RetrogeneDB ID: retro_btau_880

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 2:94064787..94065117(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DSTN
• Ensembl ID: ENSBTAG00000015434
• Aliases: None
• Description: Destrin [Source:UniProtKB/Swiss-Prot;Acc:Q5E9D5]

Sequence

>retro_btau_880
TTGGTGGGAGATGTTGGTGTCACCAAAACCGATCCTTTGAAGCATTTTGTGGGGATGCTTCCTGAAAAAGATTGTTGATA
TGCTCTGTATGATACAGGCTTTGAAACAAAGGAATCCAGAAAAGAGGAGTTGATGTTTTTCCTGTGGGCACCAGAACTGT
CTCCTCTGAAGAGTAAAATGATCTATGCGAGCTCCAAGGATGCCATCAGAAGGAAGTTCCAAGGCATAAAACACAAATGT
CAAGCAAATAGGCCAGAAAACCTCAATCGAGCTTGTACTGCTGAAAAGCTAGGTGGATCCCTAATTGTAGTTTTTGAAGG
ATGTCCTGTG

Alignment

ORF - retro_btau_880 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.18 %
• Parental protein coverage: 66.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LVGDVGVTITDPFKHFVGMLPEKDCRYALYDASFETKESRKEELMFFLWAPELAPLKSKMIYASSKDAIK
          LVGDVGVT.TDP.KHFVGMLPEKDC.YALYD..FETKESRKEELMFFLWAPEL.PLKSKMIYASSKDAI.
Retrocopy LVGDVGVTKTDPLKHFVGMLPEKDC*YALYDTGFETKESRKEELMFFLWAPELSPLKSKMIYASSKDAIR

Parental  KKFQGIKHECQANGPEDLNRACIAEKLGGSLIVAFEGCPV
          .KFQGIKH.CQAN.PE.LNRAC.AEKLGGSLIV.FEGCPV
Retrocopy RKFQGIKHKCQANRPENLNRACTAEKLGGSLIVVFEGCPV

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	44.77 RPM
ERP005899_muscle	0.26 RPM	172.30 RPM
SRP017611_brain	0.05 RPM	92.91 RPM
SRP017611_kidney	0.00 RPM	401.21 RPM
SRP017611_liver	0.00 RPM	46.59 RPM
SRP030211_testis	0.02 RPM	82.60 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_880 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_880 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_880 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015434	1 retrocopy	retro_btau_880 ,
Bos taurus	ENSBTAG00000021455	1 retrocopy	retro_btau_1382,
Choloepus hoffmanni	ENSCHOG00000003110	5 retrocopies	retro_chof_1308, retro_chof_1656, retro_chof_1758, retro_chof_2297, retro_chof_72,
Cavia porcellus	ENSCPOG00000005573	2 retrocopies	retro_cpor_700, retro_cpor_812,
Dasypus novemcinctus	ENSDNOG00000000934	1 retrocopy	retro_dnov_24,
Homo sapiens	ENSG00000125868	1 retrocopy	retro_hsap_952,
Gorilla gorilla	ENSGGOG00000009007	1 retrocopy	retro_ggor_768,
Microcebus murinus	ENSMICG00000013687	1 retrocopy	retro_mmur_765,
Macaca mulatta	ENSMMUG00000013786	1 retrocopy	retro_mmul_782,
Mus musculus	ENSMUSG00000015932	1 retrocopy	retro_mmus_3314,
Nomascus leucogenys	ENSNLEG00000009679	1 retrocopy	retro_nleu_2458,
Oryctolagus cuniculus	ENSOCUG00000027456	1 retrocopy	retro_ocun_1891,
Ochotona princeps	ENSOPRG00000000976	2 retrocopies	retro_opri_1078, retro_opri_696,
Pongo abelii	ENSPPYG00000010727	1 retrocopy	retro_pabe_812,
Pan troglodytes	ENSPTRG00000013275	1 retrocopy	retro_ptro_659,
Pteropus vampyrus	ENSPVAG00000000420	1 retrocopy	retro_pvam_1275,
Rattus norvegicus	ENSRNOG00000005924	1 retrocopy	retro_rnor_1710,
Tupaia belangeri	ENSTBEG00000017634	8 retrocopies	retro_tbel_1206, retro_tbel_1977, retro_tbel_2425, retro_tbel_2880, retro_tbel_2881, retro_tbel_4020, retro_tbel_679, retro_tbel_851,
Tursiops truncatus	ENSTTRG00000007291	1 retrocopy	retro_ttru_1503,