RetrogeneDB ID: retro_btau_241

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 11:14590047..14590362(+)
• Located in intron of: ENSBTAG00000007734

Retrocopy information

• Ensembl ID: ENSBTAG00000033887
• 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_241
ATGGTCAACGTACCTAAAACCCGCAGGACTTTCTGTAAGAAGTGTGGAAAGCATCAGCCTCACAAAGTGACCCAGTGTAA
GAAGGGCAAAGATTCCCTGTATGCCCAGGGAAAGAGGCGCTATGATCAGAAGCAGAGTGGCTACGGTGGGCAAACCAAGC
CAATTTTCCGGAAGAAGGCTAAAACCACCAAGGAGGTCGTGCTGAGACTTGAATGCGTTGAGCCCAACTGCAGATCCAAG
AGGATGCTGGCCATTAAGAGGTGCAAGCATTTTGAACTTGGAGGACATAAGAAGAGAAAGGACCAAGTGATCTAG

Alignment

ORF - retro_btau_241 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.23 %
• Parental protein coverage: 98.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVNVPKTRRTFCKKCGKHQPHKVTQYKKGKDSLYAQGKRRYDRKQSGYGGQTKPIFRKKAKTTKKIVLRL
          MVNVPKTRRTFCKKCGKHQPHKVTQ.KKGKDSLYAQGKRRYD.KQSGYGGQTKPIFRKKAKTTK..VLRL
Retrocopy MVNVPKTRRTFCKKCGKHQPHKVTQCKKGKDSLYAQGKRRYDQKQSGYGGQTKPIFRKKAKTTKEVVLRL

Parental  ECVEPNCRSKRMLAIKRCKHFELGGDKKRKGQVI
          ECVEPNCRSKRMLAIKRCKHFELGG.KKRK.QVI
Retrocopy ECVEPNCRSKRMLAIKRCKHFELGGHKKRKDQVI

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	63.88 RPM
ERP005899_muscle	0.37 RPM	213.64 RPM
SRP017611_brain	0.14 RPM	20.51 RPM
SRP017611_kidney	0.06 RPM	45.22 RPM
SRP017611_liver	0.15 RPM	21.82 RPM
SRP030211_testis	0.09 RPM	16.26 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_241 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_241 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_241 has 0 orthologous retrocopies within eutheria group .

---

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,