RetrogeneDB ID: retro_mdom_440

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:531886318..531887001(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GPR137B
• Ensembl ID: ENSMODG00000008061
• Aliases: None
• Description: G protein-coupled receptor 137B [Source:HGNC Symbol;Acc:11862]

Sequence

>retro_mdom_440
TTCTCTTTTCCTTCTTCAAAAACTTTGGCAGCCATTTCACTAGAGCCCCTTCGTCTTCCGGCTACTCTGTTGCTTTCCCG
TGAGCCTCCAGTTCTTCCCCTTGACCTTGAATGAATGTGTACTTCACGTGGATGATTTTTCAAAGCAGAATCAAATTATT
CTCCAGAATTACTGAAATACCAACGTGTTCTCTACCTGACTTCTCTCTTCCGCAGTCTTCTTTTCCAACTGGAGAATCTA
CTCTGTGTAGTGCTGAAAAGAGAAAATTGGGAGAGAAAGGTTATCATCTCAGTTCGCATAGCCATTAATGATATCGCCTT
TTTTTTTCTGCACAGTCTTGCTTTCTGTCTGCCTCTACAAGATTTCCAAGAAATCCTTAATAGATATATGTACTAGGAAT
CTAAGGGTTCATCCCTGTGTCAAGTTACCAACATTGGAGTGACAGTTAATCCTGCTTTATACATCCAGCGCCTGTTACAA
CTTGTTCATGTCACCCGGTTCCCAGAATAAGAATGTCCATTCCTTTGATTACAACTGACACAATGCATCAGACCAGGCAG
ATCTGAACAGTCAGCTTGGAAATGCTGGAGATGTAGTGTTCAGAGTGTGTCTCTTTATGTGGGAGCTCTGCTCACTACCG
CCATCTTTACTTCTTTGGAGTTAGAAAGGACTTAACAGAACCG

Alignment

ORF - retro_mdom_440 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.45 %
• Parental protein coverage: 57.5 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  FSFYFKDFVAANSL-SPFVFWLLYCFPVCLQFFTLTL-MNLYFTQVIF-KAKSKYSPELLKYRLPLYLAS
          FSF......AA.SL.SPFVF.LL.CFPV.LQFF.LTL.MN.YFT..IF.KA.S.YSPELLKY...LYL.S
Retrocopy FSFPSSKTLAAISL>SPFVFRLLCCFPVSLQFFPLTL>MNVYFTWMIF>KAESNYSPELLKYQRVLYLTS

Parental  LFISLLFLLVNLTCAVLVKTENWERKIIVSVRVAINDTLFVLCAISLSVCLYKISKMSLANIYL--ESKG
          LF.SLLF.L.NL.C.VL.K.ENWERK.I.SVR.AIND........SL..CL.........N.Y...ESKG
Retrocopy LFRSLLFQLENLLCVVL-KRENWERKVIISVRIAIND-IAXXXLHSLAFCLPLQDFQEILNRYMY*ESKG

Parental  SSVCQVTAIGVTV-ILLYASRACYNLFILSFSQNKNVHSFDYDWYNVSDQADLKNQLGDAGYVVFGVVLF
          SS.CQVT.IGVTV.ILLY.S.ACYNLF....SQNKNVHSFDY...N.SDQADL..QLG.AG.VVF.V.LF
Retrocopy SSLCQVTNIGVTV>ILLYTSSACYNLFMSPGSQNKNVHSFDYN*HNASDQADLNSQLGNAGDVVFRVCLF

Parental  VWEL-LPTTLV-VYFFRVRNPTKDLTNP
          .WEL.L.TT....YFF.VR...KDLT.P
Retrocopy MWEL<LLTTAI<LYFFGVR---KDLTEP

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	0.12 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	3.73 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_440 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_440 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006090	1 retrocopy	retro_chof_120,
Monodelphis domestica	ENSMODG00000008061	1 retrocopy	retro_mdom_440 ,