RetrogeneDB ID: retro_mmus_1340

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 15:40537382..40538224(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Arpc1b
• Ensembl ID: ENSMUSG00000029622
• Aliases: None
• Description: actin related protein 2/3 complex, subunit 1B [Source:MGI Symbol;Acc:MGI:1343142]

Sequence

>retro_mmus_1340
GAGAAGAGCCGTGCCAAGTGGAACAAGGTGCACGAGCTCAAGAAGGACAACGGGTAGGTGACAGGCATCAACTGGGACCC
TGAGCATAACCGCATTGTGACCTGCGGCACAGACCACAATGCCTATGTGTGGACGCTGAAGGGCCGCACGTTGAAGTCCA
CACTGGTCAATCTCCAGATCAATCGAGCAGTTTGCTGTGTTCACTGGCCCCCCGGTGAGAACAAGTTCATCCTGGGCAGC
AGCTCCCGGGTCATTTTCATCTGTTATTTGGAACAGGAGAATGACTGCTGGCTGTGCCAACACATCATAAAACCCATCCG
CTCCACTGTCCTCAGCCTGGATTGGCATCTCAACAACGTGCTCCTGGCTGTAGGCTCTTGTGACTTCAAGTGCAGGATCT
TCTCTGCCTATATAAAGGAGATGGAGGAACGAAACAGCCAGCCCCTACACGGTGGGGCTCCAAGATGCCCTTTGGGAAGC
TGATGTTTGAATCAAGCAGCAGCTGTGGCTGAGTGCATGGCGTCTGCTTCTTGGCCAATGGGAGCCGAGTTGCTTGGGTT
AGCCATGACAGCACTGTATGCCTGGTAGATGCTGACAAGAAGATGGCTTTGGCAACCCTGGCATCTGAGACATTACCACT
CCTGGCCGTCATCTTCATCACAGAAAATAGTCTAGTGGCAGCGGGCCACGACTGCTTCCCAGTGTTGTTTGCCTATGACA
GTGCTGCGGTCACATTGAGCTTCGGTGGCCGGCTGGATGTGCCCAAGCAGAGCTCCCAGTGTGGCATGACAGCCCGAGAG
CGCTTCCAGAACCTAGACGAGAAGGCCTGCTCTGAGGGAGGG

Alignment

ORF - retro_mmus_1340 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.69 %
• Parental protein coverage: 75. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EKSGAKWNKVHELKEHNGQVTGIDWAPESNRIVTCGTDRNAYVWTLKGRTWKPTLVILRINRAARCVRWA
          EKS.AKWNKVHELK..NG.VTGI.W.PE.NRIVTCGTD.NAYVWTLKGRT.K.TLV.L.INRA..CV.W.
Retrocopy EKSRAKWNKVHELKKDNG*VTGINWDPEHNRIVTCGTDHNAYVWTLKGRTLKSTLVNLQINRAVCCVHWP

Parental  PNENKFAVGSGSRVISICYFEQENDWWVCKHIKKPIRSTVLSLDWHPNNVLLAAGSCDFKCRIFSAYIKE
          P.ENKF..GS.SRVI.ICY.EQEND.W.C.HI.KPIRSTVLSLDWH.NNVLLA.GSCDFKCRIFSAYIKE
Retrocopy PGENKFILGSSSRVIFICYLEQENDCWLCQHIIKPIRSTVLSLDWHLNNVLLAVGSCDFKCRIFSAYIKE

Parental  VEERPA-PTP--WGSKMPFGELMFESSSSCGWVHGVCFSASGSRVAWVSHDSTVCLVDADKKMAVATLAS
          .EER...P.P..WGSKMPFG.LMFESSSSCG.VHGVCF.A.GSRVAWVSHDSTVCLVDADKKMA.ATLAS
Retrocopy MEERNS<PAPTRWGSKMPFGKLMFESSSSCG*VHGVCFLANGSRVAWVSHDSTVCLVDADKKMALATLAS

Parental  ETLPLLAVTFITENSLVAAGHDCFPVLFTYDNAAVTLSFGGRLDVPKQSSQRGMTARERFQNLDKKASSE
          ETLPLLAV.FITENSLVAAGHDCFPVLF.YD.AAVTLSFGGRLDVPKQSSQ.GMTARERFQNLD.KA.SE
Retrocopy ETLPLLAVIFITENSLVAAGHDCFPVLFAYDSAAVTLSFGGRLDVPKQSSQCGMTARERFQNLDEKACSE

Parental  GG
          GG
Retrocopy GG

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	11.10 RPM
SRP007412_cerebellum	0.04 RPM	10.38 RPM
SRP007412_heart	0.03 RPM	50.31 RPM
SRP007412_kidney	0.02 RPM	52.03 RPM
SRP007412_liver	0.03 RPM	39.60 RPM
SRP007412_testis	0.82 RPM	25.02 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1340 was not detected

EST

No EST(s) were mapped for retro_mmus_1340 retrocopy.

TSS

No TSS is located nearby retro_mmus_1340 retrocopy 5' end.

Lab

retro_mmus_1340 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1340 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000046248	2 retrocopies	retro_btau_1547, retro_btau_473,
Canis familiaris	ENSCAFG00000015081	1 retrocopy	retro_cfam_1568,
Callithrix jacchus	ENSCJAG00000015849	1 retrocopy	retro_cjac_2365,
Echinops telfairi	ENSETEG00000009924	2 retrocopies	retro_etel_1076, retro_etel_1275,
Gorilla gorilla	ENSGGOG00000013186	2 retrocopies	retro_ggor_1337, retro_ggor_1455,
Microcebus murinus	ENSMICG00000017424	1 retrocopy	retro_mmur_602,
Myotis lucifugus	ENSMLUG00000010933	1 retrocopy	retro_mluc_974,
Mustela putorius furo	ENSMPUG00000016522	1 retrocopy	retro_mputfur_1578,
Mus musculus	ENSMUSG00000029621	1 retrocopy	retro_mmus_1373,
Mus musculus	ENSMUSG00000029622	2 retrocopies	retro_mmus_1340 , retro_mmus_3623,
Otolemur garnettii	ENSOGAG00000010872	2 retrocopies	retro_ogar_2380, retro_ogar_3087,
Rattus norvegicus	ENSRNOG00000000991	2 retrocopies	retro_rnor_1105, retro_rnor_967,
Sus scrofa	ENSSSCG00000007625	1 retrocopy	retro_sscr_374,