RetrogeneDB ID: retro_ocun_197

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 11:51112680..51114036(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000004082
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TUBA1A
• Ensembl ID: ENSOCUG00000027812
• Aliases: None
• Description: tubulin, alpha 1a [Source:HGNC Symbol;Acc:20766]

Sequence

>retro_ocun_197
ATGCGTGAGTGCATCTCCATCCACGTCGGCCAGGCTGGTGTCCAGATCGGCAATGCCTGCTGGGAGCTCTACTGCCTGGA
ACACGGCATCCAGCCCGATGGCCAGATGCCAAGTGACAAGACCATTGGGGGAGGAGACGACTCCTTCAACACCTTCTTCA
GTGAGACGGGCGCTGGCAAGCACGTGCCCAGGGCCGTGTTTGTAGACCTGGAGCCCACGGTCATTGATGAAGTTCGCACC
GGCACCTACCGCCAGCTCTTCCACCCCGAGCAGCTCATCACGGGCAAGGAAGATGCTGCCAATAACTATGCCCGCGGGCA
CTACACCATTGGCAAGGAGATCATTGACCTCGTCCTGGACCGAATTCGCAAGCTGGCTGACCAGTGCACGGGCCTGCAGG
GCTTCTTGGTTTTCCACAGCTTTGGTGGGGGAACTGGTTCTGGGTTCACCTCCCTGCTGATGGAACGCCTCTCTGTCGAT
TACGGCAAGAAGTCCAAGCTGGAGTTCTCCATCTACCCAGCCCCCCAGGTTTCCACAGCTGTGGTGGAGCCCTACAACTC
CATCCTCACCACCCACACCACCCTGGAGCACTCTGATTGTGCCTTCATGGTAGACAACGAGGCCATCTATGACATCTGTC
GTAGAAACCTCGATATCGAGCGCCCCACCTACACTAACCTGAACCGCCTTATTAGCCAGATCGTGTCCTCTATCACGGCT
TCCCTGCGGTTTGACGGAGCCCTGAATGTTGACCTGACAGAATTCCAGACCAACCTGGTGCCCTACCCCCGCATCCACTT
CCCTCTGGCCACATACGCCCCCGTCATCTCTGCTGAGAAAGCCTACCACGAGCAGCTTTCTGTAGCAGAGATCACCAATG
CCTGCTTTGAGCCGGCCAACCAGATGGTGAAATGTGACCCTCGCCACGGTAAATACATGGCTTGCTGCCTGCTGTACCGT
GGCGACGTGGTTCCCAAAGATGTCAATGCTGCCATTGCTACCATCAAGACCAAGCGCAGCATCCAGTTTGTGGATTGGTG
CCCCACTGGCTTCAAGGTTGGCATTAACTACCAGCCTCCCACGGTGGTGCCTAGTGGAGACCTGGCCAAGGTGCAGCGAG
CTGTGTGCATGCTGAGCAACACCACAGCCATTGCTGAGGCCTGGGCTCGCCTGGACCACAAGTTTGACCTGATGTATGCC
AAGCGTGCCTTTGTTCACTGGTACGTGGGGGAGGGCATGGAGGAGGGAGAGTTTTCTGAAGCTCGTGAGGACATGGCTGC
CCTGGAGAAGGATTACGAGGAGGTTGGTGTGGATTCTGTTGAAGGTGAGGGTGAGGAGGAAGGAGAGGAATACTAA

Alignment

ORF - retro_ocun_197 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.33 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDL
          MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDL
Retrocopy MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDL

Parental  EPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHS
          EPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHS
Retrocopy EPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHS

Parental  FGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIY
          FGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIY
Retrocopy FGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIY

Parental  DICRRNLDIERPTYTNLNRLIGQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEK
          DICRRNLDIERPTYTNLNRLI.QIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEK
Retrocopy DICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEK

Parental  AYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTG
          AYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKR.IQFVDWCPTG
Retrocopy AYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTG

Parental  FKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
          FKVGINYQPPTVVP.GDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
Retrocopy FKVGINYQPPTVVPSGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE

Parental  AREDMAALEKDYEEVGVDSVEGEGEEEGEEY
          AREDMAALEKDYEEVGVDSVEGEGEEEGEEY
Retrocopy AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

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	43.87 RPM	513.97 RPM
SRP017611_kidney	10.95 RPM	28.38 RPM
SRP017611_liver	3.78 RPM	7.32 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_197 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_197 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_197 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 21 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 ,
Oryctolagus cuniculus	ENSOCUG00000028032	1 retrocopy	retro_ocun_111,
Pteropus vampyrus	ENSPVAG00000004645	2 retrocopies	retro_pvam_1283, retro_pvam_414,
Rattus norvegicus	ENSRNOG00000004559	3 retrocopies	retro_rnor_1200, retro_rnor_2006, retro_rnor_446,
Vicugna pacos	ENSVPAG00000005749	4 retrocopies	retro_vpac_157, retro_vpac_210, retro_vpac_429, retro_vpac_72,