RetrogeneDB ID: retro_mmul_2261

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 7:129632906..129633530(-)
• Located in intron of: ENSMMUG00000009520

Retrocopy information

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

Parental gene information

• Parental gene symbol: GLTP
• Ensembl ID: ENSMMUG00000022761
• Aliases: None
• Description: glycolipid transfer protein [Source:RefSeq peptide;Acc:NP_001247719]

Sequence

>retro_mmul_2261
ATGGCGCTGCTGGCTGAACACCTGCTGAAGCCGCTGCCCGCGGACAATCAGATCGAGACTAGGCACTTCCTCCAGGCGGT
GTCCCACCTGCCGCCCTTCTTCGATTACCTTGGGTCCCCAGTGTTTACTCCCATCAAGGCAAACATAAGCGGCAACATCA
CGAAAATCAAAGCCGTGTACGACACCAACCCAGCCAAGTTCTGGACCCTGCAGAACATCCTGGAGGTGGAGAAAGAAATG
TATGGAGCAGAGTGGCCCAAAGTAGAGGCCACACTGGCAATGATGTGGCTGAAAAGAGGCCTCCACTTCATCCAGGTCTT
CCTCCAGAGCACCTGTGACGGGGAGCGGGACGAGAACCACCCCAACCTCATCCGCGTCAACGCCACCAAGGCCTACGAGA
TGGCCCTCAAGAAGTACCATGGCTGGATCATGCAGATCTTCCAGGCAGCACTGTACGCAGCCCCCTATAAGTCCGACATC
CTGAAAGCGCTCTCCAAGGGGCAGAATGTGACAGAGGAGGAGTGCCTGGAGAAGATCCGCCTCTTCCTAGTCAACTACAC
GGCCACCATCGATGTCATCTATGAGATGTACACCCAGATGATGGCCGAGCTTAACTACAAGGTG

Alignment

ORF - retro_mmul_2261 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.82 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MALLAEHLLKPLPADKQIETGPFLEAVSHLPPFFDCLGSPVFTPIKADISGNITKIKAVYDTNPAKFRTL
          MALLAEHLLKPLPAD.QIET..FL.AVSHLPPFFD.LGSPVFTPIKA.ISGNITKIKAVYDTNPAKF.TL
Retrocopy MALLAEHLLKPLPADNQIETRHFLQAVSHLPPFFDYLGSPVFTPIKANISGNITKIKAVYDTNPAKFWTL

Parental  QNILEVEKEMYGAEWPKVGATLALMWLKRGLRFIQVFLQSICDGERDENHPNLIRVNATKAYEMALKKYH
          QNILEVEKEMYGAEWPKV.ATLA.MWLKRGL.FIQVFLQS.CDGERDENHPNLIRVNATKAYEMALKKYH
Retrocopy QNILEVEKEMYGAEWPKVEATLAMMWLKRGLHFIQVFLQSTCDGERDENHPNLIRVNATKAYEMALKKYH

Parental  GWIVQKIFQAALYAAPYKSDFLKALSKGQNVTEEECLEKIRLFLVNYTATIDVIYEMYTQMNAELNYKV
          GWI.Q.IFQAALYAAPYKSD.LKALSKGQNVTEEECLEKIRLFLVNYTATIDVIYEMYTQM.AELNYKV
Retrocopy GWIMQ-IFQAALYAAPYKSDILKALSKGQNVTEEECLEKIRLFLVNYTATIDVIYEMYTQMMAELNYKV

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	0.00 RPM	5.04 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	8.81 RPM
SRP007412_cerebellum	0.06 RPM	5.30 RPM
SRP007412_heart	0.00 RPM	5.06 RPM
SRP007412_kidney	0.12 RPM	15.38 RPM
SRP007412_liver	0.08 RPM	4.39 RPM
SRP007412_testis	0.04 RPM	5.65 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2261 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2261 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2261 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000034092	1 retrocopy	retro_cjac_1284,
Homo sapiens	ENSG00000139433	1 retrocopy	retro_hsap_755,
Myotis lucifugus	ENSMLUG00000012545	5 retrocopies	retro_mluc_1056, retro_mluc_1902, retro_mluc_2135, retro_mluc_2397, retro_mluc_658,
Macaca mulatta	ENSMMUG00000022761	1 retrocopy	retro_mmul_2261 ,
Pongo abelii	ENSPPYG00000004939	1 retrocopy	retro_pabe_28,
Pan troglodytes	ENSPTRG00000005431	1 retrocopy	retro_ptro_41,