RetrogeneDB ID: retro_mmus_3661

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:93988455..93988799(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000080995
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Bod1
• Ensembl ID: ENSMUSG00000044502
• Aliases: Bod1, 2310022M17Rik, BOD2.1, Fam44b
• Description: biorientation of chromosomes in cell division 1 [Source:MGI Symbol;Acc:MGI:1916806]

Sequence

>retro_mmus_3661
GCAGGCGCGGCGGGCCAGGCCTAGGGACTGGCGCGGGGTGCGAGTGGGGCAGGAGGCCCGGTCAATCCCGCTTCCCTGCC
TCCCGCAGCTCATCGCTCTCATAGAGGAGCAGCTCGAGAGCCGTGGGTTCTTTGACAGCTTCCGCTGGGACTGCCTAGCC
AACATGGACACTCAGCCAGCTTACCAGACCCCTGAGATGGAAGGCGGATAATTTTGTGTCTACACATCTGTACAAACAGG
AACGGAATCCTGCAATGAACAAGAGCCGGTTGGGAAATGGGCTGAGGCAGAGCGTGGTTCAGTTAGGCATGTTGGAAGCA
GGAGTGGACAGGATCGTTTCTCAA

Alignment

ORF - retro_mmus_3661 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.1 %
• Parental protein coverage: 65.9 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AGQASGPSGGSSGAGGPVNPASLP-PGDPQLIALIVEQLKSRGLFDSFRRDCLADVDTKPAYQN-LRQKV
          AG.A....G...GA.G...P.....P..PQLIALI.EQL.SRG.FDSFR.DCLA..DT.PAYQ..LR.K.
Retrocopy AGAAGQA*GLARGASGAGGPVNPA>PCLPQLIALIEEQLESRGFFDSFRWDCLANMDTQPAYQT>LRWKA

Parental  DNFVSTHLDKQEWNPAMNKNQLRNGLRQSVVQSGMLEAGVDRIISQ
          DNFVSTHL.KQE.NPAMNK..L.NGLRQSVVQ.GMLEAGVDRI.SQ
Retrocopy DNFVSTHLYKQERNPAMNKSRLGNGLRQSVVQLGMLEAGVDRIVSQ

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	48.20 RPM
SRP007412_cerebellum	0.00 RPM	38.82 RPM
SRP007412_heart	0.00 RPM	81.25 RPM
SRP007412_kidney	0.00 RPM	67.95 RPM
SRP007412_liver	0.00 RPM	19.25 RPM
SRP007412_testis	0.05 RPM	68.38 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3661 was not detected

EST

No EST(s) were mapped for retro_mmus_3661 retrocopy.

TSS

No TSS is located nearby retro_mmus_3661 retrocopy 5' end.

Lab

retro_mmus_3661 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3661 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000034598	1 retrocopy	retro_btau_663,
Canis familiaris	ENSCAFG00000016776	1 retrocopy	retro_cfam_1374,
Callithrix jacchus	ENSCJAG00000031971	4 retrocopies	retro_cjac_1154, retro_cjac_1515, retro_cjac_1536, retro_cjac_953,
Homo sapiens	ENSG00000145919	3 retrocopies	retro_hsap_102, retro_hsap_1867, retro_hsap_993,
Gorilla gorilla	ENSGGOG00000010925	2 retrocopies	retro_ggor_1365, retro_ggor_794,
Microcebus murinus	ENSMICG00000002626	1 retrocopy	retro_mmur_1126,
Macaca mulatta	ENSMMUG00000013793	2 retrocopies	retro_mmul_803, retro_mmul_869,
Mus musculus	ENSMUSG00000044502	1 retrocopy	retro_mmus_3661 ,
Nomascus leucogenys	ENSNLEG00000000476	1 retrocopy	retro_nleu_1224,
Oryctolagus cuniculus	ENSOCUG00000014283	1 retrocopy	retro_ocun_1071,
Otolemur garnettii	ENSOGAG00000001107	3 retrocopies	retro_ogar_1477, retro_ogar_2663, retro_ogar_3112,
Pongo abelii	ENSPPYG00000016057	2 retrocopies	retro_pabe_1567, retro_pabe_1587,
Pan troglodytes	ENSPTRG00000017544	2 retrocopies	retro_ptro_1282, retro_ptro_757,
Ictidomys tridecemlineatus	ENSSTOG00000013505	1 retrocopy	retro_itri_1164,
Tupaia belangeri	ENSTBEG00000014046	1 retrocopy	retro_tbel_3451,
Tarsius syrichta	ENSTSYG00000007617	1 retrocopy	retro_tsyr_818,
Tursiops truncatus	ENSTTRG00000000384	2 retrocopies	retro_ttru_1004, retro_ttru_457,
Vicugna pacos	ENSVPAG00000004260	1 retrocopy	retro_vpac_452,