RetrogeneDB ID: retro_ocun_1183

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 3:12774040..12774856(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000021100
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CS
• Ensembl ID: ENSOCUG00000007216
• Aliases: None
• Description: Citrate synthase [Source:UniProtKB/TrEMBL;Acc:G1SSK8]

Sequence

>retro_ocun_1183
CGGCTCTTGGGAGCCAAGAATTCATCCTGTCTTGTTCTTGCTGCCCGACATGCTAGTGCTTCTTCCACGAATTTGAAAGA
TGTGTTGGCTGACCTGATCCCTAAGGAGCAGGCCAGAATTAAGACCTTCAGGCAGCAACATGGCAAGACAGTGGTGGGCC
AAATCACTGTGGACATGATGTATGGTGGCATGAGAGGCATGAAGGGACTGGTATATGAAACTTCAGTTCTTGATCCTGAT
GAGGGCATTCGTTTCCGAGGTCATAGTATCCCTGAATGCCAGAAACTGCTGCCCAAGGCTAAGGGTGGGGAAGAACCCCT
GCCTGAGGGCTTATTTTGGCTGCTGGTAACCGGACAGATCCCAACAGAGGAACAGGTTTCTTGGCTTTCAAAAGAGTGGG
CAAAGAGGGCAGCCCTGCCTTCTCATGTGGTCACCATGCTGGACAACTTTCCCACCAACCTACACCCCATGTCTCAGCTC
AGTGCAGCCATTACAGCACTCAACAGTGAAAGTACCTTTGCCCGAGCATATGCAGAGGGTATCAACCGAGCCAAGTACTG
GGAGTTGATTTATGAAGACTTTATGAATCTGATCACAAAGCTACCTTGTGTTGCCGCAAAGATCTACCGAAATCTCTACC
GGGAAGGAAGCAGTATTGGAGCCATTGACTCCAAACTGGACTGGTCCCACAATTTCACCAACATGTTAGGTTATACTGAT
GCTCAGTTCACTGAGCTGATGCGCTTGTACCTCACCATCCACAGTGACCATGAGGGTGGCAATGTAAGTGCCCATACTAG
CCACTTGGTAGGCAGT

Alignment

ORF - retro_ocun_1183 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.79 %
• Parental protein coverage: 58.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RLVKLQNSSCLVLAARHASASSTNLKDVLADLIPKEQARIKTFRQQHGKTVVGQITVDMMYGGMRGMKGL
          RL....NSSCLVLAARHASASSTNLKDVLADLIPKEQARIKTFRQQHGKTVVGQITVDMMYGGMRGMKGL
Retrocopy RLLGAKNSSCLVLAARHASASSTNLKDVLADLIPKEQARIKTFRQQHGKTVVGQITVDMMYGGMRGMKGL

Parental  VYETSVLDPDEGIRFRGHSIPECQKLLPKAKGGEEPLPEGLFWLLVTGQIPTEEQVSWLSKEWAKRAALP
          VYETSVLDPDEGIRFRGHSIPECQKLLPKAKGGEEPLPEGLFWLLVTGQIPTEEQVSWLSKEWAKRAALP
Retrocopy VYETSVLDPDEGIRFRGHSIPECQKLLPKAKGGEEPLPEGLFWLLVTGQIPTEEQVSWLSKEWAKRAALP

Parental  SHVVTMLDNFPTNLHPMSQLSAAITALNSESTFARAYAEGINRAKYWELIYEDSMNLIAKLPCVAAKIYR
          SHVVTMLDNFPTNLHPMSQLSAAITALNSESTFARAYAEGINRAKYWELIYED.MNLI.KLPCVAAKIYR
Retrocopy SHVVTMLDNFPTNLHPMSQLSAAITALNSESTFARAYAEGINRAKYWELIYEDFMNLITKLPCVAAKIYR

Parental  NLYREGSSIGAIDSKLDWSHNFTNMLGYTDAQFTELMRLYLTIHSDHEGGNVSAHTSHLVGS
          NLYREGSSIGAIDSKLDWSHNFTNMLGYTDAQFTELMRLYLTIHSDHEGGNVSAHTSHLVGS
Retrocopy NLYREGSSIGAIDSKLDWSHNFTNMLGYTDAQFTELMRLYLTIHSDHEGGNVSAHTSHLVGS

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	7.73 RPM	117.39 RPM
SRP017611_kidney	12.37 RPM	194.91 RPM
SRP017611_liver	1.46 RPM	28.90 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1183 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1183 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1183 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004371	1 retrocopy	retro_btau_386,
Canis familiaris	ENSCAFG00000000115	1 retrocopy	retro_cfam_765,
Choloepus hoffmanni	ENSCHOG00000000397	1 retrocopy	retro_chof_1803,
Callithrix jacchus	ENSCJAG00000011275	1 retrocopy	retro_cjac_2031,
Dasypus novemcinctus	ENSDNOG00000010907	2 retrocopies	retro_dnov_205, retro_dnov_468,
Echinops telfairi	ENSETEG00000012035	1 retrocopy	retro_etel_584,
Homo sapiens	ENSG00000062485	2 retrocopies	retro_hsap_1972, retro_hsap_3621,
Gorilla gorilla	ENSGGOG00000009096	2 retrocopies	retro_ggor_1432, retro_ggor_2445,
Macropus eugenii	ENSMEUG00000005657	2 retrocopies	retro_meug_1078, retro_meug_1304,
Microcebus murinus	ENSMICG00000017659	2 retrocopies	retro_mmur_1322, retro_mmur_394,
Macaca mulatta	ENSMMUG00000002483	2 retrocopies	retro_mmul_1502, retro_mmul_1840,
Mus musculus	ENSMUSG00000005683	1 retrocopy	retro_mmus_258,
Nomascus leucogenys	ENSNLEG00000017514	2 retrocopies	retro_nleu_1201, retro_nleu_809,
Oryctolagus cuniculus	ENSOCUG00000007216	1 retrocopy	retro_ocun_1183 ,
Pongo abelii	ENSPPYG00000004654	1 retrocopy	retro_pabe_2972,
Rattus norvegicus	ENSRNOG00000023520	1 retrocopy	retro_rnor_2518,
Sorex araneus	ENSSARG00000010093	2 retrocopies	retro_sara_360, retro_sara_628,
Sus scrofa	ENSSSCG00000021091	1 retrocopy	retro_sscr_321,
Sus scrofa	ENSSSCG00000022858	1 retrocopy	retro_sscr_322,
Tupaia belangeri	ENSTBEG00000006425	1 retrocopy	retro_tbel_4652,
Tarsius syrichta	ENSTSYG00000004483	1 retrocopy	retro_tsyr_1659,