RetrogeneDB ID: retro_btau_183

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 15:54468040..54468361(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000027610
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RPL36A
• Ensembl ID: ENSBTAG00000019253
• Aliases: None
• Description: 60S ribosomal protein L36a [Source:UniProtKB/Swiss-Prot;Acc:Q3SZ59]

Sequence

>retro_btau_183
ATGGTGAACGTTCCAAAAACCCGTCGGACTTTCTGTAAGAAGTGTGGGAAGCACCAGCCCCACAAAGTGACACAGTACAA
GAAGGGCAAGGATTCTCTGTATGCCCAGGGAAAGCGGCGTTATGACAGGAAACAGAGTGGCTATGGTGGGCAGACTAAGC
CGATTTTCCGGAAAAAGGCTAAAACTACAAAGAAGATTGTACTGAGGCTTGAATGTGTTGAGCCCAACTGTAGATCAAAG
AGAATGCTGGCTATTAAGAGATGCAAGCATTTTGAGCTGGGAGGTGATAAGAAGAGAAAGGGCCAAGTGATCCAGTTTTG
A

Alignment

ORF - retro_btau_183 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  MVNVPKTRRTFCKKCGKHQPHKVTQYKKGKDSLYAQGKRRYDRKQSGYGGQTKPIFRKKAKTTKKIVLRL
          MVNVPKTRRTFCKKCGKHQPHKVTQYKKGKDSLYAQGKRRYDRKQSGYGGQTKPIFRKKAKTTKKIVLRL
Retrocopy MVNVPKTRRTFCKKCGKHQPHKVTQYKKGKDSLYAQGKRRYDRKQSGYGGQTKPIFRKKAKTTKKIVLRL

Parental  ECVEPNCRSKRMLAIKRCKHFELGGDKKRKGQVIQF
          ECVEPNCRSKRMLAIKRCKHFELGGDKKRKGQVIQF
Retrocopy ECVEPNCRSKRMLAIKRCKHFELGGDKKRKGQVIQF

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	0.65 RPM	63.88 RPM
ERP005899_muscle	1.00 RPM	213.64 RPM
SRP017611_brain	0.23 RPM	20.51 RPM
SRP017611_kidney	0.59 RPM	45.22 RPM
SRP017611_liver	0.30 RPM	21.82 RPM
SRP030211_testis	0.17 RPM	16.26 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_183 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_183 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_183 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000008503	1 retrocopy	retro_acar_98,
Bos taurus	ENSBTAG00000019253	3 retrocopies	retro_btau_183 , retro_btau_241, retro_btau_92,
Loxodonta africana	ENSLAFG00000017385	1 retrocopy	retro_lafr_114,
Monodelphis domestica	ENSMODG00000025578	2 retrocopies	retro_mdom_1878, retro_mdom_971,
Sarcophilus harrisii	ENSSHAG00000013479	1 retrocopy	retro_shar_467,