RetrogeneDB ID: retro_btau_693

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 18:24855853..24856535(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.63774
• Ensembl ID: ENSBTAG00000006884
• Aliases: None
• Description: Polyadenylate-binding protein 2 [Source:UniProtKB/Swiss-Prot;Acc:Q28165]

Sequence

>retro_btau_693
CCGGGAGCTCCGGGCCCTGGGCCTGGCTCGGGAGCCCCCGGCAACCAGGAGGAGGAGGAGGAGGAGTCGGGACTGGTCGA
GGGTGACCCGGGGGGACGGCGCCATTTAGGACCCGGAGCTGGAAGCGATCAAAGCTCGAGTTAGGGAGATGGAGGAAGAA
GCTGAGAAGCTAAAGGAGCTACAGAATGAGGTAGAGAAGCAGATGAATATGAGTCCACCTCCGGGCAATGCTGGCCCAGT
GATCATGTCCATTGAGGAGAAGATAGAGGCTGATGCCCGTTCCATCTATGTTGGCAATGTGGACTATGGTGCAACAGCGG
AAGAGCTAGAAGCACACTTTCATGGCTGTGGTTCAGTCAACCGTGTTACTATACTCTGTGACAAATTTAGTGGCCATCCG
AAAGGGTTTGCGTATATAGAGTTCTCAGACAAAGAGTCAGTGAGGACTTCCCTGGCCTTAGATGAATCCTTATTTAGAGG
AAGACAGATCAAGGTGATCCCTAAACGAACCAACAGACCAGGCATCAGCACAACAGACCGAGGCTTCCCACGAACCCGAT
ACCGTGCCCGAACCACCAACTACAACAGTACCCGCTCTCGATTCTACAGTGGTTTTAACAGCAGGCCCCGGGGTCGCGTC
TACAGGGGCCGGGCTAGAGCGACATCATGGTATTCCCCTTAC

Alignment

ORF - retro_btau_693 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.74 %
• Parental protein coverage: 73.86 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PGAPGPGPGSGAPGNQEEEEE-SGLVEGDPG-DGAIEDPELEAIKARVREMEEEAEKLKELQNEVEKQMN
          PGAPGPGPGSGAPGN.......SGLVEGDPG.DGAI.DPELEAIKARVREMEEEAEKLKELQNEVEKQMN
Retrocopy PGAPGPGPGSGAPGNXXXXXXXSGLVEGDPG>DGAI*DPELEAIKARVREMEEEAEKLKELQNEVEKQMN

Parental  MSPPPGNAGPVIMSIEEKMEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYI
          MSPPPGNAGPVIMSIEEK.EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYI
Retrocopy MSPPPGNAGPVIMSIEEKIEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYI

Parental  EFSDKESVRTSLALDESLFRGRQIKVIPKRTNRPGISTTDRGFPRARYRARTTNYNSSRSRFYSGFNSRP
          EFSDKESVRTSLALDESLFRGRQIKVIPKRTNRPGISTTDRGFPR.RYRARTTNYNS.RSRFYSGFNSRP
Retrocopy EFSDKESVRTSLALDESLFRGRQIKVIPKRTNRPGISTTDRGFPRTRYRARTTNYNSTRSRFYSGFNSRP

Parental  RGRVYRGRARATSWYSPY
          RGRVYRGRARATSWYSPY
Retrocopy RGRVYRGRARATSWYSPY

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	0.07 RPM	80.10 RPM
ERP005899_muscle	0.26 RPM	63.93 RPM
SRP017611_brain	0.50 RPM	161.61 RPM
SRP017611_kidney	0.24 RPM	112.79 RPM
SRP017611_liver	0.08 RPM	37.23 RPM
SRP030211_testis	1.00 RPM	217.45 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_693 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_693 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_693 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006884	1 retrocopy	retro_btau_693 ,
Bos taurus	ENSBTAG00000023752	1 retrocopy	retro_btau_972,
Callithrix jacchus	ENSCJAG00000007960	4 retrocopies	retro_cjac_1263, retro_cjac_2291, retro_cjac_3278, retro_cjac_3836,
Dipodomys ordii	ENSDORG00000002873	1 retrocopy	retro_dord_606,
Homo sapiens	ENSG00000100836	1 retrocopy	retro_hsap_4855,
Gorilla gorilla	ENSGGOG00000022683	2 retrocopies	retro_ggor_1454, retro_ggor_3030,
Mustela putorius furo	ENSMPUG00000006775	1 retrocopy	retro_mputfur_496,
Mus musculus	ENSMUSG00000022194	1 retrocopy	retro_mmus_403,
Nomascus leucogenys	ENSNLEG00000015009	2 retrocopies	retro_nleu_2066, retro_nleu_3023,
Otolemur garnettii	ENSOGAG00000008710	1 retrocopy	retro_ogar_797,
Pongo abelii	ENSPPYG00000005663	2 retrocopies	retro_pabe_1645, retro_pabe_3773,
Pan troglodytes	ENSPTRG00000006168	2 retrocopies	retro_ptro_1339, retro_ptro_3232,
Sus scrofa	ENSSSCG00000002023	1 retrocopy	retro_sscr_625,