RetrogeneDB ID: retro_btau_878

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 2:89699631..89699997(-)
• Located in intron of: ENSBTAG00000038878

Retrocopy information

• Ensembl ID: ENSBTAG00000047849
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BLOC1S1
• Ensembl ID: ENSBTAG00000011918
• Aliases: None
• Description: Biogenesis of lysosome-related organelles complex 1 subunit 1 [Source:UniProtKB/Swiss-Prot;Acc:Q2NKW0]

Sequence

>retro_btau_878
ATGCTGTCTCACCTGCTGAAAGACCACCAGGCCAAGCAGAACAAATGCAAAAAGCTGCGGCCGAAGAGGCGAGAGGCCAT
CACTCCAGCCACCTGCCTGACAGAAGTTTTGGTGGATCACCTCAATGTGGGTGTGGCCCAGGCCAACAGGAGCCAGAGAA
AGCTGGACAACAAGGTGAAGACCCTACAGATTCAGGCTGCCCAGTCTGCCAAGAGTACAGGTCAGTGGCTTGGGATGGTG
GAGAACTTCAACCAGGTACAAATCAGGAATGTGCAGAACTGGGCTCAGAAAATCGAGCTGGACATGTGCACCATCACCAC
CATGCTGAAGTACATCTACAAAGGGCAGTGGCAGTCGGCCCCCTCC

Alignment

ORF - retro_btau_878 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.8 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLSRLLKEHQAKQNERKELQEKRRREAITAATCLTEALVDHLNVGVAQAYMNQRKLDHEVKTLQVQAAQF
          MLS.LLK.HQAKQN..K.L..KRR.EAIT.ATCLTE.LVDHLNVGVAQA...QRKLD..VKTLQ.QAAQ.
Retrocopy MLSHLLKDHQAKQNKCKKLRPKRR-EAITPATCLTEVLVDHLNVGVAQANRSQRKLDNKVKTLQIQAAQS

Parental  AKQTGQWIGMVENFNQALKEIGDVENWARSIELDMRTIATALEYVYKGQLQSAPS
          AK.TGQW.GMVENFNQ....I..V.NWA..IELDM.TI.T.L.Y.YKGQ.QSAPS
Retrocopy AKSTGQWLGMVENFNQV--QIRNVQNWAQKIELDMCTITTMLKYIYKGQWQSAPS

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	13.84 RPM
ERP005899_muscle	0.00 RPM	31.62 RPM
SRP017611_brain	0.00 RPM	17.95 RPM
SRP017611_kidney	0.00 RPM	26.26 RPM
SRP017611_liver	0.00 RPM	24.84 RPM
SRP030211_testis	0.00 RPM	13.92 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_878 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_878 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_878 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011918	1 retrocopy	retro_btau_878 ,
Callithrix jacchus	ENSCJAG00000008026	1 retrocopy	retro_cjac_148,
Cavia porcellus	ENSCPOG00000001818	2 retrocopies	retro_cpor_1260, retro_cpor_846,
Macropus eugenii	ENSMEUG00000001570	3 retrocopies	retro_meug_12, retro_meug_1307, retro_meug_242,
Oryctolagus cuniculus	ENSOCUG00000010114	1 retrocopy	retro_ocun_1023,
Pteropus vampyrus	ENSPVAG00000017748	1 retrocopy	retro_pvam_121,
Sus scrofa	ENSSSCG00000000359	1 retrocopy	retro_sscr_850,
Ictidomys tridecemlineatus	ENSSTOG00000010338	1 retrocopy	retro_itri_467,