RetrogeneDB ID: retro_mmus_3087

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:128997338..128998021(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rnd2
• Ensembl ID: ENSMUSG00000001313
• Aliases: None
• Description: Rho family GTPase 2 [Source:MGI Symbol;Acc:MGI:1338755]

Sequence

>retro_mmus_3087
ATGGAAGGGCAGAGTGGCTGCTGCAAGATCACAGTGGTGGGGGACACGGAGTGCGGCAAGACAGTGCTGATGCATGTGTT
CGCCAAGGATGCCTACCCTGGGAGTTATGTCCCCATGGTGTTTGAGAACTACACTGCCAGCTTCGAGATCGACAAGCGCT
GCATTGAGCTCAACATGTGGGATACTTCAGGTTCCTCTTACTATGACAATGTCCGGCCTCTGACCTACCCGGATTCTGAT
GCTGTGCTTAGCTGCTTTGACATTAGCCGGCCAGAAACACTGGACAGTGTCCTCAAGAAGTGGCAAGGAGAGACTCAGGA
GTTTTGCCCCCAATGCCAAGGTGGTGCTGGTTGGCTGTAAGCTGGACATGAGGACTGACCTGGCCACACTGAGGGAGCTA
TCCAAGCAGAGACTTATCCCTGTCACACATGAGCAGGGTACTGTACTGTACCAAGCAGGTGGGAGCTGTGTCCTTCGTGG
AATGCTCCTCCCGATCTTCCGAGCGCAGTGTCCGGGATGTCTTTCATGTGGCCACAGTGGCTTCAATTGACCGTGGCCAT
AGGCAGCTACGCCGTACTGACTCTGGCCGGGGACTGCAGCGATCCACTCAACTGTCGGGATGGCCAGACCGGGGAAACGA
GGGCGAGATGCATAAGGATCGAGCCAAGAGCTGTAACCTCATG

Alignment

ORF - retro_mmus_3087 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.14 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MEGQSGRCKIVVVGDAECGKTALLQVFAKDAYPGSYVPTVFENYTASFEIDKRRIELNMWDTSGSSYYDN
          MEGQSG.CKI.VVGD.ECGKT.L..VFAKDAYPGSYVP.VFENYTASFEIDKR.IELNMWDTSGSSYYDN
Retrocopy MEGQSGCCKITVVGDTECGKTVLMHVFAKDAYPGSYVPMVFENYTASFEIDKRCIELNMWDTSGSSYYDN

Parental  VRPLAYPDSDAVLICFDISRPETLDSVLKKWQGETQEFCP-NAKVVLVGCKLDMRTDLATLRELSKQRLI
          VRPL.YPDSDAVL.CFDISRPETLDSVLKKWQGETQEFCP.NAKVVLVGCKLDMRTDLATLRELSKQRLI
Retrocopy VRPLTYPDSDAVLSCFDISRPETLDSVLKKWQGETQEFCP>NAKVVLVGCKLDMRTDLATLRELSKQRLI

Parental  PVTHEQGTVL-AKQVGAVSYVECSSRSSERSVRDVFHVATVASLGRGHRQLRRTDSRRGLQRSTQLSGRP
          PVTHEQGTVL..KQVGAVS.VECSSRSSERSVRDVFHVATVAS..RGHRQLRRTDS.RGLQRSTQLSG.P
Retrocopy PVTHEQGTVL>TKQVGAVSFVECSSRSSERSVRDVFHVATVASIDRGHRQLRRTDSGRGLQRSTQLSGWP

Parental  DRGNEGEMHKDRAKSCNLM
          DRGNEGEMHKDRAKSCNLM
Retrocopy DRGNEGEMHKDRAKSCNLM

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	0.05 RPM	84.01 RPM
SRP007412_cerebellum	0.00 RPM	108.60 RPM
SRP007412_heart	0.03 RPM	5.01 RPM
SRP007412_kidney	0.00 RPM	8.99 RPM
SRP007412_liver	0.05 RPM	28.35 RPM
SRP007412_testis	0.00 RPM	14.09 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3087 was not detected

EST

No EST(s) were mapped for retro_mmus_3087 retrocopy.

TSS

No TSS is located nearby retro_mmus_3087 retrocopy 5' end.

Lab

retro_mmus_3087 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3087 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013018	1 retrocopy	retro_cjac_3930,
Myotis lucifugus	ENSMLUG00000004129	4 retrocopies	retro_mluc_1125, retro_mluc_1356, retro_mluc_2145, retro_mluc_459,
Mus musculus	ENSMUSG00000001313	1 retrocopy	retro_mmus_3087 ,
Mus musculus	ENSMUSG00000007815	9 retrocopies	retro_mmus_178, retro_mmus_191, retro_mmus_2041, retro_mmus_2507, retro_mmus_3728, retro_mmus_3729, retro_mmus_3964, retro_mmus_3965, retro_mmus_3966,