RetrogeneDB ID: retro_btau_638

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 16:9705338..9705617(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTP4A2
• Ensembl ID: ENSBTAG00000039121
• Aliases: PTP4A2, PTP4A3
• Description: protein tyrosine phosphatase type IVA 3 [Source:RefSeq peptide;Acc:NP_001098468]

Sequence

>retro_btau_638
TGGCTAAGCCTACTAAAACCAAATATCCTGAAGAACAAGGTTGCTGTGTTGTAGCGCACTGCGTTGCAGGATTGGGAAGG
GGACCTGTACCGGTTGCACTTGCTTTGATTGAATGTGGAATGTTGAATGAAGTACACATGTGGAATGAAGATGCATTTCA
ATTTATAAGACAAAAAAAGAAGGGGAGCATTCAATTCCAAACAGCTTCTTTACCTGGAGAAATACCAACCTAAGATGTGA
TTATGCTTCAGAGATACCAACAGGCATTACTGTGTTCAG

Alignment

ORF - retro_btau_638 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.47 %
• Parental protein coverage: 52.1 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  WLNLLK-TKFREEPGCCVAVHCVAGLGRA--PVLVALA----LIECGMKYEDAVQFIRQ-KRRGAFNSKQ
          WL.LLK.TK..EE.GCCV..HCVAGLGR...PV..AL.....L.E..M..EDA.QFIRQ.KRRGAFNSKQ
Retrocopy WLSLLK<TKYPEEQGCCVVAHCVAGLGRGPVPVALALIECGMLNEVHMWNEDAFQFIRQ>KRRGAFNSKQ

Parental  LLYLEKYRPKMRLRFRDTNGHCCVQ
          LLYLEKY.PKM.L.FRDTN.H.CVQ
Retrocopy LLYLEKYQPKM*LCFRDTNRHYCVQ

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	95.53 RPM
ERP005899_muscle	0.00 RPM	128.12 RPM
SRP017611_brain	0.00 RPM	77.88 RPM
SRP017611_kidney	0.00 RPM	89.09 RPM
SRP017611_liver	0.00 RPM	83.44 RPM
SRP030211_testis	0.01 RPM	63.08 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_638 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_638 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_638 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002275	3 retrocopies	retro_btau_1051, retro_btau_1186, retro_btau_859,
Bos taurus	ENSBTAG00000039121	1 retrocopy	retro_btau_638 ,
Bos taurus	ENSBTAG00000046467	1 retrocopy	retro_btau_380,
Callithrix jacchus	ENSCJAG00000006539	2 retrocopies	retro_cjac_3257, retro_cjac_566,
Homo sapiens	ENSG00000184007	4 retrocopies	retro_hsap_1069, retro_hsap_1754, retro_hsap_4331, retro_hsap_944,
Mus musculus	ENSMUSG00000028788	2 retrocopies	retro_mmus_1894, retro_mmus_2432,
Nomascus leucogenys	ENSNLEG00000002137	3 retrocopies	retro_nleu_2880, retro_nleu_2956, retro_nleu_3015,
Oryctolagus cuniculus	ENSOCUG00000002060	1 retrocopy	retro_ocun_1673,
Otolemur garnettii	ENSOGAG00000029603	1 retrocopy	retro_ogar_3341,
Pongo abelii	ENSPPYG00000001606	3 retrocopies	retro_pabe_1507, retro_pabe_808, retro_pabe_890,
Rattus norvegicus	ENSRNOG00000050044	1 retrocopy	retro_rnor_305,
Sus scrofa	ENSSSCG00000003605	1 retrocopy	retro_sscr_1186,
Ictidomys tridecemlineatus	ENSSTOG00000002775	2 retrocopies	retro_itri_1165, retro_itri_152,
Tupaia belangeri	ENSTBEG00000006790	1 retrocopy	retro_tbel_4601,
Tursiops truncatus	ENSTTRG00000016571	2 retrocopies	retro_ttru_1396, retro_ttru_1402,