RetrogeneDB ID: retro_btau_688

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 18:13387835..13388672(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DYNC1LI1
• Ensembl ID: ENSBTAG00000014700
• Aliases: None
• Description: cytoplasmic dynein 1 light intermediate chain 1 [Source:RefSeq peptide;Acc:NP_001039517]

Sequence

>retro_btau_688
CAGTGTGATGCCATTAGTGTGTTGGAGAAAGAACATGACTACAGAGATGAGCATTTTGATTTTATTCAGTCACATATCCG
GAAGTTTTGTTTACAGTATGGTGCAGCACTTATATACGCTTCAGTAAAAGAAAATAAAAATATAGATTTAGTATATAAGT
ACATCGTCCAGAAACTCTATGGATTTCCTTATAAGATTCCTGCTGTTGTTGTGGAAAAAGATGCAGTATTTATTCCAGCA
GGGTGGGATAATGATAAGAAAATAGGAATATTACATGAAAACTTTCAAACGTTAAAAGCAGAAGATAATTTTGAAGACAT
CATAACTAAACCACCTGTCCGAAAGTTTGTGCATGAGAAAGAAATTATGGCGGAAGATGACCAAGTGTTTCCTATGAAGC
TACAGTCCCTTTTAGCAAAGCAACCACCAACTGCAGCTGGAAGGCCTGTGGATGCCTCACCAAGAGTCCCAAGAGGCTCC
CCTCGAACACCAAACAGATCTGTGTCATCCAACGTTGCTAGCGTATCACCCATCCCTGCTGGGTCAAAAAAGATCGATCC
AAACATGAAAGCTGGAGCTACAAGTGAAGGTGTCCTGGCAAATTTCTTTAACAGTTTGCTGAGTAAAAAGACTGGCTCCC
CAGGAGGCCCTGGTGTTGGTGGTGGTAGCCCTGGAGGTGGGGCTGCAGGCGGAGGCGGCGGTTTACCACCGTCTGCCAAA
AAGTCAGGCCAGAAGCCTGTCCTGTAAGACGTTCATGCGGAGCTGGACAGAATCGCACGGAAACCAGTGACGGTCTCCAC
TACCACACCTACATCTCCTGCAGAAGGAGAAGCTTCT

Alignment

ORF - retro_btau_688 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.57 %
• Parental protein coverage: 53.24 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KCDAISVLEKEHDYRDEHFDFIQSHIRKFCLQYGAALIYASVKENKNIDLVYKYIVQKLYGFPYKIPAVV
          .CDAISVLEKEHDYRDEHFDFIQSHIRKFCLQYGAALIYASVKENKNIDLVYKYIVQKLYGFPYKIPAVV
Retrocopy QCDAISVLEKEHDYRDEHFDFIQSHIRKFCLQYGAALIYASVKENKNIDLVYKYIVQKLYGFPYKIPAVV

Parental  VEKDAVFIPAGWDNDKKIGILHENFQTLKAEDNFEDIITKPPVRKFVHEKEIMAEDDQVFLMKLQSLLAK
          VEKDAVFIPAGWDNDKKIGILHENFQTLKAEDNFEDIITKPPVRKFVHEKEIMAEDDQVF.MKLQSLLAK
Retrocopy VEKDAVFIPAGWDNDKKIGILHENFQTLKAEDNFEDIITKPPVRKFVHEKEIMAEDDQVFPMKLQSLLAK

Parental  QPPTAAGRPVDASPRVPGGSPRTPNRSVSSNVASVSPIPAGSKKIDPNMKAGATSEGVLANFFNSLLSKK
          QPPTAAGRPVDASPRVP.GSPRTPNRSVSSNVASVSPIPAGSKKIDPNMKAGATSEGVLANFFNSLLSKK
Retrocopy QPPTAAGRPVDASPRVPRGSPRTPNRSVSSNVASVSPIPAGSKKIDPNMKAGATSEGVLANFFNSLLSKK

Parental  TGSPGGPGVGGGSPGGGAAGGGGGLPPSAKKSGQKPVLSDVHAELDRIARKPVTVSTTTPTSPAEGEAS
          TGSPGGPGVGGGSPGGGAAGGGGGLPPSAKKSGQKPVL.DVHAELDRIARKPVTVSTTTPTSPAEGEAS
Retrocopy TGSPGGPGVGGGSPGGGAAGGGGGLPPSAKKSGQKPVL*DVHAELDRIARKPVTVSTTTPTSPAEGEAS

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	2.60 RPM	15.43 RPM
ERP005899_muscle	0.00 RPM	33.47 RPM
SRP017611_brain	0.09 RPM	33.67 RPM
SRP017611_kidney	0.06 RPM	32.24 RPM
SRP017611_liver	0.38 RPM	12.84 RPM
SRP030211_testis	1.35 RPM	42.07 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

1 EST(s) were mapped to retro_btau_688 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
DY143863	13388065	13388207	100	142	0	142

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_688 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_688 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014700	1 retrocopy	retro_btau_688 ,