RetrogeneDB ID: retro_rnor_1105

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 15:41869701..41870810(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000050940
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_1105
ATGACCTACCACAGCTTCCTGGTGGAGCCCATCAGCTGCCATGCTTGGAACAAGGACCGTACTCAGATCGCCATCTGCCC
CAACAACCACGAGGTGCACATCTATGAGAAGAGCAGTGCCAAGTGGAACAAGGTGCACGAACTCAAGGAGCACAATGGGC
AGGTGACAGGCATCGACTGGGCCCCTGAGAGTAACCGCATTGTGACCTGCGGCACAGACCGCAATGCCTATGTATGGACG
CTGAAGGGCCGCACGTGGAAGCCCACACTGGTCATCCTTCGGAATAATCGAGCTGCCCGCTGCGTGCGCTGGGCCCCCAG
TGAGAACAAGTTCGCCATGGTCAGTGGTTCCCGTGTCATTTCCATCTGTTATTTTGAGCAGGAGAATGACTGGTGGGTGT
GCAAACACATCAAAAAGCCCATCCGCTCCACTGTCCTTAGCCCGGACTGGCATCCCAACAACGTGCTCCTGGCTGCAGGC
TCCTGTGACTTCAACTGCAGGATCTTCTCTGCCTATATCAAGGAGGTGGAGAAATGGCCGCCCCTACACCATGGGGCTCC
AAGATGCCCTTTGGGGAGCTGATGTTTGAATCGAGCAGCAGCTGTGGCTGGGTGCATTGTGTCTGCTTCTTGGCCAGTGG
GAGCCGAGTTGCTTGGGTCAGCCATGACAGCACTGTGTGCCTGGTAGATACTGAGAAAAGATGGCGGTGGCAACCCTGGC
CTCTGAGACATGTACCGCTCCTGGCCATCACCTTCATCACAGAAAATAGTCTCGTAGCGGCAGGCCACGACTGCTTCCCG
GTGCTGTTTACCTATGACAACGCTGCAGGGACATTGAGCTTTGGTGGCCGGCTGGATGTACCCAAGCAGAACTCCCAGCG
TGGCCTGACAGCCCAAGAGCGCTTCCAGAACCTCGACAAGAAGGGCAGCACTGAAGGGGGTGCAGCCACAGGGGCTGGCC
TGGATTCACTGCACAAGAACAGCGTCAGTCAAATCTCGGTGCTCAGCGGGGGCAAGGCCAAGTGCTCGCAGTTCTGCACC
ACAGGCATGGACGGTGGCATGAGCATCTGGGATGTGAAGAGCTTGGAGTCAGCCTTGAAGGATCTGAAG

Alignment

ORF - retro_rnor_1105 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.37 %
• Parental protein coverage: 99.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAYHSFLVEPISCHAWNKDRTQIAICPNNHEVHIYEKSGAKWNKVHELKEHNGQVTGIDWAPESNRIVTC
          M.YHSFLVEPISCHAWNKDRTQIAICPNNHEVHIYEKS.AKWNKVHELKEHNGQVTGIDWAPESNRIVTC
Retrocopy MTYHSFLVEPISCHAWNKDRTQIAICPNNHEVHIYEKSSAKWNKVHELKEHNGQVTGIDWAPESNRIVTC

Parental  GTDRNAYVWTLKGRTWKPTLVILRINRAARCVRWAPNENKFAVGSGSRVISICYFEQENDWWVCKHIKKP
          GTDRNAYVWTLKGRTWKPTLVILR.NRAARCVRWAP.ENKFA..SGSRVISICYFEQENDWWVCKHIKKP
Retrocopy GTDRNAYVWTLKGRTWKPTLVILRNNRAARCVRWAPSENKFAMVSGSRVISICYFEQENDWWVCKHIKKP

Parental  IRSTVLSLDWHPNNVLLAAGSCDFKCRIFSAYIKEVEERP-APTPWGSKMPFGELMFESSSSCGWVHGVC
          IRSTVLS.DWHPNNVLLAAGSCDF.CRIFSAYIKEVE..P.APTPWGSKMPFGELMFESSSSCGWVH.VC
Retrocopy IRSTVLSPDWHPNNVLLAAGSCDFNCRIFSAYIKEVEKWP<APTPWGSKMPFGELMFESSSSCGWVHCVC

Parental  FSAGGSRVAWVSHDSTVCLVDAEK-KMAVATLASET-LPLLAITFITENSLVAAGHDCFPVLFTYDNAAG
          F.A.GSRVAWVSHDSTVCLVD.EK.KMAVATLASET..PLLAITFITENSLVAAGHDCFPVLFTYDNAAG
Retrocopy FLASGSRVAWVSHDSTVCLVDTEK<KMAVATLASET>VPLLAITFITENSLVAAGHDCFPVLFTYDNAAG

Parental  TLSFGGRLDVPKQNSQRGLTARERFQNLDKKASSEGGAATGAGLDSLHKNSVSQISVLSGGKAKCSQFCT
          TLSFGGRLDVPKQNSQRGLTA.ERFQNLDKK.S.EGGAATGAGLDSLHKNSVSQISVLSGGKAKCSQFCT
Retrocopy TLSFGGRLDVPKQNSQRGLTAQERFQNLDKKGSTEGGAATGAGLDSLHKNSVSQISVLSGGKAKCSQFCT

Parental  TGMDGGMSIWDVKSLESALKDLK
          TGMDGGMSIWDVKSLESALKDLK
Retrocopy TGMDGGMSIWDVKSLESALKDLK

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	0.07 RPM	12.37 RPM
SRP017611_kidney	0.14 RPM	73.97 RPM
SRP017611_liver	0.07 RPM	21.92 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1105 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1105 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1105 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,