RetrogeneDB ID: retro_mmus_1373

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 15:95715191..95715920(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Arpc1a
• Ensembl ID: ENSMUSG00000029621
• Aliases: Arpc1a, 0610010H08Rik, 1110030K07Rik, 41kDa, AA407347, Sid32, Sid329
• Description: actin related protein 2/3 complex, subunit 1A [Source:MGI Symbol;Acc:MGI:1928896]

Sequence

>retro_mmus_1373
ATGTTTCTGCATCAGTTTCTGCTAGAGCCAATAACCTACCATGCCTGGAACAGGGATGGTACCCACATCGCCCTGAGCCC
CAATAGTCATGAAGTGCACATCTACAAGAAGAATGGGAGTCAGTGGACGAAAGCTCGTGAGCTGAAGGAACATAACAGAC
ACATCATAGGTATTGACTAGGCTCCTAAGAGTGATTGTAATATCACTTGCGGGGCAGACCTCGATGCCTATGTCTGGAGT
CAGAAAGATGGCAGCTGGAAGCCCACCTGGTGATCCTGAGAATTAACGGTGCAGCCACTTTTGTGAATTGGTCCCCACTT
GAGAACGAGTTTGCTGTGGGGAGCAGAGACCCCGATCATCTCTATTTGTTACTCAGAGTTTGAAAATGACTGGTGGGCGA
GCAAGCACATGAAGAAGCCAATTCGCTCCACAGTCCTCAGCTTGGACTGGCATTCCAACAATGTTTTGTTGGCTGCAGGC
TCTTGTGACTTCGAAAGAAGAGTGTCTTCTGCCTACATCAAAGAGGTGAACAAGAAGCCAGCCAACATGCCCTGGGGCAG
CAAGATGCCTTTTGGTCAGCTGATGTCTGAGTTTGGTGGCAGTGGCACGGGCAGCTGGGTGCGTGGGGTCAGCTTCTCTG
CCAGTGGGAGCCGCCTGGTCTGGGTCAGCCAGGTCAGTACAGCGCCCGTTGTGGATGCCTCAAAAAGCATGCAGGTTTCA
ACTCTAAGA

Alignment

ORF - retro_mmus_1373 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.82 %
• Parental protein coverage: 65.68 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSLHQFLLEPITCHAWNRDRTQIALSPNNHEVHIYKKNGSQWTKAHELKEHNGHITGIDWAPKSDRIVTC
          M.LHQFLLEPIT.HAWNRD.T.IALSPN.HEVHIYKKNGSQWTKA.ELKEHN.HI.GID.APKSD...TC
Retrocopy MFLHQFLLEPITYHAWNRDGTHIALSPNSHEVHIYKKNGSQWTKARELKEHNRHIIGID*APKSDCNITC

Parental  GADRNAYVWSQKDGIWKPT-LVILRINRAATFVKWSPLENKFAVGS-GARLISVCYFESENDWWVSKHIK
          GAD..AYVWSQKDG.WKPT.LVILRIN.AATFV.WSPLEN.FAVGS.....IS.CY.E.ENDWW.SKH.K
Retrocopy GADLDAYVWSQKDGSWKPT<LVILRINGAATFVNWSPLENEFAVGS>ETPIISICYSEFENDWWASKHMK

Parental  KPIRSTVLSLDWHPNNVLLAAGSCDFKCRVFSAYIKEVDEKPASTPWGSKMPFGQLMSEFGGSGTGGWVH
          KPIRSTVLSLDWH.NNVLLAAGSCDF..RV.SAYIKEV..KPA..PWGSKMPFGQLMSEFGGSGTG.WV.
Retrocopy KPIRSTVLSLDWHSNNVLLAAGSCDFERRVSSAYIKEVNKKPANMPWGSKMPFGQLMSEFGGSGTGSWVR

Parental  GVSFSASGNRLAWVSHDSTVSVADASKSVQVSTLR
          GVSFSASG.RL.WVS..ST..V.DASKS.QVSTLR
Retrocopy GVSFSASGSRLVWVSQVSTAPVVDASKSMQVSTLR

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	0.09 RPM	107.70 RPM
SRP007412_cerebellum	0.00 RPM	68.08 RPM
SRP007412_heart	0.00 RPM	33.50 RPM
SRP007412_kidney	0.00 RPM	48.80 RPM
SRP007412_liver	0.00 RPM	37.85 RPM
SRP007412_testis	0.00 RPM	62.98 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1373 was not detected

EST

No EST(s) were mapped for retro_mmus_1373 retrocopy.

TSS

No TSS is located nearby retro_mmus_1373 retrocopy 5' end.

Lab

retro_mmus_1373 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1373 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 56 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006322	1 retrocopy	retro_amel_1431,
Bos taurus	ENSBTAG00000004242	1 retrocopy	retro_btau_1486,
Callithrix jacchus	ENSCJAG00000015859	3 retrocopies	retro_cjac_2141, retro_cjac_2165, retro_cjac_2263,
Cavia porcellus	ENSCPOG00000001777	2 retrocopies	retro_cpor_452, retro_cpor_981,
Dipodomys ordii	ENSDORG00000016059	1 retrocopy	retro_dord_593,
Equus caballus	ENSECAG00000016467	1 retrocopy	retro_ecab_185,
Homo sapiens	ENSG00000241685	2 retrocopies	retro_hsap_2010, retro_hsap_3191,
Loxodonta africana	ENSLAFG00000014024	1 retrocopy	retro_lafr_1006,
Macropus eugenii	ENSMEUG00000005609	8 retrocopies	retro_meug_1033, retro_meug_1081, retro_meug_1495, retro_meug_1668, retro_meug_1755, retro_meug_1912, retro_meug_2179, retro_meug_492,
Myotis lucifugus	ENSMLUG00000010912	1 retrocopy	retro_mluc_1432,
Macaca mulatta	ENSMMUG00000019342	2 retrocopies	retro_mmul_1383, retro_mmul_2012,
Monodelphis domestica	ENSMODG00000001303	9 retrocopies	retro_mdom_1360, retro_mdom_1380, retro_mdom_1438, retro_mdom_1551, retro_mdom_1796, retro_mdom_1917, retro_mdom_686, retro_mdom_699, retro_mdom_808,
Mus musculus	ENSMUSG00000029621	1 retrocopy	retro_mmus_1373 ,
Mus musculus	ENSMUSG00000029622	2 retrocopies	retro_mmus_1340, retro_mmus_3623,
Nomascus leucogenys	ENSNLEG00000010852	2 retrocopies	retro_nleu_1663, retro_nleu_2069,
Oryctolagus cuniculus	ENSOCUG00000003944	1 retrocopy	retro_ocun_1130,
Otolemur garnettii	ENSOGAG00000010870	6 retrocopies	retro_ogar_1547, retro_ogar_2690, retro_ogar_2697, retro_ogar_381, retro_ogar_610, retro_ogar_656,
Pongo abelii	ENSPPYG00000025816	4 retrocopies	retro_pabe_1647, retro_pabe_1648, retro_pabe_2537, retro_pabe_2647,
Pan troglodytes	ENSPTRG00000033819	2 retrocopies	retro_ptro_1340, retro_ptro_2253,
Sarcophilus harrisii	ENSSHAG00000010673	2 retrocopies	retro_shar_180, retro_shar_727,
Ictidomys tridecemlineatus	ENSSTOG00000001660	1 retrocopy	retro_itri_1834,
Tupaia belangeri	ENSTBEG00000011381	3 retrocopies	retro_tbel_1237, retro_tbel_1241, retro_tbel_82,