RetrogeneDB ID: retro_btau_1152

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 28:18349475..18349742(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000040018
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DDA1
• Ensembl ID: ENSBTAG00000017068
• Aliases: DDA1, PCIA1
• Description: DET1- and DDB1-associated protein 1 [Source:UniProtKB/Swiss-Prot;Acc:Q5E9A9]

Sequence

>retro_btau_1152
AGCAATTTTAGTAGATTTCATGCCGACTCTGTGTGCAAAGCCTCGAACCGACGTCCCTCAGTCTACCTGCCCACTAGGGA
GTACCCGTCTGAACAGATCATCGTGACAGAGAAAACAAACATTCTTTTGCGCTACCTACATCAGCAATGGGACAAAAAGA
ATGCCGCCAAGAAGAGAGACCAGGAGCAAGTGGAGCTAGCGGGCGAGAGCTCGGCGCCGCCCCGCAAGGTCGCGCGGACC
GACAGCCCGGACATGCACGAGGACACT

Alignment

ORF - retro_btau_1152 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.88 %
• Parental protein coverage: 87.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SNFSRFHADSVCKASNRRPSVYLPTREYPSEQIIVTEKTNILLRYLHQQWDKKNAAKKRDQEQVELEGES
          SNFSRFHADSVCKASNRRPSVYLPTREYPSEQIIVTEKTNILLRYLHQQWDKKNAAKKRDQEQVEL.GES
Retrocopy SNFSRFHADSVCKASNRRPSVYLPTREYPSEQIIVTEKTNILLRYLHQQWDKKNAAKKRDQEQVELAGES

Parental  SAPPRKVARTDSPDMHEDT
          SAPPRKVARTDSPDMHEDT
Retrocopy SAPPRKVARTDSPDMHEDT

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	1.15 RPM
ERP005899_muscle	0.05 RPM	8.24 RPM
SRP017611_brain	0.18 RPM	15.58 RPM
SRP017611_kidney	0.00 RPM	8.59 RPM
SRP017611_liver	0.00 RPM	4.76 RPM
SRP030211_testis	0.14 RPM	35.18 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1152 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1152 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1152 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017068	3 retrocopies	retro_btau_1152 , retro_btau_536, retro_btau_74,
Canis familiaris	ENSCAFG00000031251	3 retrocopies	retro_cfam_1089, retro_cfam_2033, retro_cfam_475,
Cavia porcellus	ENSCPOG00000006944	1 retrocopy	retro_cpor_435,
Felis catus	ENSFCAG00000001001	1 retrocopy	retro_fcat_487,
Homo sapiens	ENSG00000130311	1 retrocopy	retro_hsap_1409,
Gorilla gorilla	ENSGGOG00000005802	1 retrocopy	retro_ggor_1093,
Microcebus murinus	ENSMICG00000001763	1 retrocopy	retro_mmur_1162,
Myotis lucifugus	ENSMLUG00000003990	1 retrocopy	retro_mluc_1014,
Macaca mulatta	ENSMMUG00000016231	1 retrocopy	retro_mmul_2248,
Nomascus leucogenys	ENSNLEG00000005738	2 retrocopies	retro_nleu_1427, retro_nleu_1428,
Otolemur garnettii	ENSOGAG00000003701	1 retrocopy	retro_ogar_2375,
Pongo abelii	ENSPPYG00000009710	2 retrocopies	retro_pabe_1167, retro_pabe_1214,
Pan troglodytes	ENSPTRG00000010668	1 retrocopy	retro_ptro_966,
Rattus norvegicus	ENSRNOG00000039417	1 retrocopy	retro_rnor_1511,