RetrogeneDB ID: retro_rnor_2006

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:210393502..210394854(+)
• Located in intron of: ENSRNOG00000008157

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tuba1a
• Ensembl ID: ENSRNOG00000004559
• Aliases: Tuba1a, Tuba1
• Description: Tubulin alpha-1A chain [Source:UniProtKB/Swiss-Prot;Acc:P68370]

Sequence

>retro_rnor_2006
ATGCGTGAGTGCATCTCCATCCACGCTGGCCAGGCTGGTGTCCAGACCGGCAATGCCTGCTGGGAGCTCTACTGCCTGGA
ACATGGCATCCAGCCTGATGGCCAGATGCCAAGCGACAAGACCATTGGGGGAGGAGATGACTCCTTCAACACCTTCTTCA
GTGAGACAGGAGCTGGCAAGCACGTGCTCCGGGCAGTGTTCGTAGACTGAACCCACAGTTATTGATGAAGTTCGCACTGG
CACCTACTGCCAGCTCTTCCACCCTGAGTAGCTCATCACAGGCAAGGAAGATGCTGCCAATAACTATGCCTGTGGCCACT
ACACCATTGGCAAGGAGATCATTGACCTTATCTTGGACAGAATTCGCAAGCTGGCTGACCAGTGCACGGGTCTCCAGGGC
TTCTTGGTTTTCCACAGCTTTGGAGGGGGAACTGGCTCTGGGTTCACCTCCCTGCTGATGGAGCGGCTCTCTGTCGATTA
CGGAAAGAAGTCCAAGCTGGAGTTCTCCATTTACCCAACCCGCCCAGGTTTCCACTGCTGTAGTTGAGTCCTACAATTCC
ATCCTCACCACCCACACCACCCTGGAGCACTCTGATTGTGCCTTCATGGTAGACAATGAGGCCATCTATGACATCTGTCG
TAGAAACCTCGACATTGAGCGCCCAACCTACACTAACTTTAACCGCCTTATTAGCCAGATTGTGTCTTCCATCACTGCTC
CCCTCAGATTTGATGGGGCCCTGAATGTTGATCTGACAGAATTCCAGACCAACCTGGTGCCCTACCCTCGCATCCACTTC
CCTCTGGCCACTTATGCCCCTGTCATCTTTGCTGAGAAAGCCTACCATGAGCAGCTTTCTGTAGCAGAGATCACCAATGC
CTGCTTTGAGCCAGCCAACCAGATGGTGAAATGTGACCCTCACCATGGTAAATACATGGCTTGCTGCCTGCTGTACCGTG
GTGATGTGGTCCCCAAAGATGTCAATGCTGCCATTGCCACCATCAAGACCAAGCGCAGCATCCAGTTTGTGGACTGGTGC
CCCACTGGCTTCAAGGTTGGCATTAATTACCAGCCTCCCACTGTGGTACTTGGTGGCGACCTGGCCAAGGTCCAGAGAGC
TGTGTGTATGCTGAGCAACACCACAGCCATTGCTAAGGCCTGGGCTCGCCTGGATCGCAAGTTTGATATGATGTATGCCA
AGCGTGCCTTTGTGCACTGGTACGTGGGTGAGGGCATGGAGGAGGGAGAGTTCTCTGAGGCCCGTGAGGACATGGCTGCC
CTAGAGAAGGATTATGAGGAGGTTGGTGTGGATTCTGTGGAGGGTGAGGGTGAGGAAGAAGGAGAGGAATAC

Alignment

ORF - retro_rnor_2006 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.71 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVD-
          MRECISIH.GQAGVQ.GNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHV.RAVFVD.
Retrocopy MRECISIHAGQAGVQTGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVLRAVFVD<

Parental  LEP-TVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVF
          L.P.TVIDEVRTGTY.QLFHPE.LITGKEDAANNYA.GHYTIGKEIIDL.LDRIRKLADQCTGLQGFLVF
Retrocopy LNP<TVIDEVRTGTYCQLFHPE*LITGKEDAANNYACGHYTIGKEIIDLILDRIRKLADQCTGLQGFLVF

Parental  HSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPA-PQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNE
          HSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYP...QVSTAVVE.YNSILTTHTTLEHSDCAFMVDNE
Retrocopy HSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPT>AQVSTAVVESYNSILTTHTTLEHSDCAFMVDNE

Parental  AIYDICRRNLDIERPTYTNLNRLIGQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVIS
          AIYDICRRNLDIERPTYTN.NRLI.QIVSSITA.LRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVI.
Retrocopy AIYDICRRNLDIERPTYTNFNRLISQIVSSITAPLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVIF

Parental  AEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWC
          AEKAYHEQLSVAEITNACFEPANQMVKCDP.HGKYMACCLLYRGDVVPKDVNAAIATIKTKR.IQFVDWC
Retrocopy AEKAYHEQLSVAEITNACFEPANQMVKCDPHHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWC

Parental  PTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGE
          PTGFKVGINYQPPTVV.GGDLAKVQRAVCMLSNTTAIA.AWARLD.KFD.MYAKRAFVHWYVGEGMEEGE
Retrocopy PTGFKVGINYQPPTVVLGGDLAKVQRAVCMLSNTTAIAKAWARLDRKFDMMYAKRAFVHWYVGEGMEEGE

Parental  FSEAREDMAALEKDYEEVGVDSVEGEGEEEGEEY
          FSEAREDMAALEKDYEEVGVDSVEGEGEEEGEEY
Retrocopy FSEAREDMAALEKDYEEVGVDSVEGEGEEEGEEY

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	3.45 RPM	701.13 RPM
SRP017611_kidney	0.91 RPM	71.46 RPM
SRP017611_liver	0.34 RPM	17.82 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2006 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2006 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2006 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001489	3 retrocopies	retro_btau_251, retro_btau_350, retro_btau_929,
Callithrix jacchus	ENSCJAG00000020894	2 retrocopies	retro_cjac_1209, retro_cjac_3157,
Dasypus novemcinctus	ENSDNOG00000004121	1 retrocopy	retro_dnov_43,
Equus caballus	ENSECAG00000013798	1 retrocopy	retro_ecab_223,
Homo sapiens	ENSG00000167552	1 retrocopy	retro_hsap_3313,
Nomascus leucogenys	ENSNLEG00000017836	2 retrocopies	retro_nleu_245, retro_nleu_2757,
Oryctolagus cuniculus	ENSOCUG00000027812	1 retrocopy	retro_ocun_197,
Pteropus vampyrus	ENSPVAG00000004645	2 retrocopies	retro_pvam_1283, retro_pvam_414,
Rattus norvegicus	ENSRNOG00000003597	1 retrocopy	retro_rnor_2819,
Rattus norvegicus	ENSRNOG00000004559	3 retrocopies	retro_rnor_1200, retro_rnor_2006 , retro_rnor_446,
Rattus norvegicus	ENSRNOG00000015544	3 retrocopies	retro_rnor_1193, retro_rnor_2260, retro_rnor_960,
Vicugna pacos	ENSVPAG00000005749	4 retrocopies	retro_vpac_157, retro_vpac_210, retro_vpac_429, retro_vpac_72,