RetrogeneDB ID: retro_btau_509

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 13:18011797..18012276(+)
• Located in intron of: ENSBTAG00000016445

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM96A
• Ensembl ID: ENSBTAG00000002012
• Aliases: None
• Description: MIP18 family protein FAM96A precursor [Source:RefSeq peptide;Acc:NP_001030282]

Sequence

>retro_btau_509
ATGGGGCAAGTGTCCGGACTGCTCTCCTGGACACTGAGCAGAGTCCTGTAGCTCTCAGATCTCTCTGAGTGGGGAGCTGA
CCAGCAACCCCGCATCATGGAAGAGAAAAGAGCTAGAAGTTTATGACCTGATTCAAACTTTCTGGGACCCAGAGAAGCCC
AATACTTTAGAAGAAATGGAAGTGGTAACAGAAAGTTGTGTGGAGGTTCAAGAGATAAATGAAGACGACTATTTGGTCAT
TATAAGGTTCACACCAACAGTACCTCATGCCTCTTCAGCAACTCTTATTGGGCTGTGCTTAAGAGTAAAACTTCAACGGT
GTTTACCATTTAAATATATGTTGGAAATCTAAATTTCTGACGGAAACCACTCAACAGAGGAAGTTATGAACAAACAGATA
AATGACAAAGAGCTAGTGGCGGCTGCAATGGAGAAACCCAACTTAATGGGAAATCGTGAAACAGTGTCTCCTTGCCCCT

Alignment

ORF - retro_btau_509 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.37 %
• Parental protein coverage: 99.38 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MERVSGLLSWTLSRFLWLSGLSERGAARQPRIMEEKA-LEVYDLIRTIRDPEKPNTLEELEVVTESCVEV
          M..VSGLLSWTLSR.L.LS.LSE.GA..QPRIMEEK..LEVYDLI.T..DPEKPNTLEE.EVVTESCVEV
Retrocopy MGQVSGLLSWTLSRVL*LSDLSEWGADQQPRIMEEKR>LEVYDLIQTFWDPEKPNTLEEMEVVTESCVEV

Parental  QEINEDDYLVIIRFTPTVPHCSLATLIGLCLRVKLQRCLPFKHKLEIYISEGTHSTEEDINKQINDKERV
          QEINEDDYLVIIRFTPTVPH.S.ATLIGLCLRVKLQRCLPFK..LEI.IS.G.HSTEE..NKQINDKE.V
Retrocopy QEINEDDYLVIIRFTPTVPHASSATLIGLCLRVKLQRCLPFKYMLEI*ISDGNHSTEEVMNKQINDKELV

Parental  AAAMENPNLR-EIVEQCVLEP
          AAAME.PNL..EIV.QC.L.P
Retrocopy AAAMEKPNLM>EIVKQCLLAP

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	77.21 RPM
ERP005899_muscle	0.00 RPM	38.17 RPM
SRP017611_brain	0.00 RPM	14.25 RPM
SRP017611_kidney	0.06 RPM	104.61 RPM
SRP017611_liver	0.00 RPM	29.07 RPM
SRP030211_testis	0.21 RPM	18.43 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_509 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_509 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_509 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002448	1 retrocopy	retro_amel_1707,
Bos taurus	ENSBTAG00000002012	2 retrocopies	retro_btau_509 , retro_btau_984,
Bos taurus	ENSBTAG00000013931	1 retrocopy	retro_btau_609,
Canis familiaris	ENSCAFG00000017035	2 retrocopies	retro_cfam_1450, retro_cfam_439,
Callithrix jacchus	ENSCJAG00000004834	1 retrocopy	retro_cjac_1751,
Equus caballus	ENSECAG00000010303	1 retrocopy	retro_ecab_364,
Erinaceus europaeus	ENSEEUG00000000854	1 retrocopy	retro_eeur_323,
Felis catus	ENSFCAG00000004178	1 retrocopy	retro_fcat_1379,
Homo sapiens	ENSG00000166797	2 retrocopies	retro_hsap_2763, retro_hsap_522,
Gorilla gorilla	ENSGGOG00000016550	2 retrocopies	retro_ggor_1921, retro_ggor_481,
Loxodonta africana	ENSLAFG00000011114	1 retrocopy	retro_lafr_758,
Macropus eugenii	ENSMEUG00000005979	2 retrocopies	retro_meug_471, retro_meug_85,
Microcebus murinus	ENSMICG00000011072	1 retrocopy	retro_mmur_233,
Myotis lucifugus	ENSMLUG00000028233	2 retrocopies	retro_mluc_578, retro_mluc_893,
Mustela putorius furo	ENSMPUG00000000605	1 retrocopy	retro_mputfur_722,
Mus musculus	ENSMUSG00000032381	1 retrocopy	retro_mmus_1919,
Nomascus leucogenys	ENSNLEG00000026932	3 retrocopies	retro_nleu_156, retro_nleu_2577, retro_nleu_667,
Ochotona princeps	ENSOPRG00000015229	5 retrocopies	retro_opri_476, retro_opri_522, retro_opri_828, retro_opri_84, retro_opri_999,
Pongo abelii	ENSPPYG00000006544	1 retrocopy	retro_pabe_224,
Pan troglodytes	ENSPTRG00000007153	2 retrocopies	retro_ptro_1870, retro_ptro_390,
Sorex araneus	ENSSARG00000002068	3 retrocopies	retro_sara_54, retro_sara_597, retro_sara_742,
Tarsius syrichta	ENSTSYG00000004186	2 retrocopies	retro_tsyr_195, retro_tsyr_62,