RetrogeneDB ID: retro_btau_1598

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 8:17707436..17707905(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSN
• Ensembl ID: ENSBTAG00000006059
• Aliases: TSN, C3PO
• Description: Translin [Source:UniProtKB/Swiss-Prot;Acc:Q08DM8]

Sequence

>retro_btau_1598
ACGTCTTTGAAGACCAAGTTTCCTGCGGGATAGCATTACAGGTTTCATGAGCACTGAAGGTTTGTGCTGCAGTGCCTGGT
CTTCTTGGCAGCATTTGGTGTGTACTTGGAGACCGAAACCATAGTGAACCGAGAAGCAGTTACCGAGATCCTTGGCACTG
AGCCTGATCAGGAGAAGGGATTTCACCTGGATGTGGATGATTATCTCTCGGGGGTTCTCATTCTCACTAGTGAACTGTTG
AGGTTGTCCATCAACAGAGTGACCGCCGGAGACTACTCCCGGCCCCTGCACATTTCCACCTTCATCAAACGAGCTGGATT
CCGGCTTGTGCCTCCTCAACCTCAAAAATGATTCCCTGAGGAAGCGCTACGAGGGCCTGAAGTACGATGTGAAGAAAGTG
AAGGAGGTGGTCTATGATCTCTCCATCCAGGGCTGCAACAGGGAGCCAGCAGCCGCCTGCGTGAAGCAG

Alignment

ORF - retro_btau_1598 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.8 %
• Parental protein coverage: 68.42 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TSLKTKFPAEQYYRFHEHWRFVLQRLVFLAAFVVYLESETLVTREAVTEILGIEPDREKGFHLDVEDYLS
          TSLKTKFPA...YRFHEH.RFVLQ.LVFLAAF.VYLE.ET.V.REAVTEILG.EPD.EKGFHLDV.DYLS
Retrocopy TSLKTKFPAG*HYRFHEH*RFVLQCLVFLAAFGVYLETETIVNREAVTEILGTEPDQEKGFHLDVDDYLS

Parental  GVLILASELSRLSVNSVTAGDYSRPLHISTFI-NELDSGFRLLNLKNDSLRKRYDGLKYDVKKVEEVVYD
          GVLIL.SEL.RLS.N.VTAGDYSRPLHISTFI.NELDSG..LLNLKNDSLRKRY.GLKYDVKKV.EVVYD
Retrocopy GVLILTSELLRLSINRVTAGDYSRPLHISTFI>NELDSGLCLLNLKNDSLRKRYEGLKYDVKKVKEVVYD

Parental  LSIRGFNKETAAACVEK
          LSI.G.N.E.AAACV..
Retrocopy LSIQGCNREPAAACVKQ

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	8.87 RPM
ERP005899_muscle	0.00 RPM	14.73 RPM
SRP017611_brain	0.00 RPM	20.01 RPM
SRP017611_kidney	0.00 RPM	20.57 RPM
SRP017611_liver	0.00 RPM	13.74 RPM
SRP030211_testis	0.00 RPM	25.95 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1598 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1598 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1598 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006059	1 retrocopy	retro_btau_1598 ,
Dasypus novemcinctus	ENSDNOG00000025740	2 retrocopies	retro_dnov_1581, retro_dnov_907,
Felis catus	ENSFCAG00000027149	1 retrocopy	retro_fcat_1577,
Homo sapiens	ENSG00000211460	1 retrocopy	retro_hsap_3760,
Gorilla gorilla	ENSGGOG00000002216	2 retrocopies	retro_ggor_2528, retro_ggor_2610,
Myotis lucifugus	ENSMLUG00000012656	1 retrocopy	retro_mluc_1420,
Macaca mulatta	ENSMMUG00000021119	1 retrocopy	retro_mmul_1718,
Monodelphis domestica	ENSMODG00000000147	1 retrocopy	retro_mdom_1896,
Nomascus leucogenys	ENSNLEG00000001202	1 retrocopy	retro_nleu_170,
Ornithorhynchus anatinus	ENSOANG00000003457	1 retrocopy	retro_oana_120,
Oryctolagus cuniculus	ENSOCUG00000023529	1 retrocopy	retro_ocun_271,
Otolemur garnettii	ENSOGAG00000030436	3 retrocopies	retro_ogar_1221, retro_ogar_2875, retro_ogar_3426,
Pan troglodytes	ENSPTRG00000012420	1 retrocopy	retro_ptro_2551,
Tarsius syrichta	ENSTSYG00000004395	1 retrocopy	retro_tsyr_1593,