RetrogeneDB ID: retro_btau_861

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 2:25336692..25336932(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LSM6
• Ensembl ID: ENSBTAG00000014060
• Aliases: None
• Description: U6 snRNA-associated Sm-like protein LSm6 [Source:RefSeq peptide;Acc:NP_001107991]

Sequence

>retro_btau_861
ATGAGTCTGTGGAAGCAAACGCCCAGTGACTTCCTGAAGCAGATCACTGGGCGACCAGTTGTGGTGAAGCTAAATTCGGG
AGTGGATTATCGAGGGGTCCTGGCTTGCCTGGATGGCTACATGAATATAGTCTTGGAGCAGACAGAGGAGTATGTAAATG
GACAGCTGAAGAATACATACGGGGATGCATTTATCCAAGGAAACAATGTGTTGTATATAAGTACGCAGAAGAGGAGGATG

Alignment

ORF - retro_btau_861 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.75 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSLRKQTPSDFLKQIIGRPVVVKLNSGVDYRGVLACLDGYMNIALEQTEEYVNGQLKNKYGDAFIRGNNV
          MSL.KQTPSDFLKQI.GRPVVVKLNSGVDYRGVLACLDGYMNI.LEQTEEYVNGQLKN.YGDAFI.GNNV
Retrocopy MSLWKQTPSDFLKQITGRPVVVKLNSGVDYRGVLACLDGYMNIVLEQTEEYVNGQLKNTYGDAFIQGNNV

Parental  LYISTQKRRM
          LYISTQKRRM
Retrocopy LYISTQKRRM

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	0.22 RPM	16.58 RPM
ERP005899_muscle	0.11 RPM	13.41 RPM
SRP017611_brain	0.00 RPM	13.02 RPM
SRP017611_kidney	0.00 RPM	20.75 RPM
SRP017611_liver	0.08 RPM	12.31 RPM
SRP030211_testis	0.07 RPM	20.39 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_861 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_861 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_861 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014060	1 retrocopy	retro_btau_861 ,
Bos taurus	ENSBTAG00000016271	1 retrocopy	retro_btau_765,
Cavia porcellus	ENSCPOG00000015389	1 retrocopy	retro_cpor_368,
Dasypus novemcinctus	ENSDNOG00000009322	5 retrocopies	retro_dnov_1118, retro_dnov_176, retro_dnov_2092, retro_dnov_301, retro_dnov_664,
Homo sapiens	ENSG00000164167	2 retrocopies	retro_hsap_1948, retro_hsap_2107,
Gorilla gorilla	ENSGGOG00000001310	2 retrocopies	retro_ggor_1417, retro_ggor_1638,
Myotis lucifugus	ENSMLUG00000026355	1 retrocopy	retro_mluc_1859,
Monodelphis domestica	ENSMODG00000000526	4 retrocopies	retro_mdom_1027, retro_mdom_1383, retro_mdom_1983, retro_mdom_621,
Nomascus leucogenys	ENSNLEG00000005584	2 retrocopies	retro_nleu_1275, retro_nleu_1479,
Otolemur garnettii	ENSOGAG00000026665	1 retrocopy	retro_ogar_233,
Sus scrofa	ENSSSCG00000009036	2 retrocopies	retro_sscr_474, retro_sscr_475,
Tarsius syrichta	ENSTSYG00000012759	4 retrocopies	retro_tsyr_1332, retro_tsyr_1727, retro_tsyr_340, retro_tsyr_653,