RetrogeneDB ID: retro_mdom_1042

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:335829977..335830721(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GSR
• Ensembl ID: ENSMODG00000019004
• Aliases: None
• Description: glutathione reductase [Source:HGNC Symbol;Acc:4623]

Sequence

>retro_mdom_1042
GTACTTCAATCTTTCCATGCATTAATTGTTTCCAACTGCACTGAAGAACTGGAGAATGCTGTCATCAAGGTCCCAAAGTA
CTCCCAGGTCAAGGAAGTGAAGATCTCCTTAAACTTGAAACTGACCATAGTGATGGCGAAGCCCATCTGCACAGTCCCTG
GTATTGACTCCCTATTGTTGGCCATTGGGTACACCCTAAACATCCAGAGCTTGAATCTGAACAAGGTAGGCTTTCAGAGT
GATGATAAAGGGTACATCCTGGTTGATGAATTCCAGAACCCCAACAGAAAGGGCATCTATCCTGTTGGGGGATGTGTGTG
GAAAAACTCTTCTTACTCCAGTCTCAATCACACTTGCACACAGAATTTTTTTAATACAAATTGTACTCCACACTAAACTA
TGAAAACATCCCAACTGTAGTGTTCAGTCACCTGTTGATTGTCACACAGGGACTCGTGGAAGATAAAGCCATTTCTAAAA
ATGGAAAAGGAAATGTGAAGATATTTCTGACTTCCTTTACCCCTATGTACCAAGAGGTGACAAGAAGGAAAACCAAGTGA
GTGATGAAGCTGTGTGTGATATGCCCAAAATGAAGAGAAGTTGGTGGGTATCTGCATTCAAGGAATTGGGTGTGATGAGA
TGCTGCAAGATTTTGCAGTGCCTGTGAAGATGGATGCCACATATAATAACTTTGACAACATGGTCATCAGCCACTAGATC
TCTTCTGAACAGCTGGTCACTCTC

Alignment

ORF - retro_mdom_1042 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.54 %
• Parental protein coverage: 53.78 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VLRSFDALISSNCTEELEHAGVEVLRYSQVKEVKKTSSGLELTVVTARPSGKPTFCTVSDVDCLLWAIGR
          VL.SF.ALI.SNCTEELE.A...V..YSQVKEVK..S..L.LT.V.A....KP..CTV...D.LL.AIG.
Retrocopy VLQSFHALIVSNCTEELENAVIKVPKYSQVKEVK-ISLNLKLTIVMA----KP-ICTVPGIDSLLLAIGY

Parental  TPNIQGLNLNKLGIQTDDKGHIVVDEFQNTNRKGIYAVG-DVCGKALLTPVAIAAGRKLAHRLFEC-KLD
          T.NIQ.LNLNK.G.Q.DDKG.I.VDEFQN.NRKGIY.VG.DVCGK.LLTPV.I.....LAHR.F...KL.
Retrocopy TLNIQSLNLNKVGFQSDDKGYILVDEFQNPNRKGIYPVG>DVCGKTLLTPVSIT----LAHRIFLI>KLY

Parental  SKLDYENIPTVVFSHPPIGTVGLTEDEAISKYGKENVKIYLTSFTPMYHAVTRRKTKCVMKL-VCAQKEE
          S.L.YENIPTVVFSH..I.T.GL.ED.AISK.GK.NVKI.LTSFTPMY..VTRRKTK.VMKL.V...K..
Retrocopy STLNYENIPTVVFSHLLIVTQGLVEDKAISKNGKGNVKIFLTSFTPMYQEVTRRKTK*VMKLCVICPK*R

Parental  KV-VGIHMQGIGCDEMLQGFAVAVKMGATKADFDNTVAIHPTSAEELVTL
          .V.VGI..QGIGCDEMLQ.FAV.VKM.AT...FDN.V..H..S.E.LVTL
Retrocopy EV>VGICIQGIGCDEMLQDFAVPVKMDATYNNFDNMVISH*ISSEQLVTL

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_1042 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1042 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
Bos taurus	ENSBTAG00000007115	1 retrocopy	retro_btau_1296,
Choloepus hoffmanni	ENSCHOG00000009523	1 retrocopy	retro_chof_2437,
Monodelphis domestica	ENSMODG00000019004	1 retrocopy	retro_mdom_1042 ,