RetrogeneDB ID: retro_btau_593

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 15:34088430..34088797(-)
• Located in intron of: ENSBTAG00000013989

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZFAND6
• Ensembl ID: ENSBTAG00000012321
• Aliases: ZFAND6, ZA20D3
• Description: AN1-type zinc finger protein 6 [Source:UniProtKB/Swiss-Prot;Acc:Q3SZY7]

Sequence

>retro_btau_593
GTGGCTTAAGAAACTAATCACAGCCAAGTGCCTGTGCTTTGTTCTGCTGGCTGCAGATTTTATGGAAACCCTAGTACGAA
TGGCATGTGTTCAGTGCGCAATAAAGAACATCTTCAAATAGTAGTTCAGAATAGTGATGGTAGAATAAGCCCCCCTGTAC
TTTCTGTCTCTAGTCTGTCTGAGTCTTTACCAGCCCAGAGCACAGATGGCAGTGTCCCAGAAGCTCAGTCAGCGCTAGAC
ACTACGTCTTCGTCCATGTAGCCAAGCCCTGTATCACATCAGTCACTTTTATCAGAATCTGTAGTGTCTTCCCCAAGTGG
ACAGTACATCTATGGACAAAGCAATACTGGAAACAGATGACCTGCAA

Alignment

ORF - retro_btau_593 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.42 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAQETNHSQVPMLCSTGCGFYGNPRTNGMCSVCYKEHLQRQ-NSSNGRISPPAPSVTSLSESLPVQCTDG
          .A.ETNHSQVP.LCS.GC.FYGNP.TNGMCSV..KEHLQ.....S.GRISPP..SV.SLSESLP.Q.TDG
Retrocopy VA*ETNHSQVPVLCSAGCRFYGNPSTNGMCSVRNKEHLQIVVQNSDGRISPPVLSVSSLSESLPAQSTDG

Parental  SVPEAQSALDSTASSVQPSPVSNQSLLSESVASS-QVDSTSVDKAIPETEDLQ
          SVPEAQSALD.T.SS..PSPVS.QSLLSESV.SS.QVDSTS.DKAI.ET.DLQ
Retrocopy SVPEAQSALDTTSSSM*PSPVSHQSLLSESVVSS>QVDSTSMDKAILETDDLQ

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	4.33 RPM
ERP005899_muscle	0.00 RPM	20.38 RPM
SRP017611_brain	0.00 RPM	5.02 RPM
SRP017611_kidney	0.00 RPM	25.37 RPM
SRP017611_liver	0.00 RPM	10.65 RPM
SRP030211_testis	0.03 RPM	66.24 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_593 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_593 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_593 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012321	1 retrocopy	retro_btau_593 ,
Choloepus hoffmanni	ENSCHOG00000009491	2 retrocopies	retro_chof_1516, retro_chof_2072,
Felis catus	ENSFCAG00000012931	2 retrocopies	retro_fcat_1024, retro_fcat_1998,
Homo sapiens	ENSG00000086666	1 retrocopy	retro_hsap_4153,
Gorilla gorilla	ENSGGOG00000015621	1 retrocopy	retro_ggor_2790,
Loxodonta africana	ENSLAFG00000006722	1 retrocopy	retro_lafr_587,
Monodelphis domestica	ENSMODG00000019428	1 retrocopy	retro_mdom_685,
Nomascus leucogenys	ENSNLEG00000008870	1 retrocopy	retro_nleu_1387,
Pan troglodytes	ENSPTRG00000007361	2 retrocopies	retro_ptro_1375, retro_ptro_2824,
Rattus norvegicus	ENSRNOG00000013506	1 retrocopy	retro_rnor_2019,
Sus scrofa	ENSSSCG00000001779	2 retrocopies	retro_sscr_1206, retro_sscr_1207,