RetrogeneDB ID: retro_rnor_1193

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 16:49869142..49870218(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tuba1c
• Ensembl ID: ENSRNOG00000015544
• Aliases: None
• Description: Tubulin alpha-1C chain [Source:UniProtKB/Swiss-Prot;Acc:Q6AYZ1]

Sequence

>retro_rnor_1193
ATGTGTGAACGCATCTCTATCCACGTTGGCCAGGCTCGTGTCCAGATTGGCAATGCCTGCTGGGAGCTCTACTGCCTGGA
ACGTGGCATCCAGCCTGATGGGCAGAGGCCACGCGTCAAAACCACTGGGGGAGGAGAGGACTCATTCAACACCTTCTTCA
GTGAGACAGGAGCTGGCAAGCACGTGACCCAGGTTCATAGACCTGGAACCCACAGTTATTGATAAAGTTCGCACTGGCAC
CTACTGCCAGCTCTTCCACCCCGAGCAGCTCCTCACAGGCAAGGAAGATGCTGCCAAGAACTATGCCTGTGACCACTACA
CCATTGGCAAGGAGATCATTGACCTTGTCTTGGACAGAATTTGAAAGCTGGCTGACCAGTGCACAGGTCTCCAGGGCTTC
TTGGTTTTCCACAGCTTTGGTGGGGGAACTGACTCTGGGTTCACTTCCCCGCTAATGAAGTGTCTCTCTGTTGATTATGG
AAAGAAATGCAAGCTGGAGTTCTCCATTTACCCAGTCCCCCAAGTTTTCACTGCTGTGGTTGAGCCCTACAATTCATCCT
TACATCCAAAATACCCTGGATCACTCTGATTATGCCTTCTTGATAGACAATGAAGCCATCTATGACATCTGTCGTAGAAA
CATCAACATTGAGTGCCCAACTTACACTAACCTTTACCACCTTCTTAGCCATATTGTATCTTCCACCACTGCTTCCCTTA
GATTTGATGAGACCTTGAATGTTGATCTGACAGAATTCTAGACCAACCTGGTGCCCTACCCTCGCATCCACTTCCCTCTG
GCCACTTATGCCTTTGCCATCTCTGCTGAGAAAGCCTACCATGAACAGTTTTCTGTAGCAGAGATCACTAATGCCTACTT
TGAGCCAGCCAACCAGATGGTGAAATGTGACCCTCACCAGGGTAAACACATTGCTTGCTGCCCACTTGGTGATATGGTTC
CCAAGGATGTCAGTGCTGCCATTGCCACCATCAAGACCAAGTGAAGCATCCAGTTTATGGACTGGTGTCCCACTGGCTTC
AAGGTTGGCATTAATTACCAGTCCCACCTGGTGATG

Alignment

ORF - retro_rnor_1193 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.42 %
• Parental protein coverage: 80.85 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHV-PRAVFVD
          M.E.ISIHVGQA.VQIGNACWELYCLE.GIQPDGQ.P..KT.GGG.DSFNTFFSETGAGKHV.PR..F.D
Retrocopy MCERISIHVGQARVQIGNACWELYCLERGIQPDGQRPRVKTTGGGEDSFNTFFSETGAGKHV>PR--FID

Parental  LEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFH
          LEPTVID.VRTGTY.QLFHPEQL.TGKEDAA.NYA..HYTIGKEIIDLVLDRI.KLADQCTGLQGFLVFH
Retrocopy LEPTVIDKVRTGTYCQLFHPEQLLTGKEDAAKNYACDHYTIGKEIIDLVLDRI*KLADQCTGLQGFLVFH

Parental  SFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNS-ILTT-HTTLEHSDCAFMVDNE
          SFGGGT.SGFTS.LM..LSVDYGKK.KLEFSIYP.PQV.TAVVEPYNS.ILT....TL.HSD.AF..DNE
Retrocopy SFGGGTDSGFTSPLMKCLSVDYGKKCKLEFSIYPVPQVFTAVVEPYNS<ILTS<QNTLDHSDYAFLIDNE

Parental  AIYDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVIS
          AIYDICRRN..IE.PTYTNL..L.S.IVSS.TASLRFD..LNVDLTEF.TNLVPYPRIHFPLATYA..IS
Retrocopy AIYDICRRNINIECPTYTNLYHLLSHIVSSTTASLRFDETLNVDLTEF*TNLVPYPRIHFPLATYAFAIS

Parental  AEKAYHEQLTVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWC
          AEKAYHEQ..VAEITNA.FEPANQMVKCDP..GK..ACC.L..GD.VPKDV.AAIATIKTK..IQF.DWC
Retrocopy AEKAYHEQFSVAEITNAYFEPANQMVKCDPHQGKHIACCPL--GDMVPKDVSAAIATIKTK*SIQFMDWC

Parental  PTGFKVGINYQPPTVV
          PTGFKVGINYQ...V.
Retrocopy PTGFKVGINYQSHLVM

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	29.84 RPM
SRP017611_kidney	0.00 RPM	78.51 RPM
SRP017611_liver	0.00 RPM	32.81 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1193 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1193 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1193 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000039992	1 retrocopy	retro_btau_840,
Choloepus hoffmanni	ENSCHOG00000008444	2 retrocopies	retro_chof_179, retro_chof_360,
Equus caballus	ENSECAG00000009504	1 retrocopy	retro_ecab_1041,
Felis catus	ENSFCAG00000024852	1 retrocopy	retro_fcat_361,
Felis catus	ENSFCAG00000028689	3 retrocopies	retro_fcat_1802, retro_fcat_254, retro_fcat_798,
Macropus eugenii	ENSMEUG00000010779	2 retrocopies	retro_meug_1648, retro_meug_2174,
Mus musculus	ENSMUSG00000043091	1 retrocopy	retro_mmus_843,
Oryctolagus cuniculus	ENSOCUG00000028032	1 retrocopy	retro_ocun_111,
Otolemur garnettii	ENSOGAG00000009435	1 retrocopy	retro_ogar_240,
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,