RetrogeneDB ID: retro_mmus_1511

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 16:38685314..38685869(-)
• Located in intron of: ENSMUSG00000022799

Retrocopy information

• Ensembl ID: ENSMUSG00000081651
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Anapc10
• Ensembl ID: ENSMUSG00000036977
• Aliases: Anapc10, 1500026N15Rik, A830003M23Rik, APC10
• Description: anaphase promoting complex subunit 10 [Source:MGI Symbol;Acc:MGI:1916249]

Sequence

>retro_mmus_1511
ATAACCACACCGAACAAGACACCTCCTGGTGCTGATCCTAAGTAGTTGGAGAGGACAGCAACAGTCAGGGAAATTGGGTC
TCAGGCTGTTTGGTCACTCTCTTCCTGCAAACCAGGGTTTGGAGTGGATCAATTACAGGATGACAATCTAGAAACTTACT
GGCAATCTGATGGCTCTCAGCCTCATTTAGTGAGCATCCAATTCAGAAGAAAAACAACAGTGAAGGCATTTTGTATTTAT
GCAGACTATAAGTCTGATGAAAGCTACACTCCAAGGAAAATCTCAGTCAGAGTAGGAAATAATTTTCACAACCTTCAAGA
AATCCGGCAACTTGGATTGGTTGAACCAAGCGGCTGGATTCACGTTCCTTTAACTGACAATCATAAGAAGCCAATTCGCA
CATTCATGATACAGATTGCTGTTCTAGCCAATCATCAAAATGGAAGAGATACCCACATGAGACAAATTAAAATATACACA
CCAGTGGAAGAGAGCTCCATTGGGAAATTCCCTAGATGCACAACCATTGATTTCATGATGTATCATTCAATACAG

Alignment

ORF - retro_mmus_1511 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.05 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTTPNKTPPGADPKQLERTATVREIGSQAVWSLSSCKPGFGVDQLRDDNLETYWQSDGSQPHLVNIQFRR
          .TTPNKTPPGADPK.LERTATVREIGSQAVWSLSSCKPGFGVDQL.DDNLETYWQSDGSQPHLV.IQFRR
Retrocopy ITTPNKTPPGADPK*LERTATVREIGSQAVWSLSSCKPGFGVDQLQDDNLETYWQSDGSQPHLVSIQFRR

Parental  KTTVKTLCIYADYKSDESYTPSKISVRVGNNFHNLQEIRQLELVEPSGWIHVPLTDNHKKPTRTFMIQIA
          KTTVK..CIYADYKSDESYTP.KISVRVGNNFHNLQEIRQL.LVEPSGWIHVPLTDNHKKP.RTFMIQIA
Retrocopy KTTVKAFCIYADYKSDESYTPRKISVRVGNNFHNLQEIRQLGLVEPSGWIHVPLTDNHKKPIRTFMIQIA

Parental  VLANHQNGRDTHMRQIKIYTPVEESSIGKFPRCTTIDFMMYRSIR
          VLANHQNGRDTHMRQIKIYTPVEESSIGKFPRCTTIDFMMY.SI.
Retrocopy VLANHQNGRDTHMRQIKIYTPVEESSIGKFPRCTTIDFMMYHSIQ

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	5.61 RPM
SRP007412_cerebellum	0.00 RPM	4.34 RPM
SRP007412_heart	0.03 RPM	2.52 RPM
SRP007412_kidney	0.02 RPM	3.21 RPM
SRP007412_liver	0.00 RPM	1.37 RPM
SRP007412_testis	0.09 RPM	14.68 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1511 was not detected

EST

No EST(s) were mapped for retro_mmus_1511 retrocopy.

TSS

No TSS is located nearby retro_mmus_1511 retrocopy 5' end.

Lab

retro_mmus_1511 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1511 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002663	2 retrocopies	retro_cjac_2683, retro_cjac_2999,
Dipodomys ordii	ENSDORG00000016690	1 retrocopy	retro_dord_202,
Homo sapiens	ENSG00000164162	1 retrocopy	retro_hsap_152,
Gorilla gorilla	ENSGGOG00000025091	1 retrocopy	retro_ggor_241,
Myotis lucifugus	ENSMLUG00000008607	1 retrocopy	retro_mluc_1679,
Macaca mulatta	ENSMMUG00000004432	1 retrocopy	retro_mmul_374,
Mus musculus	ENSMUSG00000036977	1 retrocopy	retro_mmus_1511 ,
Nomascus leucogenys	ENSNLEG00000005453	1 retrocopy	retro_nleu_1498,
Otolemur garnettii	ENSOGAG00000006902	2 retrocopies	retro_ogar_1649, retro_ogar_2510,
Pongo abelii	ENSPPYG00000015096	1 retrocopy	retro_pabe_468,
Pan troglodytes	ENSPTRG00000016480	1 retrocopy	retro_ptro_149,
Pteropus vampyrus	ENSPVAG00000013169	2 retrocopies	retro_pvam_1245, retro_pvam_1450,