RetrogeneDB ID: retro_btau_271

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 1:96642033..96642732(+)
• Located in intron of: ENSBTAG00000017490

Retrocopy information

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

Parental gene information

• Parental gene symbol: KLF3
• Ensembl ID: ENSBTAG00000017488
• Aliases: None
• Description: Krueppel-like factor 3 [Source:RefSeq peptide;Acc:NP_001192907]

Sequence

>retro_btau_271
ATGCTCATGTTTGACCCAGTCCCTGTCAAGCAAGAGGCCATGGACCCTGTCTCGGTGTCATACCCGTCTAATTACATGAA
GTCGATGAAGCCCAACAAGTACGGCGTCATCTACTCCACGCCATTGTCGGATAAGTTCTTCCAGACGCCGGAAGGCCTGT
CTCACGGGATGCAGATGGAGCCGGTGGACCTCACGGTCAACAAGCGGAGCTCGCCGCCCTCGGCCGGGAACTCGCCGTCC
TCCCTGAAGTTCCAGTCCTCCCACAGGCGCGCCTCGCCCGGGCTGAGCCTGCCCTCGTCCAGCCCGCCGGGGAAGAAGTA
CTCGCCGCCGCCGCCGCCCGGCGTGCAGCCCTTCAGCGTGCCGCTGTCCATGCCGCCGGTGATGGCCGCGGCCCTGTCCC
GCCACGGCATCCGGAGCCCGGGCATCCTGCCCGTCATCCAGCCCGTCGTCGTGCAGCCTGTCCCCTTCATGTACACCAGC
CACCTCCAGCAGCCGCTCATGGTCTCCTTGTCGGAGGAGATGGAAAATTCCAGTAGTAGCATGCAAGTACCTGTAATTGA
ATCATATGAGAAGCCTATATTGCAGAAAAAAATTAAAATAGAACCTGGGATCGAACCACAGAGGACAGATTATTATCCCG
AAGAAATGTCACCCCCTTTAATGAACTCAGTGTCCCCCCCGCAAGCATTGTTGCAAGAG

Alignment

ORF - retro_btau_271 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.57 %
• Parental protein coverage: 67.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLMFDPVPVKQEAMDPVSVSYPSNYMESMKPNKYGVIYSTPLSDKFFQTPEGLSHGMQMEPVDLTVNKRS
          MLMFDPVPVKQEAMDPVSVSYPSNYM.SMKPNKYGVIYSTPLSDKFFQTPEGLSHGMQMEPVDLTVNKRS
Retrocopy MLMFDPVPVKQEAMDPVSVSYPSNYMKSMKPNKYGVIYSTPLSDKFFQTPEGLSHGMQMEPVDLTVNKRS

Parental  SPPSAGNSPSSLKFQSSHRRASPGLSLPSSSPPGKKYSPPPPPGVQPFSVPLSMPPVMAAALSRHGIRSP
          SPPSAGNSPSSLKFQSSHRRASPGLSLPSSSPPGKKYSPPPPPGVQPFSVPLSMPPVMAAALSRHGIRSP
Retrocopy SPPSAGNSPSSLKFQSSHRRASPGLSLPSSSPPGKKYSPPPPPGVQPFSVPLSMPPVMAAALSRHGIRSP

Parental  GILPVIQPVVVQPVPFMYTSHLQQPLMVSLSEEMENSSSSMQVPVIESYEKPILQKKIKIEPGIEPQRTD
          GILPVIQPVVVQPVPFMYTSHLQQPLMVSLSEEMENSSSSMQVPVIESYEKPILQKKIKIEPGIEPQRTD
Retrocopy GILPVIQPVVVQPVPFMYTSHLQQPLMVSLSEEMENSSSSMQVPVIESYEKPILQKKIKIEPGIEPQRTD

Parental  YYPEEMSPPLMNSVSPPQALLQE
          YYPEEMSPPLMNSVSPPQALLQE
Retrocopy YYPEEMSPPLMNSVSPPQALLQE

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	3.24 RPM
ERP005899_muscle	0.84 RPM	16.73 RPM
SRP017611_brain	0.64 RPM	5.71 RPM
SRP017611_kidney	0.59 RPM	9.66 RPM
SRP017611_liver	0.38 RPM	3.25 RPM
SRP030211_testis	0.51 RPM	1.07 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_271 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_271 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_271 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 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,
Choloepus hoffmanni	ENSCHOG00000004256	1 retrocopy	retro_chof_181,
Macaca mulatta	ENSMMUG00000003363	1 retrocopy	retro_mmul_2118,
Nomascus leucogenys	ENSNLEG00000017046	1 retrocopy	retro_nleu_2431,
Otolemur garnettii	ENSOGAG00000006524	1 retrocopy	retro_ogar_1686,