RetrogeneDB ID: retro_mmus_3710

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:150222365..150223336(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000048592
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Bmi1
• Ensembl ID: ENSMUSG00000026739
• Aliases: Bmi1, AW546694, Bmi-1, Pcgf4
• Description: Bmi1 polycomb ring finger oncogene [Source:MGI Symbol;Acc:MGI:88174]

Sequence

>retro_mmus_3710
ATGTATCAAAAAACCAGAATCAAGATCACTGAGCTAAATCCCCACTTAATGTGTGTCCTGTGTGGAGGGTACTTCATTGA
TGCCACTACCATAATAGAATGTCTACATTCCTTCTGTAAAACATGTATTGTGCGTTATTTGGAGAGCAGCAAGTATTGTC
CTATTTGTGATGTCCAAGTTCACAAAACTAGACCACTCCTGAACATAAGGTCAAATAAAACTCTTCAAGATATTGTATAC
AAATTAGTCCCAGGGCTTTTCAAAAATGAAATGAAGAGAAGAAGAGATTTTTATGCAGCTCACCCTTCAGCTGATGCTGC
CAATGGCTCCAACGAAGACCGAGGAGAAGTTGCAGATGAGGAGAAGCGGATTATAACTGATGATGAGATAATAAGCTTGT
CTATTGAGTTCTTTGATCAGAACAGATTGGATCAGAAAGTAAATAAAAAGAAGCCTATGAAAGAGATGAATGATAAAAGG
TACTTACGATGCCCAGGAGCAATGACTGTGATGCACTTGAGAAAGTTTCTCAGGAGTAAAATGGACATACCTAATACTTT
CCAGATTGACATCATGTATGAAGAGGAACCTTTAAAGGATTATTACACACTAATGGACATTGCCTACATTTATACCTGGA
GAAGAAATGGCCCACTACCTTTGAAATACAGAGTTCAGCCAACTTGCAAAAGAATGAAGATGAGTCACCAGAGGGATGGA
CTGACGAATGCTGGAGAGCTGGAAAGTGATTCGGGGAGTGACAAGGCCAACAGCCCAGCAGGAGGTGTTCCCTCCACCTC
TTCCTGCTTGCCCAGTCCCAGCACTCCAGTGCAGTCTCCTCACCCACAGTTCCTCACATTTCCAGTACCATGAATGGAAC
CAGCAACAGCCCCAACGGTAACCACCAATCTTCCTTTGCCAGTAGACCTCGAAAATTATCATTAAATGGGTCATCAGCAA
CTTCATCTGGT

Alignment

ORF - retro_mmus_3710 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.46 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MHRTTRIKITELNPHLMCVLCGGYFIDATTIIECLHSFCKTCIVRYLETSKYCPICDVQVHKTRPLLNIR
          M...TRIKITELNPHLMCVLCGGYFIDATTIIECLHSFCKTCIVRYLE.SKYCPICDVQVHKTRPLLNIR
Retrocopy MYQKTRIKITELNPHLMCVLCGGYFIDATTIIECLHSFCKTCIVRYLESSKYCPICDVQVHKTRPLLNIR

Parental  SDKTLQDIVYKLVPGLFKNEMKRRRDFYAAHPSADAANGSNEDRGEVADEEKRIITDDEIISLSIEFFDQ
          S.KTLQDIVYKLVPGLFKNEMKRRRDFYAAHPSADAANGSNEDRGEVADEEKRIITDDEIISLSIEFFDQ
Retrocopy SNKTLQDIVYKLVPGLFKNEMKRRRDFYAAHPSADAANGSNEDRGEVADEEKRIITDDEIISLSIEFFDQ

Parental  SRLDRKVNKEKPKEEVNDKRYLRCPAAMTVMHLRKFLRSKMDIPNTFQIDVMYEEEPLKDYYTLMDIAYI
          .RLD.KVNK.KP..E.NDKRYLRCP.AMTVMHLRKFLRSKMDIPNTFQID.MYEEEPLKDYYTLMDIAYI
Retrocopy NRLDQKVNKKKPMKEMNDKRYLRCPGAMTVMHLRKFLRSKMDIPNTFQIDIMYEEEPLKDYYTLMDIAYI

Parental  YTWRRNGPLPLKYRVRPTCKRMKMSHQRDGLTNAGELESDSGSDKANSPAGGVPSTSSCLPSPSTPVQSP
          YTWRRNGPLPLKYRV.PTCKRMKMSHQRDGLTNAGELESDSGSDKANSPAGGVPSTSSCLPSPSTPVQSP
Retrocopy YTWRRNGPLPLKYRVQPTCKRMKMSHQRDGLTNAGELESDSGSDKANSPAGGVPSTSSCLPSPSTPVQSP

Parental  HPQF-PHISSTMNGTSNSPSANHQSSFASRPRKSSLNGSSATSSG
          HPQF.PHISSTMNGTSNSP..NHQSSFASRPRK.SLNGSSATSSG
Retrocopy HPQF<PHISSTMNGTSNSPNGNHQSSFASRPRKLSLNGSSATSSG

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	0.02 RPM	36.03 RPM
SRP007412_cerebellum	0.00 RPM	30.61 RPM
SRP007412_heart	0.06 RPM	37.51 RPM
SRP007412_kidney	0.06 RPM	38.10 RPM
SRP007412_liver	0.00 RPM	18.79 RPM
SRP007412_testis	0.18 RPM	74.10 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3710 was not detected

EST

No EST(s) were mapped for retro_mmus_3710 retrocopy.

TSS

No TSS is located nearby retro_mmus_3710 retrocopy 5' end.

Lab

retro_mmus_3710 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3710 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011962	1 retrocopy	retro_chof_709,
Callithrix jacchus	ENSCJAG00000036548	1 retrocopy	retro_cjac_2437,
Cavia porcellus	ENSCPOG00000015427	2 retrocopies	retro_cpor_1209, retro_cpor_546,
Gorilla gorilla	ENSGGOG00000025243	1 retrocopy	retro_ggor_3025,
Loxodonta africana	ENSLAFG00000016845	1 retrocopy	retro_lafr_591,
Macaca mulatta	ENSMMUG00000000881	1 retrocopy	retro_mmul_2591,
Mus musculus	ENSMUSG00000026739	1 retrocopy	retro_mmus_3710 ,
Mus musculus	ENSMUSG00000069678	1 retrocopy	retro_mmus_2722,
Oryctolagus cuniculus	ENSOCUG00000005420	1 retrocopy	retro_ocun_489,
Tupaia belangeri	ENSTBEG00000015631	1 retrocopy	retro_tbel_2369,