RetrogeneDB ID: retro_mmul_1136

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 15:17327398..17327937(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BCAS4
• Ensembl ID: ENSMMUG00000012127
• Aliases: None
• Description: breast carcinoma-amplified sequence 4 [Source:RefSeq peptide;Acc:NP_001253400]

Sequence

>retro_mmul_1136
CAACCGGACCCCGCCGCCCTCCTGATGCTGCTTGTGAACGCCGATCCGAGCCCGTGCGCAGCGGAGCGCGGGAGCTCGCG
CTCTTCCTGACCCCCGAGCCTGGGGCCGAGGCGAAGGAGGTGGAGGAGACCATCGAGGCCATGCTCCTCAGGCTGGAAGA
GTTTTGCAGCCTGGCTGACCTGATCAGGAGTGATACGTCACAGATCCTGGAGGAAAACATCCCAGTCCTTAAGGCCAAAC
TGACAGAAATGCGTGGCATCTACGCCATAGTGGACCGGCTAGAGGCCTTCGTCAAGATGGTCGGACACCATGTCGCGTTC
CTGGAAGCGGACGTACTTCAGACTGAGCGGGACCATGGGGCCTTCCCGCAGGCCCTGCGGAGGTGGCTGGGATCCGCAGG
GCTCCCCTCCTTCAGGAACAAGTCGCCTGCACCAGTACCCGTGACGTATGAGCTGCCCACGCTGTACAGGACGGAGGACT
ATTTTCCTGCGGACACCAGGGAGGCACAGCACCACCCCCGCACCTGCCCTCGGCCTTTG

Alignment

ORF - retro_mmul_1136 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.6 %
• Parental protein coverage: 89.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QPDSAALLMLLVNADRPEP-VRSGARELALFLTPEPGAEAKEVEETIEGMLLRLEEFCSLADLIRSDTSQ
          QPD.AALLMLLVNAD.P.P.VRSGARELALFLTPEPGAEAKEVEETIE.MLLRLEEFCSLADLIRSDTSQ
Retrocopy QPDPAALLMLLVNAD-PSP<VRSGARELALFLTPEPGAEAKEVEETIEAMLLRLEEFCSLADLIRSDTSQ

Parental  ILEENIPVLKAKLTEMRGIYAKVDRLEAFVKMVGHHVAFLEADVLQAERDHGAFPQALRRWLGSAGLPSF
          ILEENIPVLKAKLTEMRGIYA.VDRLEAFVKMVGHHVAFLEADVLQ.ERDHGAFPQALRRWLGSAGLPSF
Retrocopy ILEENIPVLKAKLTEMRGIYAIVDRLEAFVKMVGHHVAFLEADVLQTERDHGAFPQALRRWLGSAGLPSF

Parental  RNKSPAPVPVTYELPTLYRTEDYFPADAREAQHHPRTCPRPL
          RNKSPAPVPVTYELPTLYRTEDYFPAD.REAQHHPRTCPRPL
Retrocopy RNKSPAPVPVTYELPTLYRTEDYFPADTREAQHHPRTCPRPL

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
SRP007412_brain	0.11 RPM	2.80 RPM
SRP007412_brain_prefrontal_cortex	0.16 RPM	7.38 RPM
SRP007412_cerebellum	0.06 RPM	1.42 RPM
SRP007412_heart	0.00 RPM	0.24 RPM
SRP007412_kidney	0.00 RPM	1.53 RPM
SRP007412_liver	0.00 RPM	0.20 RPM
SRP007412_testis	0.41 RPM	1.39 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1136 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1136 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1136 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000012127	1 retrocopy	retro_mmul_1136 ,
Oryctolagus cuniculus	ENSOCUG00000014694	1 retrocopy	retro_ocun_853,