RetrogeneDB ID: retro_mmus_3460

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:60548018..60548459(+)
• Located in intron of: ENSMUSG00000062949

Retrocopy information

• Ensembl ID: ENSMUSG00000082226
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: 1810013L24Rik
• Ensembl ID: ENSMUSG00000022507
• Aliases: 1810013L24Rik, 1110017P05Rik, 3010002C02Rik, AA792997, AW124177, Gm19906, R74903
• Description: RIKEN cDNA 1810013L24 gene [Source:MGI Symbol;Acc:MGI:1916303]

Sequence

>retro_mmus_3460
ATGGAGGACCAGCCGAAGGACCGTGAGGCCGAGGTCGCCGGGCCCTGGTTTTCTAAGTGGGAGCGCCAGTGCCTTGCAGA
GGCGGAGCAGGCGGAGCAGCTGTCCCCGGAGCTGCAGGAGGAGGCGGCTGCCGATGCGGCGGGGCTCAAGATCGAGCGCC
AGAGGCTCTGGCACCTCTTCCAGATCTCAGCCACGGCAGTGGCCCAGCTCTACAAAGATTCCGGGTGCCAGCAGCCAGGA
CTCTCTATGTGGGACCCCTTCCAGAACGCGGCCATGGCCGTGACCAGCCTCTACAAAGAGAGCGGGGATGCCTACCAGAG
AAGTTTTGAACTGGGCGTCCAGGTTGGCTACCAGCGTCGTGTGAGAGACGTGCTGGAGTGGGTGAAGAAGGGTAGGAGCA
TCATTCGTCGGGAAGACCTCATAAGCTTCCTCTGTGGCAAA

Alignment

ORF - retro_mmus_3460 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.87 %
• Parental protein coverage: 54.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEERKEEGEAEIQEHGPEHWFSKWERQCLAEAEQDEQLSPELQEEAAA-AAQPEHKQQKLWHLFQNSATA
          ME......EAE....GP..WFSKWERQCLA.......LSPELQEEAAA.AA......Q.LWHLFQ.SATA
Retrocopy MEDQPKDREAEVA--GP--WFSKWERQCLAXXXXXXXLSPELQEEAAADAAGLKIERQRLWHLFQISATA

Parental  VAQLYKDRVCQQPGLSLWVPFQNAATAVTNLYKESVDTHQRSFDIGIQIGYQRRNKDVLAWVKKRRRTIR
          VAQLYKD..CQQPGLS.W.PFQNAA.AVT.LYKES.D..QRSF..G.Q.GYQRR..DVL.WVKK.R..IR
Retrocopy VAQLYKDSGCQQPGLSMWDPFQNAAMAVTSLYKESGDAYQRSFELGVQVGYQRRVRDVLEWVKKGRSIIR

Parental  REDLISFLCGK
          REDLISFLCGK
Retrocopy REDLISFLCGK

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	0.61 RPM	47.57 RPM
SRP007412_cerebellum	0.39 RPM	41.55 RPM
SRP007412_heart	0.03 RPM	49.09 RPM
SRP007412_kidney	0.04 RPM	54.61 RPM
SRP007412_liver	0.03 RPM	35.01 RPM
SRP007412_testis	0.37 RPM	102.96 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3460 was not detected

EST

No EST(s) were mapped for retro_mmus_3460 retrocopy.

TSS

No TSS is located nearby retro_mmus_3460 retrocopy 5' end.

Lab

retro_mmus_3460 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3460 has 8 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4765
Pan troglodytes	retro_ptro_3172
Gorilla gorilla	retro_ggor_2968
Pongo abelii	retro_pabe_163
Rattus norvegicus	retro_rnor_156
Sus scrofa	retro_sscr_1177
Canis familiaris	retro_cfam_147
Equus caballus	retro_ecab_1091

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010719	2 retrocopies	retro_amel_1715, retro_amel_88,
Canis familiaris	ENSCAFG00000018981	1 retrocopy	retro_cfam_147,
Cavia porcellus	ENSCPOG00000010925	1 retrocopy	retro_cpor_101,
Dasypus novemcinctus	ENSDNOG00000015893	3 retrocopies	retro_dnov_1575, retro_dnov_2266, retro_dnov_827,
Equus caballus	ENSECAG00000009430	1 retrocopy	retro_ecab_1091,
Homo sapiens	ENSG00000182831	1 retrocopy	retro_hsap_4765,
Gorilla gorilla	ENSGGOG00000010744	1 retrocopy	retro_ggor_2968,
Monodelphis domestica	ENSMODG00000005378	2 retrocopies	retro_mdom_1716, retro_mdom_299,
Mustela putorius furo	ENSMPUG00000014707	1 retrocopy	retro_mputfur_44,
Mus musculus	ENSMUSG00000022507	1 retrocopy	retro_mmus_3460 ,
Nomascus leucogenys	ENSNLEG00000010106	1 retrocopy	retro_nleu_2348,
Otolemur garnettii	ENSOGAG00000003909	1 retrocopy	retro_ogar_74,
Pongo abelii	ENSPPYG00000007088	1 retrocopy	retro_pabe_163,
Pan troglodytes	ENSPTRG00000007751	1 retrocopy	retro_ptro_3172,
Rattus norvegicus	ENSRNOG00000002545	2 retrocopies	retro_rnor_156, retro_rnor_1928,
Sus scrofa	ENSSSCG00000028454	1 retrocopy	retro_sscr_1177,
Ictidomys tridecemlineatus	ENSSTOG00000009324	1 retrocopy	retro_itri_137,