RetrogeneDB ID: retro_btau_1343

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 4:34666075..34666441(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C6ORF106
• Ensembl ID: ENSBTAG00000034493
• Aliases: C23H6orf106, C6orf106
• Description: None

Sequence

>retro_btau_1343
TATGACTTTGAGAGCCCAAACATCACTGTCCCCTCTGCATCCTTTGTTGAAGATGTCACCCTGGGAGAAGAGGAGTCCAT
ACCTCCTGATGCTCAGTTTATAAAAACCTGGCAGATGGAGAATTCTGGGGCAGAGGCCTGGCCTCTACGGGTTTGTCTTA
AGTATGTCAGGGGAGACCAGATTGGATGTATGAACGTGGTGATAGTGACATCGCTGGAGTCCCGAGAGATTGCAGGATTC
AGCGTCGGGTGTACAGCCGGGGAGCAGGGATGAGTCAGGACCGGCGCTGATGAGCGCTGCTGCAGGCTCTACCGTGGAGG
CGCTAGCCGAGTCCTCCTTGTGGAGGTGGGTGGACTTTTAGGAGTG

Alignment

ORF - retro_btau_1343 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.6 %
• Parental protein coverage: 59.52 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YDFESPNISVPSMSFVEDVTIGEGESIPPDTQFIKTWRIQNSGAEAWPPGVCLKYVGGDQFGHVNMVMVR
          YDFESPNI.VPS.SFVEDVT.GE.ESIPPD.QFIKTW...NSGAEAWP..VCLKYV.GDQ.G..N.V.V.
Retrocopy YDFESPNITVPSASFVEDVTLGEEESIPPDAQFIKTWQMENSGAEAWPLRVCLKYVRGDQIGCMNVVIVT

Parental  SLEPQEIADVSVQMCSPSRAGMYQGQWRMCTATGLYYGDVIWVILSVEVGGLLGV
          SLE..EIA..SV............G....C....LY.G....V.L.VEVGGLLGV
Retrocopy SLESREIAGFSVGCTAGEQG*VRTGADERCCR--LYRGGASRVLL-VEVGGLLGV

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	6.63 RPM
ERP005899_muscle	0.00 RPM	21.70 RPM
SRP017611_brain	0.05 RPM	20.46 RPM
SRP017611_kidney	0.00 RPM	16.95 RPM
SRP017611_liver	0.00 RPM	24.77 RPM
SRP030211_testis	0.02 RPM	76.64 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1343 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1343 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1343 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000034493	1 retrocopy	retro_btau_1343 ,
Callithrix jacchus	ENSCJAG00000015304	1 retrocopy	retro_cjac_2788,
Homo sapiens	ENSG00000196821	1 retrocopy	retro_hsap_2137,
Gorilla gorilla	ENSGGOG00000000388	1 retrocopy	retro_ggor_1653,
Microcebus murinus	ENSMICG00000013442	1 retrocopy	retro_mmur_1615,
Macaca mulatta	ENSMMUG00000022824	1 retrocopy	retro_mmul_2155,
Nomascus leucogenys	ENSNLEG00000008387	2 retrocopies	retro_nleu_1933, retro_nleu_2739,
Otolemur garnettii	ENSOGAG00000011264	1 retrocopy	retro_ogar_3245,
Ochotona princeps	ENSOPRG00000009350	1 retrocopy	retro_opri_559,
Pongo abelii	ENSPPYG00000016519	2 retrocopies	retro_pabe_1265, retro_pabe_1928,
Pan troglodytes	ENSPTRG00000018068	1 retrocopy	retro_ptro_1564,