RetrogeneDB ID: retro_mmus_1370

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 15:91822777..91823147(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083083
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rap1b
• Ensembl ID: ENSMUSG00000052681
• Aliases: Rap1b, 2810443E11Rik
• Description: RAS related protein 1b [Source:MGI Symbol;Acc:MGI:894315]

Sequence

>retro_mmus_1370
ACGATACAAGATTCTTATAAGAAAGCATGCTGAGGTAGATGTGCAACAGTGTATGCTTGAAATCCAGGATGCTGCAGGAA
CAGAACAACTTACAACAATGGGAAATTTGTACATGCAGGCTGGACAAGGCTTTGCTTTGGTTTAGTCCGTCACAGCCCAG
TGCACATTTAAAGACTGACACCATCTGAGAGAACTGATTCTTCGGGTCAAAGACACTGGTGAAGTTCCAGTGACTCTGGT
TGGTAATAAATGTGACTTGGAAGATGAAATACTTGTAGGAAAGGAACAAGGTCAAAACCTAGTAAGGCAATGGAGCCTCT
GTGCGTTCTTAGAATCCTCTTCAAAATCCAGAATAAATGTTAAGGAAATC

Alignment

ORF - retro_mmus_1370 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.39 %
• Parental protein coverage: 66.85 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TIEDSY-RKQVEVDAQQCMLEILDTAGTEQFTAMRDLYMKNGQGFALVYSITAQSTFNDLQDLREQILRV
          TI.DSY.RK..EVD.QQCMLEI.D.AGTEQ.T.M..LYM..GQGFALV.S.TAQ.TF.D...LRE.ILRV
Retrocopy TIQDSY>RKHAEVDVQQCMLEIQDAAGTEQLTTMGNLYMQAGQGFALV*SVTAQCTFKD*HHLRELILRV

Parental  KDTDDVPMILVGNKCDLEDERVVGKEQGQNLARQWNNCAFLESSAKSKINVNEI
          KDT..VP..LVGNKCDLEDE..VGKEQGQNL.RQW..CAFLESS.KS.INV.EI
Retrocopy KDTGEVPVTLVGNKCDLEDEILVGKEQGQNLVRQWSLCAFLESSSKSRINVKEI

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	0.30 RPM	54.88 RPM
SRP007412_cerebellum	0.22 RPM	38.60 RPM
SRP007412_heart	0.09 RPM	50.74 RPM
SRP007412_kidney	0.85 RPM	75.17 RPM
SRP007412_liver	0.03 RPM	53.52 RPM
SRP007412_testis	0.05 RPM	22.87 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1370 was not detected

EST

No EST(s) were mapped for retro_mmus_1370 retrocopy.

TSS

No TSS is located nearby retro_mmus_1370 retrocopy 5' end.

Lab

retro_mmus_1370 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1370 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_2479

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008637	1 retrocopy	retro_amel_103,
Callithrix jacchus	ENSCJAG00000007261	3 retrocopies	retro_cjac_1435, retro_cjac_2371, retro_cjac_607,
Cavia porcellus	ENSCPOG00000008272	4 retrocopies	retro_cpor_1194, retro_cpor_632, retro_cpor_739, retro_cpor_85,
Gorilla gorilla	ENSGGOG00000025649	1 retrocopy	retro_ggor_2836,
Loxodonta africana	ENSLAFG00000016460	1 retrocopy	retro_lafr_482,
Mus musculus	ENSMUSG00000052681	1 retrocopy	retro_mmus_1370 ,
Mus musculus	ENSMUSG00000068798	2 retrocopies	retro_mmus_1963, retro_mmus_3027,
Nomascus leucogenys	ENSNLEG00000003573	2 retrocopies	retro_nleu_1034, retro_nleu_481,
Otolemur garnettii	ENSOGAG00000005746	2 retrocopies	retro_ogar_2260, retro_ogar_272,
Sarcophilus harrisii	ENSSHAG00000011497	1 retrocopy	retro_shar_425,
Sus scrofa	ENSSSCG00000030014	2 retrocopies	retro_sscr_435, retro_sscr_909,
Tupaia belangeri	ENSTBEG00000013380	4 retrocopies	retro_tbel_2145, retro_tbel_4650, retro_tbel_4658, retro_tbel_613,