RetrogeneDB ID: retro_btau_952

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 21:32090305..32090640(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARPP19
• Ensembl ID: ENSBTAG00000011022
• Aliases: ARPP19, ARPP-16, ARPP-19
• Description: cAMP-regulated phosphoprotein 19 [Source:UniProtKB/Swiss-Prot;Acc:Q28055]

Sequence

>retro_btau_952
ATGTCTGCGGAAGTCCCCCAGGCAGCCTCCGCAGAGGAGCAGAAGGAAATGGAAGATAAAGTGATTAGTCCAGAGAAAGC
TGAAGAAGCAAAAGTTAAAAGCAAGATATCCTCATCTGGGACAAAATCCTGGAGGTTCAGATTTTTTAAGTAAACGATTG
CATAAAGGGTAAAAATATTTTGATTCTGGGGATTACAACATGGCTAAAGCAAAATGAAGAACAAGCAACTTCCTACTGCA
ACCCCAGATAAGACAGAGGTCACTGGTGACTACATCCCACTCCACAGGACCTTCCTCAGTGGAAACCATCTCTTGTTGCT
AGCAAGCTGGCTGGC

Alignment

ORF - retro_btau_952 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.43 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSAEVPEAASAEEQKEMEDKVTSPEKAEEAK-LKARYPHLGQKPGGSDFLRKRLQKGQKYFDSGDYNMAK
          MSAEVP.AASAEEQKEMEDKV.SPEKAEEAK.LKARYPHLGQ.PGGSDFL.KRL.KG.KYFDSGDYNMAK
Retrocopy MSAEVPQAASAEEQKEMEDKVISPEKAEEAK>LKARYPHLGQNPGGSDFLSKRLHKG*KYFDSGDYNMAK

Parental  A-KMKNKQLPTATPDKTEVTGDHI-PTPQDLPQRKPSLVASKLAG
          A.KMKNKQLPTATPDKTEVTGD.I.PTPQDLPQ.KPSLVASKLAG
Retrocopy A<KMKNKQLPTATPDKTEVTGDYI<PTPQDLPQWKPSLVASKLAG

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	23.86 RPM
ERP005899_muscle	0.00 RPM	20.22 RPM
SRP017611_brain	0.00 RPM	122.97 RPM
SRP017611_kidney	0.00 RPM	48.78 RPM
SRP017611_liver	0.00 RPM	9.74 RPM
SRP030211_testis	0.00 RPM	83.42 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_952 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_952 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_952 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011022	5 retrocopies	retro_btau_1259, retro_btau_1821, retro_btau_1845, retro_btau_952 , retro_btau_981,
Canis familiaris	ENSCAFG00000032515	2 retrocopies	retro_cfam_1375, retro_cfam_1402,
Cavia porcellus	ENSCPOG00000011228	1 retrocopy	retro_cpor_1148,
Dasypus novemcinctus	ENSDNOG00000004474	9 retrocopies	retro_dnov_1086, retro_dnov_1576, retro_dnov_1960, retro_dnov_2150, retro_dnov_2427, retro_dnov_557, retro_dnov_616, retro_dnov_644, retro_dnov_662,
Dipodomys ordii	ENSDORG00000011321	2 retrocopies	retro_dord_194, retro_dord_33,
Echinops telfairi	ENSETEG00000015550	1 retrocopy	retro_etel_585,
Homo sapiens	ENSG00000128989	2 retrocopies	retro_hsap_2130, retro_hsap_3280,
Gorilla gorilla	ENSGGOG00000025250	1 retrocopy	retro_ggor_198,
Nomascus leucogenys	ENSNLEG00000006551	2 retrocopies	retro_nleu_2533, retro_nleu_2884,
Oryctolagus cuniculus	ENSOCUG00000015489	10 retrocopies	retro_ocun_1182, retro_ocun_1297, retro_ocun_1398, retro_ocun_1573, retro_ocun_1731, retro_ocun_1768, retro_ocun_310, retro_ocun_473, retro_ocun_479, retro_ocun_698,
Otolemur garnettii	ENSOGAG00000013865	1 retrocopy	retro_ogar_591,
Pongo abelii	ENSPPYG00000006487	2 retrocopies	retro_pabe_120, retro_pabe_1923,
Pan troglodytes	ENSPTRG00000042183	1 retrocopy	retro_ptro_1559,
Sus scrofa	ENSSSCG00000004618	1 retrocopy	retro_sscr_603,
Ictidomys tridecemlineatus	ENSSTOG00000003677	7 retrocopies	retro_itri_1075, retro_itri_1290, retro_itri_1339, retro_itri_1643, retro_itri_1657, retro_itri_1865, retro_itri_594,
Tursiops truncatus	ENSTTRG00000004804	1 retrocopy	retro_ttru_172,