RetrogeneDB ID: retro_btau_1666

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 9:7645891..7646729(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRKAR1A
• Ensembl ID: ENSBTAG00000008621
• Aliases: None
• Description: cAMP-dependent protein kinase type I-alpha regulatory subunit [Source:UniProtKB/Swiss-Prot;Acc:P00514]

Sequence

>retro_btau_1666
CTGGCTCCTGGTGGCACCTCTGCTGAGGAGGAGCGCAGCTCCTGGGAACGTGAACTCTACGACCAGAAGCACACATCTAG
GCCCTGTTCAAAGAGTCCATCATGTAGCTGTGCACTGCACGGCCCGAGAGGCCATGACATTCCTCAGGGAATACTTTGAG
AGGTTGGAGAAGAAGGAGGCAAAACGGATCCAGAATCTGCAGAAAGCAAGCTCTTGTGCAGACTGAAGGAAGGATGAAGT
CTCTCTCCCTCCAACCAACCCAGCGATGAGGGGCTGGGGGCAACAAGGTGCCATCTACGCTGAGGTCTACACTAAGCAAG
ATGCCACATCCTATGTTAGGAAGGTTGGACCAGAAGGTTACAAGACAATGACTGCTTTAGCTAAAGCTGTTGAAAAGAAT
GTGCTCTCTGCACATCTTGATGATAGTGAGAGAAGCAATCATTTTGATGCCGTGTTTCCAGTTTCCTTTATTGCTGGAGA
GATTGTCATTCAGCAAGGTCGTGAAAGGAATAACTTCTTTGTGATTGATCAAGGAGAAATGGAAGTCTGTGTCAACAGTG
AATGGGCAACCAGTGTCGGGGAAGGAAGGAGTGTTGGGGAAATTGCTTCGATCATGGAGCACCTAGAGCAGCTACCTTCA
AGGCCCAGACAGATGTGAAGTTGTGGGGCATCGCCCCAAGACAACTCTAGAAGGATCCTATCGGGAAGTGTGCGAAGAAA
GCTGAAGATGTATGAGGAGTCTTTTAGCAAGGGATCTATTTTAGCATTTCTGGACAAGTGGAAACATCTCAGGGTAGCTG
ATGCCATGGAACTGGTCCAGACTGAAGACAGCCAGAAG

Alignment

ORF - retro_btau_1666 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.66 %
• Parental protein coverage: 73.68 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MASGTTASEEERSLRECELYVQKH-NIQALLKDSIVQLCTARPERP-MAFLREYFEKLEKEEAKQIQNLQ
          .A.G.T..EEERS..E.ELY.QKH..I.AL.K.SI..LCTARPERP.M.FLREYFE.LEK.EAK.IQNLQ
Retrocopy LAPGGTSAEEERSSWERELYDQKH<HI*ALFKESIM*LCTARPERP<MTFLREYFERLEKKEAKRIQNLQ

Parental  KAGSRADSREDEISPPPPNPVVKGRRRRGAISAEVYTEEDAASYVRKVIPKDYKTMAALAKAIEKNVLFS
          KA.S.AD.R.DE.S.PP.NP...G....GAI.AEVYT..DA.SYVRKV.P..YKTM.ALAKA.EKNVL..
Retrocopy KASSCAD*RKDEVSLPPTNPAMRGWGQQGAIYAEVYTKQDATSYVRKVGPEGYKTMTALAKAVEKNVLSA

Parental  HLDDNERSDIFDAMFPVSFIAGETVIQQGDEGDNFYVIDQGEMDVYVNNEWATSVGEGGSFGELALI-YG
          HLDD.ERS..FDA.FPVSFIAGE.VIQQG.E..NF.VIDQGEM.V.VN.EWATSVGEG.S.GE.A.I..G
Retrocopy HLDDSERSNHFDAVFPVSFIAGEIVIQQGRERNNFFVIDQGEMEVCVNSEWATSVGEGRSVGEIASI<HG

Parental  TPRAATVKAKTNVKLWGI-DRDSYRRILMGSTLRKRKMYEEFLSKVSILESLDKWERLTVADALEPVQFE
          .PRAAT.KA.T.VKLWGI...D..RRIL.GS..RK.KMYEE..SK.SIL..LDKW..L.VADA.E.VQ.E
Retrocopy APRAATFKAQTDVKLWGI>PQDNSRRILSGSVRRKLKMYEESFSKGSILAFLDKWKHLRVADAMELVQTE

Parental  DGQK
          D.QK
Retrocopy DSQK

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	28.05 RPM
ERP005899_muscle	0.05 RPM	90.69 RPM
SRP017611_brain	0.05 RPM	148.59 RPM
SRP017611_kidney	0.00 RPM	156.48 RPM
SRP017611_liver	0.00 RPM	47.80 RPM
SRP030211_testis	0.04 RPM	241.80 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1666 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1666 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1666 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000008621	1 retrocopy	retro_btau_1666 ,
Ictidomys tridecemlineatus	ENSSTOG00000012903	1 retrocopy	retro_itri_104,