RetrogeneDB ID: retro_btau_386

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 10:95708526..95709735(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CS
• Ensembl ID: ENSBTAG00000004371
• Aliases: None
• Description: Citrate synthase, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q29RK1]

Sequence

>retro_btau_386
TCACTGGACATGATGTATGGTGGCATGCGAGGCATGAAGGGATTGGTATATGAAACATCAGTTCTTGATCCTGATGAGGG
CATCCGTTTTAGAGGCTACAGCATCCCTGAATGCCAGAAACTGCTGCCAAAGGCTAAAGGGGGCGAAGAACCCTTGCCAG
AGGGCTTATTTTGGCTGCTGGTAACTGGACAAATCCCAACAGAGGAACAGGTATCTTGGCTCTCACAGGAGTGGGCAAAG
AGGGCAGCTCTGCCTTCCCACGTGGTCACCATGCTGGACAACTTTCCCACTAATCTACACCCCATGTCTCAGCTCAGTGC
AGCTGTTACAGCTCTCAACAGTGAAAGTAACTTTGCCCGAGCATATTCAGAGGGTATCAACTGAACCAAGTACTGGGAGT
TGATTTACGAAGACTGTATGGATCTGATCGCAAAGCTTCCTTGTGTTGCGGCAAAGATCTACTGGAACCTGTACCGAGAG
GGCAGCAGTATTGGGGCCATTGACCCTAAGCTGGACTGGTCCCACAATTTCACCAACATGTTAGGCTATACTGACGCTCA
GTTCACGGAGCTCATGCGCTTGTACCTCACCATCCACAGTGACCATGAAGGTGGCAATGTAAGTGCCCACACCAGCCACT
TGGTGGGCAGTGCCCTTTCAGACCCCTGTTTGTCCTTTGCAGCAGCCATGAATGGGCTGGCAGGGCCCCTGCATGGACTG
GCAAATCAGGAAGTGCTTGTTTGGCTGACACAACTTCAGAAGGAAGTTGGCAAAGATGTGTCAGATGAGAAGTTACGAGA
CTACATCTGGAACACACTCAACTCAGGACGGGTTGTCCCGGGCTATGGCCATGCAATACTAAGGAAGACTGATCCACGAT
ATACCTGTCAATGAGAGTTTGCTCTGAAACACCTGCCTCAGGACCCCATGTTTAAGCTGGTTGCTCAGCTGTACAAGATT
GTGCCCAATATCCTCCTAGAGCAGGGCAAGGCAAAGAATCCGTGGCCCATTGTAGATGCTCACAGCGGGGTGCTGTTCCA
GTACTACGGCATGATGGAGATGAATTACTACACAGTCCTGTTTGGGGTATCACGGGCACTAGGTGTATTAGCACAGCTCA
TTTGGAGCCGAGCCCTAGGCTTCCCTCTAGAGAGACCCAAGTCCATGAGCACAGACGGTCTGATGAAGTTTGTGGACTCT
AAGTCAGGG

Alignment

ORF - retro_btau_386 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.02 %
• Parental protein coverage: 86.48 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TVDMMYGGMRGMKGLVYETSVLDPDEGIRFRGYSIPECQKLLPKAKGGEEPLPEGLFWLLVTGQIPTEEQ
          ..DMMYGGMRGMKGLVYETSVLDPDEGIRFRGYSIPECQKLLPKAKGGEEPLPEGLFWLLVTGQIPTEEQ
Retrocopy SLDMMYGGMRGMKGLVYETSVLDPDEGIRFRGYSIPECQKLLPKAKGGEEPLPEGLFWLLVTGQIPTEEQ

Parental  VSWLSQEWAKRAALPSHVVTMLDNFPTNLHPMSQLSAAVTALNSESTFARAYSEGINRTKYWELIYEDSM
          VSWLSQEWAKRAALPSHVVTMLDNFPTNLHPMSQLSAAVTALNSES.FARAYSEGIN.TKYWELIYED.M
Retrocopy VSWLSQEWAKRAALPSHVVTMLDNFPTNLHPMSQLSAAVTALNSESNFARAYSEGIN*TKYWELIYEDCM

Parental  DLIAKLPCVAAKIYRNLYREGSSIGAIDPKLDWSHNFTNMLGYTDAQFTELMRLYLTIHSDHEGGNVSAH
          DLIAKLPCVAAKIY.NLYREGSSIGAIDPKLDWSHNFTNMLGYTDAQFTELMRLYLTIHSDHEGGNVSAH
Retrocopy DLIAKLPCVAAKIYWNLYREGSSIGAIDPKLDWSHNFTNMLGYTDAQFTELMRLYLTIHSDHEGGNVSAH

Parental  TSHLVGSALSDPYLSFAAAMNGLAGPLHGLANQEVLVWLTQLQKEVGKDVSDEKLRDYIWNTLNSGRVVP
          TSHLVGSALSDP.LSFAAAMNGLAGPLHGLANQEVLVWLTQLQKEVGKDVSDEKLRDYIWNTLNSGRVVP
Retrocopy TSHLVGSALSDPCLSFAAAMNGLAGPLHGLANQEVLVWLTQLQKEVGKDVSDEKLRDYIWNTLNSGRVVP

Parental  GYGHAVLRKTDPRYTCQREFALKHLPQDPMFKLVAQLYKIVPNILLEQGKAKNPWPNVDAHSGVLLQYYG
          GYGHA.LRKTDPRYTCQ.EFALKHLPQDPMFKLVAQLYKIVPNILLEQGKAKNPWP.VDAHSGVL.QYYG
Retrocopy GYGHAILRKTDPRYTCQ*EFALKHLPQDPMFKLVAQLYKIVPNILLEQGKAKNPWPIVDAHSGVLFQYYG

Parental  MTEMNYYTVLFGVSRALGVLAQLIWSRALGFPLERPKSMSTDGLMKFVDSKSG
          M.EMNYYTVLFGVSRALGVLAQLIWSRALGFPLERPKSMSTDGLMKFVDSKSG
Retrocopy MMEMNYYTVLFGVSRALGVLAQLIWSRALGFPLERPKSMSTDGLMKFVDSKSG

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
ERP005899_liver	0.00 RPM	21.41 RPM
ERP005899_muscle	0.21 RPM	165.39 RPM
SRP017611_brain	0.14 RPM	97.89 RPM
SRP017611_kidney	0.30 RPM	155.05 RPM
SRP017611_liver	0.00 RPM	24.16 RPM
SRP030211_testis	0.04 RPM	27.08 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_386 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_386 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_386 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,