RetrogeneDB ID: retro_mmul_945

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 12:39000478..39001390(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.2456
• Ensembl ID: ENSMMUG00000014236
• Aliases: SLC35A5, SLC35A3
• Description: probable UDP-sugar transporter protein SLC35A5 [Source:RefSeq peptide;Acc:NP_001247488]

Sequence

>retro_mmul_945
GCCATGGCTGTTGTCTTCTCAAATTTTAGAATTATAACAACAGCTCTTCTATTCAGGATAGTGCTGAAGAGGCATCTAAA
CTGGATCCAGTGGGCTTCCTTCCTGATTTTATTTTTGTCTATTTTGGCCTTGACTGCTGGGACTAAAACTTTACAGCACA
ACTTGGCAGGACATGGATTTCATCATGATGCCTTCTTCAGCCCATCCAATTCCTGCCTTCTTTTCAGAATTGAGTGTCCC
AGAAAAGACAATTGTACAACAAAGGAATGGACTTTTCCTGAAGCTAAATGGAACACCACAGTCAAGGTTTTCAGTCACGT
CCATCTTGGCATGGGCCATGTTCTTATTATAGTCCAGTGTTTTATTTCTTCGATGGCTAATATCTATAATGAAAATATAT
TGAAGGAAGGGAACCAGCTCACTGAAACCATCTTCATACAGAACAGCAAACTCTGTTTCTTTGGCATTCTGTTTAATGGG
CTGACTCTGGGCCTTCAGAGGAGTAACTGTGATCAGATTAAGAACTGTGGAATTTTTTATGGCCACAATGCATTTTCAGT
AGCCCTTATTTTTGTAACTGCATTCCAGGGCCTTTCAGTGGTTTTCACTCTGAAGTTCCTGGACAACATGTTCCATGTCT
TAAGGGCCCAGGTTACCACTGTCATTATCACAACAGTGTCTGTCCTGGTCTTTGACTTCAGGCCCTCCCTGGAATTTTTC
TTGGAAGCCCCATCAGTCCTTGTCTCTATATTTATTTATATTGCCAGCAAGCCTCAAGGTCCAGAATACACACCTAGGCA
AGAAAGGATCCGAGATCTAAGTGGCAATCTTTGAGAGAGTTCCAGTGGGGATGGAGAAGAACTAGAAAGACTTGCCAAAC
CCAAGAGTGATGAATCAGATGAAGATACTTTC

Alignment

ORF - retro_mmul_945 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.13 %
• Parental protein coverage: 71.7 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AMAVIFSNFSIITTALLFRIVLKKRLNWIQWASLLILFLSIVALTAGTKTLQHNLAGRGFHHDAFFSPSN
          AMAV.FSNF.IITTALLFRIVLK..LNWIQWAS.LILFLSI.ALTAGTKTLQHNLAG.GFHHDAFFSPSN
Retrocopy AMAVVFSNFRIITTALLFRIVLKRHLNWIQWASFLILFLSILALTAGTKTLQHNLAGHGFHHDAFFSPSN

Parental  SCLLFRSECPRKDNCTTKEWTFPEAKWNTTARVFSHIRLGMGHVLIIVQCFISSMASIYNEKILKEGNQL
          SCLLFR.ECPRKDNCTTKEWTFPEAKWNTT..VFSH..LGMGHVLIIVQCFISSMA.IYNE.ILKEGNQL
Retrocopy SCLLFRIECPRKDNCTTKEWTFPEAKWNTTVKVFSHVHLGMGHVLIIVQCFISSMANIYNENILKEGNQL

Parental  SESIFIQNSKLYFFGILFNGLTLGLQRSNRDQIKNCGFFYGHNAFSVALIFVTAFQGLSVAFILKFLDNM
          .E.IFIQNSKL.FFGILFNGLTLGLQRSN.DQIKNCG.FYGHNAFSVALIFVTAFQGLSV.F.LKFLDNM
Retrocopy TETIFIQNSKLCFFGILFNGLTLGLQRSNCDQIKNCGIFYGHNAFSVALIFVTAFQGLSVVFTLKFLDNM

Parental  FHVLMAQVTTVIITTVSVLIFDFRPSLEFLLEAPSVLLSIFIYNASKPQGPEYAPRQERIRDLSGNLWER
          FHVL.AQVTTVIITTVSVL.FDFRPSLEF.LEAPSVL.SIFIY.ASKPQGPEY.PRQERIRDLSGNL.E.
Retrocopy FHVLRAQVTTVIITTVSVLVFDFRPSLEFFLEAPSVLVSIFIYIASKPQGPEYTPRQERIRDLSGNL*ES

Parental  SSGDGEELERLTKPKSDESDEDTF
          SSGDGEELERL.KPKSDESDEDTF
Retrocopy SSGDGEELERLAKPKSDESDEDTF

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	30.37 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	22.05 RPM
SRP007412_cerebellum	0.06 RPM	19.70 RPM
SRP007412_heart	0.00 RPM	11.01 RPM
SRP007412_kidney	0.23 RPM	19.48 RPM
SRP007412_liver	0.12 RPM	10.01 RPM
SRP007412_testis	0.00 RPM	16.77 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_945 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_945 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_945 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000014236	1 retrocopy	retro_mmul_945 ,