RetrogeneDB ID: retro_ocun_8

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:116168529..116169273(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000007222
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TPM3
• Ensembl ID: ENSOCUG00000011821
• Aliases: None
• Description: tropomyosin 3 [Source:HGNC Symbol;Acc:12012]

Sequence

>retro_ocun_8
ATGGCCGGGATCACCACCATCGAGGCGGTGAAGCGCAAGATCCAGGTTCTGCAGCAGCAGGCGGATGATGCAGAGGAGAG
GGCGGAGCGCCTTCAGCGGGAGGTGGAGGGGGAAAGGCGGGCCCGAGAGCAGGCTGAGGCTGAGGTGGCTTCCTTGAACC
GCAGGATCCAGTTGGTGGAAGAGGAGCTGGATCGTGCTCAGGAGCGCCTGGCCACTGCCCTGCAAAAGTTGGAAGAAGCA
GAAAAAGCTGCTGATGAGAGTGAGAGAGGTATGAAGGTTATTGAAAACCGGGCCTTAAAAGATGAAGAAAAGATGGAACT
CCAGGAAATCCAACTCAAAGAAGCTAAGCACATTGCAGAAGAGGCAGACAGGAAGTATGAAGAGGTGGCTCGTAAATTGG
TGATTATTGAAGGAGACTTGGAACGCACAGAGGAACGAGCTGAACTGGCAGAGTCCCGTTGCCGAGAGATGGATGAGCAG
ATCAGACTGATGGACCAGAACCTGAAGTGTCTGAGTGCTGCTGAGGAAAAGTACTCTCAAAAAGAGGACAAATATGAGGA
AGAAATAAAGATTCTCACCGATAAACTCAAGGAGGCGGAGACCCGTGCTGAATTTGCTGAGAGATCGGTAGCCAAGCTGG
AAAAGACAATTGATTTGGAAGATAAACTGAAATGCACCAAAGAGGAGCACCTCTGTACACAAAGGATGCTGGACCAGACT
CTGCTTGACCTGAACGAGATGTAG

Alignment

ORF - retro_ocun_8 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.49 %
• Parental protein coverage: 85.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LAAMQKKLKGTEDELDKYSEALKDAQEKLELAEKKAADAEGEVASLNRR-QLVEEELDRAQERLATALQK
          ..A...K........D...E.....Q...E........AE.EVASLNRR.QLVEEELDRAQERLATALQK
Retrocopy IEAVKRKIQVLQQQADDAEERAERLQREVEGERRAREQAEAEVASLNRRIQLVEEELDRAQERLATALQK

Parental  LEEAEKAADESERGMKVIENRALKDEEKMELQEIQLKEAKHIAEEADRKYEEVARKLVIIEGDLERTEER
          LEEAEKAADESERGMKVIENRALKDEEKMELQEIQLKEAKHIAEEADRKYEEVARKLVIIEGDLERTEER
Retrocopy LEEAEKAADESERGMKVIENRALKDEEKMELQEIQLKEAKHIAEEADRKYEEVARKLVIIEGDLERTEER

Parental  AELAESKCSELEEELKNVTNNLKSLEAQAEKYSQKEDKYEEEIKILTDKLKEAETRAEFAERSVAKLEKT
          AELAES.C.E..E.......NLK.L.A..EKYSQKEDKYEEEIKILTDKLKEAETRAEFAERSVAKLEKT
Retrocopy AELAESRCREMDEQIRLMDQNLKCLSAAEEKYSQKEDKYEEEIKILTDKLKEAETRAEFAERSVAKLEKT

Parental  IDDLEDELYAQKLKYKAISEELDHALNDMTSM
          I.DLED.L...K.........LD..L.D...M
Retrocopy I-DLEDKLKCTKEEHLCTQRMLDQTLLDLNEM

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	13.58 RPM	33.61 RPM
SRP017611_kidney	19.36 RPM	17.53 RPM
SRP017611_liver	8.56 RPM	8.79 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_8 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_8 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_8 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011877	2 retrocopies	retro_amel_1017, retro_amel_1212,
Bos taurus	ENSBTAG00000033217	3 retrocopies	retro_btau_1166, retro_btau_210, retro_btau_933,
Canis familiaris	ENSCAFG00000017311	4 retrocopies	retro_cfam_1278, retro_cfam_1678, retro_cfam_2089, retro_cfam_983,
Cavia porcellus	ENSCPOG00000007279	1 retrocopy	retro_cpor_150,
Dasypus novemcinctus	ENSDNOG00000019156	7 retrocopies	retro_dnov_1322, retro_dnov_1767, retro_dnov_329, retro_dnov_451, retro_dnov_848, retro_dnov_878, retro_dnov_944,
Equus caballus	ENSECAG00000010942	1 retrocopy	retro_ecab_390,
Felis catus	ENSFCAG00000012596	1 retrocopy	retro_fcat_1441,
Homo sapiens	ENSG00000143549	9 retrocopies	retro_hsap_1482, retro_hsap_1639, retro_hsap_2001, retro_hsap_2011, retro_hsap_2012, retro_hsap_2237, retro_hsap_2395, retro_hsap_3711, retro_hsap_3893,
Myotis lucifugus	ENSMLUG00000013331	1 retrocopy	retro_mluc_1038,
Macaca mulatta	ENSMMUG00000010805	10 retrocopies	retro_mmul_1019, retro_mmul_1240, retro_mmul_1384, retro_mmul_1385, retro_mmul_1703, retro_mmul_1829, retro_mmul_2128, retro_mmul_2354, retro_mmul_314, retro_mmul_880,
Mustela putorius furo	ENSMPUG00000007875	1 retrocopy	retro_mputfur_604,
Mus musculus	ENSMUSG00000027940	1 retrocopy	retro_mmus_21,
Oryctolagus cuniculus	ENSOCUG00000009884	1 retrocopy	retro_ocun_1652,
Oryctolagus cuniculus	ENSOCUG00000011821	2 retrocopies	retro_ocun_699, retro_ocun_8 ,