RetrogeneDB ID: retro_btau_521

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 13:10484177..10484919(-)
• Located in intron of: ENSBTAG00000000939

Retrocopy information

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

Parental gene information

• Parental gene symbol: KLF4
• Ensembl ID: ENSBTAG00000020355
• Aliases: None
• Description: Krueppel-like factor 4 [Source:RefSeq peptide;Acc:NP_001098855]

Sequence

>retro_btau_521
CTGAGTGCTCCTGGCAGCGAGTACGGCAGCCCTTGGTTATCAGTGTTCGCACAGGCAGCCCGGATGGCAGCCACTCGGTG
GTGGTGGGCCCTATAGCAGCAGGCCACTGCGTATGTGCCCGAAGATCAAGCGGGAGGCTGTCTCCTCGTGTACTGTCGGT
TGGCCCCTCAAGGCCCGCTTGGGCACTGGATCTCTGCTCAGCAGTGGCCACCGGCTGCCTGCGCACGACTTTCCCCTGGG
GCAGCAGCTCCCTGGCAGGGCTACCCCGACCCTGGGTGCCGAGGAACTTGCTGAGCAGCCCAGACTGTCATCCTGCCCTG
CCGCTCCCCCCGGGCTTCCATCCCCACCCCGGGCCCAACCACCCTCCCTTCCTGCTCCATCAGATGCAGACGCAGGTCCC
ATCGTGCCATGACCAAGCGCGTGCCAGCCAGTTCCTGCATGCTGGAGGAGCCCAAGCCAAAAAGGAGGAGGAGGTCATGG
CTCCGGAAAAGGACGGCCTCTCACACTTGTAATTATGCAGGCTGCAGCTAAACCTGCGCGGAGAGTTCTCATCTCAAGGC
ACACCTGCACATCCCACACAGGTGCGAAACCTTACCACTGTGACTGGGATGGCTGAGGGTGGAAGTTCGCCCGCTCAGAT
GAACTGACCAGGCACTATGGCAGACAAACCGGGCAGTGTCAGAAGTGTGACCGGGCATTCTTGAGGTTGGACCACCTTGC
CTTACACATGAAGAGGCACTTT

Alignment

ORF - retro_btau_521 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.64 %
• Parental protein coverage: 52.83 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  LSAPGSEYGSP-SVISVSKGSPDGSHPVVVAP-YSGGPPRMCPKIKQEAVSSCTVGRPLEAHLGTGPPLS
          LSAPGSEYGSP..VISV..GSPDGSH.VVV.P.YS..P.RMCPKIK.EAVSSCTVG.PL.A.LGTG..LS
Retrocopy LSAPGSEYGSP<LVISVRTGSPDGSHSVVVGP<YSSRPLRMCPKIKREAVSSCTVGWPLKARLGTGSLLS

Parental  NGHRPPAHDFPLGRQLPSRTTPTLGAEE-LLSSRDCHPALPLPPGFHPHPGPNYPPFLPDQMQPQVPPLH
          .GHR.PAHDFPLG.QLP.R.TPTLGAEE.LLSS.DCHPALPLPPGFHPHPGPN.PPFL..QMQ.QVP..H
Retrocopy SGHRLPAHDFPLGQQLPGRATPTLGAEE>LLSSPDCHPALPLPPGFHPHPGPNHPPFLLHQMQTQVPSCH

Parental  YQ-ELMPPGSCMPEEPKPKRG-RRSWPRKRTATHTCDYAGCGKTYTKSSHLKAHLR-THTGEKPYHCDWD
          .Q.....P.......P..K.G.RRSW.RKRTA.HTC.YAGC..T...SSHLKAHL...HTG.KPYHCDWD
Retrocopy DQ<SACQPVPACWRSPSQKGG<RRSWLRKRTASHTCNYAGCS*TCAESSHLKAHLH>SHTGAKPYHCDWD

Parental  GCGWKFARSDELTRHYRKHTGHRPFQCQKCDRAFSRSDHLALHMKRHF
          G.GWKFARSDELTRHY...TG....QCQKCDRAF.R.DHLALHMKRHF
Retrocopy G*GWKFARSDELTRHYGRQTG----QCQKCDRAFLRLDHLALHMKRHF

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	0.07 RPM	1.44 RPM
ERP005899_muscle	0.16 RPM	69.95 RPM
SRP017611_brain	0.05 RPM	5.25 RPM
SRP017611_kidney	0.06 RPM	13.16 RPM
SRP017611_liver	0.15 RPM	2.11 RPM
SRP030211_testis	0.14 RPM	119.74 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_521 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_521 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_521 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013740	1 retrocopy	retro_btau_1617,
Bos taurus	ENSBTAG00000017488	1 retrocopy	retro_btau_271,
Bos taurus	ENSBTAG00000020355	1 retrocopy	retro_btau_521 ,
Bos taurus	ENSBTAG00000038055	1 retrocopy	retro_btau_1360,
Pongo abelii	ENSPPYG00000019478	7 retrocopies	retro_pabe_1836, retro_pabe_2020, retro_pabe_2022, retro_pabe_2024, retro_pabe_2027, retro_pabe_2037, retro_pabe_3579,
Rattus norvegicus	ENSRNOG00000016299	1 retrocopy	retro_rnor_2164,
Ictidomys tridecemlineatus	ENSSTOG00000022002	1 retrocopy	retro_itri_1862,