RetrogeneDB ID: retro_btau_1332

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 4:95536876..95537282(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJC8
• Ensembl ID: ENSBTAG00000018385
• Aliases: None
• Description: None

Sequence

>retro_btau_1332
AAGAGGTTTCGGCAACTATCCATACTGGTGTATCCTGACAAAACTCAAGATGCTGCCGACAGAGCACAAAAGGCTTCTGA
AGCCGTGGACAAAGCTTACAAGCTGCTACCGGGTCAGGAACAAAAGCAGAGGCCCTGGATGCAATTCAGGCAGGAAAAGA
AGCTGTGGAACACACCGTGAAAGAGCGAAAAAAGCAATTAAACAAGGAAGGCAGGCCTACAAATGTGGAGGAGGATGACC
CTGAGCTGTTCAAACAAGCAACATACAAACAGACCATGAAACTCTCTGCTGAGCTGTAAATTAAAAGACAGAGAGAGCCA
TGAAAGGAAGCGACAAGGGGAGGAAGAGACTGAAGTTCAAGCAAAAACCAAAGGAGAAAGGGAGTAGCAGAAAATTTTTT
AGCAAA

Alignment

ORF - retro_btau_1332 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.84 %
• Parental protein coverage: 52.11 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KRFRQLSILVHPDKNQDDADRAQKAFEAVDKAYKLLLDQEQKKR-ALDVIQAGKEYVEHTVKERKKQLKK
          KRFRQLSILV.PDK.QD.ADRAQKA.EAVDKAYKLL..QEQK.R.ALD.IQAGKE.VEHTVKERKKQL.K
Retrocopy KRFRQLSILVYPDKTQDAADRAQKASEAVDKAYKLLPGQEQKQR<ALDAIQAGKEAVEHTVKERKKQLNK

Parental  EGKPTNVEEDDPELFKQAVYKQTMKLFAELEIKRK-EREAKEMHERKRQREEEIEAQEKAKREREWQK
          EG.PTNVEEDDPELFKQA.YKQTMKL.AEL.IKR..ER..K................EK........K
Retrocopy EGRPTNVEEDDPELFKQATYKQTMKLSAEL*IKRQ<ERAMKGSDKGRKRLKFKQKPKEKGSSRKFFSK

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	14.49 RPM
ERP005899_muscle	0.05 RPM	23.81 RPM
SRP017611_brain	0.05 RPM	25.40 RPM
SRP017611_kidney	0.06 RPM	25.31 RPM
SRP017611_liver	0.00 RPM	8.61 RPM
SRP030211_testis	0.47 RPM	38.77 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1332 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1332 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1332 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 23 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011231	1 retrocopy	retro_amel_703,
Bos taurus	ENSBTAG00000018385	2 retrocopies	retro_btau_1332 , retro_btau_794,
Canis familiaris	ENSCAFG00000011885	2 retrocopies	retro_cfam_1506, retro_cfam_1663,
Choloepus hoffmanni	ENSCHOG00000009649	1 retrocopy	retro_chof_1545,
Dasypus novemcinctus	ENSDNOG00000015452	2 retrocopies	retro_dnov_133, retro_dnov_914,
Erinaceus europaeus	ENSEEUG00000011136	2 retrocopies	retro_eeur_536, retro_eeur_638,
Echinops telfairi	ENSETEG00000008348	4 retrocopies	retro_etel_374, retro_etel_502, retro_etel_745, retro_etel_846,
Felis catus	ENSFCAG00000013393	1 retrocopy	retro_fcat_203,
Homo sapiens	ENSG00000126698	3 retrocopies	retro_hsap_1319, retro_hsap_2840, retro_hsap_4119,
Gorilla gorilla	ENSGGOG00000000821	2 retrocopies	retro_ggor_1030, retro_ggor_2766,
Microcebus murinus	ENSMICG00000001222	5 retrocopies	retro_mmur_1152, retro_mmur_1355, retro_mmur_343, retro_mmur_601, retro_mmur_935,
Macaca mulatta	ENSMMUG00000017080	4 retrocopies	retro_mmul_2004, retro_mmul_2078, retro_mmul_2168, retro_mmul_228,
Mustela putorius furo	ENSMPUG00000015540	1 retrocopy	retro_mputfur_202,
Mus musculus	ENSMUSG00000054405	1 retrocopy	retro_mmus_916,
Nomascus leucogenys	ENSNLEG00000009762	3 retrocopies	retro_nleu_1401, retro_nleu_1594, retro_nleu_2701,
Otolemur garnettii	ENSOGAG00000015597	4 retrocopies	retro_ogar_2422, retro_ogar_2595, retro_ogar_3219, retro_ogar_84,
Pongo abelii	ENSPPYG00000025833	2 retrocopies	retro_pabe_2351, retro_pabe_3382,
Pelodiscus sinensis	ENSPSIG00000017721	1 retrocopy	retro_psin_34,
Pteropus vampyrus	ENSPVAG00000017619	1 retrocopy	retro_pvam_1057,
Rattus norvegicus	ENSRNOG00000013255	1 retrocopy	retro_rnor_488,
Ictidomys tridecemlineatus	ENSSTOG00000012834	2 retrocopies	retro_itri_1361, retro_itri_1775,
Tarsius syrichta	ENSTSYG00000007057	3 retrocopies	retro_tsyr_137, retro_tsyr_1389, retro_tsyr_885,
Tursiops truncatus	ENSTTRG00000000047	1 retrocopy	retro_ttru_1430,