RetrogeneDB ID: retro_ocun_132

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 17:69007918..69008446(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000001692
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000023198
• Aliases: None
• Description: None

Sequence

>retro_ocun_132
ATGGGGAAGGTGCTATCCAAAATCTTCGGGAACAAGGAAATGCGGATCCTCATGTTGGGCCTGGACGCGGCCGGCAAGAC
CACAATCCTGTACAAGTTGAAGCTGGGCCAGTCGGTGACCACCATCCCCACCGTGGGCTTCAACGTGGAGACGGTGACTT
ACAAAAACGTCAAGTTCAACGTGTGGGATGTGGGAGGCCAGGACAAGATCCGGCCGCTCTGGCGGCACTACTACACCGGG
ACCCAGGGTCTGATCTTCGTGGTGGACTGCGCCGACCGCGACCGCATCGACGAGGCCCGCCAGGAGCTGCACCGCATTAT
CAATGACCGGGAGATGAGGGACGCCATAATCCTCATCTTCGCCAACAAGCAGGACCTGCCCGATGCCATGAAACCCCATG
AGATCCAGGAGAAACTGGGCCTGACCCGGATTCGGGACAGGAACTGGTATGTGCAGCCCTCCTGTGCCACCTCAGGGGAC
GGACTCTATGAGGGGCTCACATGGTTAACCTCTAACTACAAGTCCTAA

Alignment

ORF - retro_ocun_132 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.79 %
• Parental protein coverage: 95.58 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KLFKSLFGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRP
          K.....FG.KEMRILM.GLDAAGKTTILYKLKLG..VTTIPT.GFNVETV.YKN..F.VWDVGGQDKIRP
Retrocopy KVLSKIFGNKEMRILMLGLDAAGKTTILYKLKLGQSVTTIPTVGFNVETVTYKNVKFNVWDVGGQDKIRP

Parental  LWRHYFQNTQGLIFVVDSNDRERVNEAREELTRMLAEDELRDAVLLVFVNKQDLPNAMNAAEITDKLGLH
          LWRHY...TQGLIFVVD..DR.R..EAR.EL.R.....E.RDA..L.F.NKQDLP.AM...EI..KLGL.
Retrocopy LWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFANKQDLPDAMKPHEIQEKLGLT

Parental  SLRQRSWYIQATCATSGDGLYEGLDWLSNQLKN
          ..R.R.WY.Q..CATSGDGLYEGL.WL....K.
Retrocopy RIRDRNWYVQPSCATSGDGLYEGLTWLTSNYKS

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	15.34 RPM	11.37 RPM
SRP017611_kidney	34.56 RPM	5.47 RPM
SRP017611_liver	15.03 RPM	1.08 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_132 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_132 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_132 has 12 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_36
Pan troglodytes	retro_ptro_5
Gorilla gorilla	retro_ggor_161
Pongo abelii	retro_pabe_126
Macaca mulatta	retro_mmul_174
Callithrix jacchus	retro_cjac_300
Mus musculus	retro_mmus_147
Rattus norvegicus	retro_rnor_272
Bos taurus	retro_btau_26
Sus scrofa	retro_sscr_82
Canis familiaris	retro_cfam_119
Equus caballus	retro_ecab_106

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004184	1 retrocopy	retro_amel_1639,
Bos taurus	ENSBTAG00000006785	1 retrocopy	retro_btau_26,
Ciona savignyi	ENSCSAVG00000007011	1 retrocopy	retro_csav_2,
Equus caballus	ENSECAG00000009563	1 retrocopy	retro_ecab_106,
Latimeria chalumnae	ENSLACG00000019009	1 retrocopy	retro_lcha_10,
Mus musculus	ENSMUSG00000062421	1 retrocopy	retro_mmus_2056,
Oryctolagus cuniculus	ENSOCUG00000000824	4 retrocopies	retro_ocun_1007, retro_ocun_1502, retro_ocun_1868, retro_ocun_987,
Oryctolagus cuniculus	ENSOCUG00000014090	2 retrocopies	retro_ocun_1942, retro_ocun_751,
Oryctolagus cuniculus	ENSOCUG00000023009	1 retrocopy	retro_ocun_1404,
Oryctolagus cuniculus	ENSOCUG00000023198	1 retrocopy	retro_ocun_132 ,
Oryctolagus cuniculus	ENSOCUG00000023645	2 retrocopies	retro_ocun_1137, retro_ocun_247,
Otolemur garnettii	ENSOGAG00000002503	1 retrocopy	retro_ogar_263,
Ictidomys tridecemlineatus	ENSSTOG00000019768	1 retrocopy	retro_itri_883,
Tetraodon nigroviridis	ENSTNIG00000011685	1 retrocopy	retro_tnig_19,