RetrogeneDB ID: retro_rnor_967

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 13:69394034..69394846(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Arpc1b
• Ensembl ID: ENSRNOG00000000991
• Aliases: None
• Description: Actin-related protein 2/3 complex subunit 1B [Source:UniProtKB/Swiss-Prot;Acc:O88656]

Sequence

>retro_rnor_967
TGTGTACACTGGGTACCCAGTGAGAACAAGTTTGTCGTGGGCAGTGGCTTCGTGTCATTTCCATCTGTTATTTTGAGCAG
GAGAATGATTGATGGGTGTACAAGCACATCAAAAAGCCCATCCACTTCACTGTCCTTGGCCTGGACTGGCATCCCAACAA
TGTACTGTGGCTGCAGTTTCCTGTGACTTCAAGTGCAGGATCTTCTCTGCCTATATCAAGGGGGTGGAGAAACGGCCATC
CCATACCCCATGGGGCTCCAAGATGCCCTTTGGGGAGCTGATGTTTTGAATCGAGCAGCAGCTGTGGCTGGGTACATGGT
GTCTGCTTCTCGGCCAGTGGGAGCCGAGTTGCTTGGGTCAGCCATGACAGCACTGTGTGCCTGATAGATGCTGAGAAGAT
GGCCATGGCAGCCCTGACCTCTGAGACATTACCACTCTTGACTATCACCTTAATCACAGAAAATAGTCTCATGGCAGCGG
GCCACAACTGCTTCCTGGTGCTGTTTCCCTATGACAATGCTGCGGGGACACTGAGCTTTGGTGGCCCGCTGGATGTGCCC
AAGAAGAACTCCCAGCGTGGCCTGACAGCCTGAGAACGCTTCCAGAACCTCAAGAAGGCCAGCTCTGAAGGGGGTGCAGC
CACAGGGTGCAGCCTGGATTCACTGCACAAGAACAGCATCAGTCAAATCTGGGTACTCAGCAGGGGTAAGGCCAAGTGCT
CGCAGTTCTGCACCACAGACGTAGATGGTGGTGACATGAGCATCTGGGATGTGAAGAGCTTGGAGTCAGCCTTGAAGGAC
ATGAAGATCAAA

Alignment

ORF - retro_rnor_967 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.7 %
• Parental protein coverage: 73.12 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  CVRWAPNENKFAVGSGS-RVISICYFEQENDWWVCKHIKKPIRSTVLSLDWHPNNVL-LAAGSCDFKCRI
          CV.W.P.ENKF.VGSG..RVISICYFEQEND.WV.KHIKKPI..TVL.LDWHPNNVL..AA.SCDFKCRI
Retrocopy CVHWVPSENKFVVGSGF<RVISICYFEQEND*WVYKHIKKPIHFTVLGLDWHPNNVL<VAAVSCDFKCRI

Parental  FSAYIKEVEERPAPTPWGSKMPFGELMF-ESSSSCGWVHGVCFSAGGSRVAWVSHDSTVCLVDAEKKMAV
          FSAYIK.VE.RP..TPWGSKMPFGELMF.ESSSSCGWVHGVCFSA.GSRVAWVSHDSTVCL.DAEK.MA.
Retrocopy FSAYIKGVEKRPSHTPWGSKMPFGELMF>ESSSSCGWVHGVCFSASGSRVAWVSHDSTVCLIDAEK-MAM

Parental  ATLASETLPLLAITFITENSLVAAGHDCFPVLFTYDNAAGTLSFGGRLDVPKQNSQRGLTARERFQNLDK
          A.L.SETLPLL.IT.ITENSL.AAGH.CF.VLF.YDNAAGTLSFGG.LDVPK.NSQRGLTA.ERFQNL.K
Retrocopy AALTSETLPLLTITLITENSLMAAGHNCFLVLFPYDNAAGTLSFGGPLDVPKKNSQRGLTA*ERFQNL-K

Parental  KASSEGGAATGAGLDSLHKNSVSQISVLSGGKAKCSQFCTTGMDGG-MSIWDVKSLESALKDLKIR
          KASSEGGAATG..LDSLHKNS.SQI.VLS.GKAKCSQFCTT..DGG.MSIWDVKSLESALKD.KI.
Retrocopy KASSEGGAATGCSLDSLHKNSISQIWVLSRGKAKCSQFCTTDVDGGDMSIWDVKSLESALKDMKIK

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
SRP017611_brain	0.00 RPM	12.37 RPM
SRP017611_kidney	0.00 RPM	73.97 RPM
SRP017611_liver	0.00 RPM	21.92 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_967 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_967 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_967 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 18 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	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,