RetrogeneDB ID: retro_btau_594

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 15:35974658..35975017(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDZD11
• Ensembl ID: ENSBTAG00000012860
• Aliases: None
• Description: PDZ domain-containing protein 11 [Source:UniProtKB/Swiss-Prot;Acc:Q32LE7]

Sequence

>retro_btau_594
CCTGCATGGATTCCTCCTCGTGAGAGAGTATACCATGCATACTACAATGAGCTGCCCCAATTTCTGCCCCAAATGGTCAC
ACTGAAAAAGCCCCCTGGGCTCAGTTGGGATTTCACATCTGAGTAGGAAGGGCCTCCCAGCAAGACATTTTCATCTCCAA
GGTGATTCTTGACTCTGATGCACACTGAGCAGGACTTCAGGAAGGGGACCAAGTTCTAGCTGTGAAGGATGTGGATTTCC
AGAATGCTGAGCACAGCAAGGCTACTGAGATCCTGAAGACAGCTGGTGAAGCCAGCATGCACGTCTGCTTTTTTTTTTTT
TTGTACAATTATCATCATCAGAAAGACAGGACTGTGCAC

Alignment

ORF - retro_btau_594 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.59 %
• Parental protein coverage: 85. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PAWIPPHERVYHPDYNNELTQFLPRIVTLKKPPG-AQLGFNIRGGKASQLGIFISKVIPDSDAHRAGLQE
          PAWIPP.ERVYH..Y.NEL.QFLP..VTLKKPPG.AQLGF.I..G.ASQ..IFISKVI.DSDAH.AGLQE
Retrocopy PAWIPPRERVYHA-YYNELPQFLPQMVTLKKPPG<AQLGFHI*VGRASQQDIFISKVILDSDAH*AGLQE

Parental  GDQVLAVNDVDFQDIEHSKAVEILKTAREISMRV--RFFPYNYHRQKERTVH
          GDQVLAV.DVDFQ..EHSKA.EILKTA.E.SM.V......YNYH.QK.RTVH
Retrocopy GDQVLAVKDVDFQNAEHSKATEILKTAGEASMHVCXXXXXYNYHHQKDRTVH

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	20.48 RPM
ERP005899_muscle	0.00 RPM	53.95 RPM
SRP017611_brain	0.00 RPM	21.38 RPM
SRP017611_kidney	0.00 RPM	34.50 RPM
SRP017611_liver	0.00 RPM	28.92 RPM
SRP030211_testis	0.01 RPM	8.94 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_594 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_594 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_594 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Equus caballus	retro_ecab_940

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009203	1 retrocopy	retro_amel_158,
Bos taurus	ENSBTAG00000012860	1 retrocopy	retro_btau_594 ,
Callithrix jacchus	ENSCJAG00000012432	1 retrocopy	retro_cjac_138,
Cavia porcellus	ENSCPOG00000000210	1 retrocopy	retro_cpor_143,
Echinops telfairi	ENSETEG00000008626	3 retrocopies	retro_etel_1026, retro_etel_1863, retro_etel_921,
Felis catus	ENSFCAG00000008633	3 retrocopies	retro_fcat_1356, retro_fcat_1410, retro_fcat_263,
Homo sapiens	ENSG00000120509	1 retrocopy	retro_hsap_1439,
Gorilla gorilla	ENSGGOG00000006626	1 retrocopy	retro_ggor_1108,
Macropus eugenii	ENSMEUG00000012040	1 retrocopy	retro_meug_1858,
Macaca mulatta	ENSMMUG00000013938	1 retrocopy	retro_mmul_2265,
Nomascus leucogenys	ENSNLEG00000000863	1 retrocopy	retro_nleu_1414,
Oryctolagus cuniculus	ENSOCUG00000017101	2 retrocopies	retro_ocun_1208, retro_ocun_1945,
Ochotona princeps	ENSOPRG00000001811	1 retrocopy	retro_opri_374,
Pongo abelii	ENSPPYG00000020929	1 retrocopy	retro_pabe_1193,
Pan troglodytes	ENSPTRG00000021995	1 retrocopy	retro_ptro_981,
Rattus norvegicus	ENSRNOG00000002838	1 retrocopy	retro_rnor_615,
Sarcophilus harrisii	ENSSHAG00000005380	1 retrocopy	retro_shar_149,
Ictidomys tridecemlineatus	ENSSTOG00000027107	2 retrocopies	retro_itri_1264, retro_itri_1702,
Tursiops truncatus	ENSTTRG00000007864	1 retrocopy	retro_ttru_953,