RetrogeneDB ID: retro_btau_297

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 1:66687562..66688101(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAP1B
• Ensembl ID: ENSBTAG00000008967
• Aliases: None
• Description: Ras-related protein Rap-1b [Source:UniProtKB/Swiss-Prot;Acc:P61223]

Sequence

>retro_btau_297
ATGTGTGAGTATAAGCTAGCAGTTCTTGGTTCAGGGGACATTGGAAAATTGACTCTCACTGTACACTTTATTCAAGGAAT
TTTTGTTGAAAATATAATCCTACCATAGAAGATTATTATAGAAAGCAAGTTAAAGTAGATGCAAAACAGTATACGCTTGA
AATCTTGGATAATATAGAAATAGGCCATTTACAGTGATGATAGATTTGTACATGAAACATGGACAAGGCTTTGCTTTATT
TTATTCCTACACAGCACAGTTCACATTTAATGATACACAAGATCAGAGAGAACAGATTCTTTAAGTTAAAGACACTGATG
GTGTTCCAAAATTCTGGTTGGTAGTAAGTGTGACGTGGAAGATGACAGAGTTGTAAGAAAGGAACAAGTTGAAGTCTAGC
AAGAAAATGGAACAACTGCACGTTCTTAGACTCCTCTGCAAAGTAGAAAATAACTGTTAATGAAATATTTTATAACCTAA
TGTGGCAAATTATCAGGAAAACTCCACTGTCTGGGGAGGCCTGCAAAAAGTCTCCATGT

Alignment

ORF - retro_btau_297 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.73 %
• Parental protein coverage: 98.37 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MREYKLVVLGSGGVGKSALTVQFVQGIFVE-KYDPTIEDSYRKQVEVDAQQCMLEILDTAG-TEQFTAMR
          M.EYKL.VLGSG..GK..LTV.F.QGIFVE.KY.PTIED.YRKQV.VDA.Q..LEILD.......FT.M.
Retrocopy MCEYKLAVLGSGDIGKLTLTVHFIQGIFVE<KYNPTIEDYYRKQVKVDAKQYTLEILDNIE<NRPFTVMI

Parental  DLYMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTDDVP-MILVGNKCDLEDERVVGKEQGQ-NLAR
          DLYMK.GQGFAL.YS.TAQ.TFND.QD.REQIL.VKDTD.VP..ILVG.KCD.ED.RVV.KEQ....LAR
Retrocopy DLYMKHGQGFALFYSYTAQFTFNDTQDQREQIL*VKDTDGVP<KILVGSKCDVEDDRVVRKEQVE<SLAR

Parental  QWNNCAFLESSAKSKINVNEIFYDLVRQINRKTPVPGKARKKSSC
          .WNNC.FL.SSAK.KI.VNEIFY.L..QI.RKTP..G.A.KKS.C
Retrocopy KWNNCTFLDSSAK*KITVNEIFYNLMWQIIRKTPLSGEACKKSPC

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	45.28 RPM
ERP005899_muscle	0.00 RPM	58.75 RPM
SRP017611_brain	0.00 RPM	29.69 RPM
SRP017611_kidney	0.06 RPM	61.64 RPM
SRP017611_liver	0.00 RPM	15.33 RPM
SRP030211_testis	0.00 RPM	42.45 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_297 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_297 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_297 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008637	1 retrocopy	retro_amel_103,
Bos taurus	ENSBTAG00000008967	3 retrocopies	retro_btau_1564, retro_btau_297 , retro_btau_684,
Cavia porcellus	ENSCPOG00000008272	4 retrocopies	retro_cpor_1194, retro_cpor_632, retro_cpor_739, retro_cpor_85,
Echinops telfairi	ENSETEG00000000242	1 retrocopy	retro_etel_11,
Loxodonta africana	ENSLAFG00000016460	1 retrocopy	retro_lafr_482,
Otolemur garnettii	ENSOGAG00000005746	2 retrocopies	retro_ogar_2260, retro_ogar_272,
Sus scrofa	ENSSSCG00000030014	2 retrocopies	retro_sscr_435, retro_sscr_909,