIRALRWEYGSVLPNALRFHMSSE
          E.NQ...N..K.D..S.LI.TIK..H.SLLRN..CIV..YL.DRLL.I..LRWEY..VLPNAL.F..S.E
Retrocopy EHNQYYKNDAK*DRQSNLILTIKCWHCSLLRNQSCIVR>YLCDRLL*IPVLRWEYSNVLPNALQFCTSIE

Parental  EIEWFNRYKKSLATYMRCLGGDEGLDITQDMKPPKSLYI
          E.E.FN.YKKSLATYMRCLG.DEGLD..Q.MK..KSLYI
Retrocopy ERE*FNHYKKSLATYMRCLGRDEGLDSIQAMKSCKSLYI

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	13.35 RPM
SRP007412_cerebellum	0.00 RPM	8.49 RPM
SRP007412_heart	0.00 RPM	1.99 RPM
SRP007412_kidney	0.00 RPM	2.63 RPM
SRP007412_liver	0.00 RPM	5.03 RPM
SRP007412_testis	0.00 RPM	116.49 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1191 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1191 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000002718	1 retrocopy	retro_etel_1594,
Macropus eugenii	ENSMEUG00000016481	1 retrocopy	retro_meug_1309,
Monodelphis domestica	ENSMODG00000006443	1 retrocopy	retro_mdom_1191 ,
Rattus norvegicus	ENSRNOG00000008091	1 retrocopy	retro_rnor_2888,
Sarcophilus harrisii	ENSSHAG00000017422	1 retrocopy	retro_shar_343,
Sus scrofa	ENSSSCG00000024720	1 retrocopy	retro_sscr_238,