RetrogeneDB ID: retro_mmul_2030

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 6:109216369..109217368(+)
• Located in intron of: ENSMMUG00000020488

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZRSR2
• Ensembl ID: ENSMMUG00000014054
• Aliases: None
• Description: None

Sequence

>retro_mmul_2030
GCTATGCAGAAGATGCTGGATCAGGCTGAAAATGAGTTAGAAAATGGTACCATATGGTAAAACCCTGAACCACCTGTGGA
TTTCAGAGTAATGGAGAAGGATCGAGCTAATTGTCCCTTTTACAGTAAAACAGGAGCTTGCAGATTTGGAGACAGATGTT
CACGTAAACATAATTTCCCAACATCCAGTCCTACCCTTCTTATTAAGAGCATGTTTACAACGTTTGGAATGGAGCAGTGC
AGGAGGGATGACTATGACCCTGACGCAAGCCTGGAGTATAGCGAGGAAGAAATCTACCAACAGTTCCTAGATTTCTATGA
GGATGTGTTGCCCGAGTTCAAGAACGTGGGGAAGGTGATTCAGTTCAAGGTCAGCTGCAATTTAGAACCTCACCTGAGGG
GCAATGTATATGTTCAGTACCAGTCGGAAGAAGAATGCCAAGCAGCCCTTTCTCTGTTTAATGGACGATGGTATGCAGGA
CGACAGCTGCAATGTGAATTCTGCCCAGTGACCCGGTGGAAAATGGCGATTTGTGGTTTATTTGAAATACAACAGTGTCC
AAGAGGAAAACACTGCAACTTTCTTCATGTGTTCAGAAATCCCAACAATGAATTCTGGGAAGCTAACAGAGACATCCACT
TGTCTCCAGATCAGACTGGCTCCTCCTTTGGCAAGAACTCCGAGAGGAGGGAGAGGATGCGCCACCACGACCACTACTCT
AGCAGGCTGCGGGGAAGGAGAAACCCTAGTCCAGACCACTCCTACAAAAGAAATGGGGAATCTGAGAGGAAAAGGAGTAG
TCACAGGGTGAAGAAATCTCACAAACACACATCAAAGAGTCGGGAGAAGCACAATTCACCAAGCAGAGGAAGAAACAGGC
ACCGCAGCCAGGGCCAGGGCCGCCGGAGCCAGAGCCGCAGGAGCCACCGCAGCCGGAGCCAAAGTTCCTCTAGGTCCTGA
AGTCGTGGCAGGAGGAGGTCGGGTAATAGAGGCAGAACC

Alignment

ORF - retro_mmul_2030 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.09 %
• Parental protein coverage: 69.52 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ALQKMLDQAENELENGTTWQNPEPPVDFRVMEKDRANCPFYSKTGACRFGDRCSRKHNFPTSSPTLLIKS
          A.QKMLDQAENELENGT.W.NPEPPVDFRVMEKDRANCPFYSKTGACRFGDRCSRKHNFPTSSPTLLIKS
Retrocopy AMQKMLDQAENELENGTIW*NPEPPVDFRVMEKDRANCPFYSKTGACRFGDRCSRKHNFPTSSPTLLIKS

Parental  MFTTFGMEQCRRDDYDPDASLEYSEEETYQQFLDFYEDVLPEFKNVGKVIQFKVSCNLEPHLRGNVYVQY
          MFTTFGMEQCRRDDYDPDASLEYSEEE.YQQFLDFYEDVLPEFKNVGKVIQFKVSCNLEPHLRGNVYVQY
Retrocopy MFTTFGMEQCRRDDYDPDASLEYSEEEIYQQFLDFYEDVLPEFKNVGKVIQFKVSCNLEPHLRGNVYVQY

Parental  QSEEECQAALSLFNGRWYAGRQLQCEFCPVTRWKMAICGLFEIQQCPRGKHCNFLHVFRNPNNEFWEANR
          QSEEECQAALSLFNGRWYAGRQLQCEFCPVTRWKMAICGLFEIQQCPRGKHCNFLHVFRNPNNEFWEANR
Retrocopy QSEEECQAALSLFNGRWYAGRQLQCEFCPVTRWKMAICGLFEIQQCPRGKHCNFLHVFRNPNNEFWEANR

Parental  DIYLSPDRTGSSFGKNSERRERMGHHDDYYSRLRGRRNPSPDHSYKRNGESERKRSSHRGKKSHKRTSKS
          DI.LSPD.TGSSFGKNSERRERM.HHD.Y.SRLRGRRNPSPDHSYKRNGESERKRSSHR.KKSHK.TSKS
Retrocopy DIHLSPDQTGSSFGKNSERRERMRHHDHYSSRLRGRRNPSPDHSYKRNGESERKRSSHRVKKSHKHTSKS

Parental  RERHNSRSRGRNKDRSRDRSRGRGSRSRSRSRRSRRSRSQSSSRSRSRGRRRS
          RE.HNS.SRGRN..RS....................SRS.S..R.RS..R.R.
Retrocopy REKHNSPSRGRNRHRSQXXXXXXXXXXXXXXXXXSSSRS*SRGRRRSGNRGRT

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	2.69 RPM	11.99 RPM
SRP007412_brain_prefrontal_cortex	1.82 RPM	7.22 RPM
SRP007412_cerebellum	5.49 RPM	12.14 RPM
SRP007412_heart	1.24 RPM	14.90 RPM
SRP007412_kidney	2.23 RPM	7.51 RPM
SRP007412_liver	0.51 RPM	2.49 RPM
SRP007412_testis	2.37 RPM	4.22 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2030 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2030 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2030 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000009333	1 retrocopy	retro_fcat_44,
Homo sapiens	ENSG00000169249	1 retrocopy	retro_hsap_39,
Gorilla gorilla	ENSGGOG00000011962	1 retrocopy	retro_ggor_1422,
Macaca mulatta	ENSMMUG00000014054	1 retrocopy	retro_mmul_2030 ,
Macaca mulatta	ENSMMUG00000022769	2 retrocopies	retro_mmul_1071, retro_mmul_2126,
Mus musculus	ENSMUSG00000031370	1 retrocopy	retro_mmus_233,
Nomascus leucogenys	ENSNLEG00000009496	1 retrocopy	retro_nleu_1,
Pan troglodytes	ENSPTRG00000021693	1 retrocopy	retro_ptro_25,
Rattus norvegicus	ENSRNOG00000033176	1 retrocopy	retro_rnor_176,
Tarsius syrichta	ENSTSYG00000005278	1 retrocopy	retro_tsyr_1826,