RetrogeneDB ID: retro_mmul_604

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 10:43666603..43667775(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SDAD1
• Ensembl ID: ENSMMUG00000017503
• Aliases: None
• Description: None

Sequence

>retro_mmul_604
ATGCATGATCCCCAAGATTTTGCAGAAAAACTATTAAAGCAGCTTGAGTGCTGTAAGGAGAGGTTTGAAGCGAAGATGAT
GCTCATGAACCTCATCTCCAGATTGGTAGGAATTCATGAGCTCTTCCTCTTCAATTTCTATCCCTTTTGCAAAGGTTTCT
GCAGCCCCACCAAAGAGAAGTAACAAAAATCTTCTGCTTGATGCACAAGCATCTCATCACCTAGTGCCCCCAGAGATAAT
TCAATCATTGCCTATGATTTTGGCATACAATTTTGTTACTGACAAGAACTCTGGAGAAGTCATGACAGTAGGAATCAATG
CTATAAAAGAGATAACACCTTGATGTCCTCTGGCCGTGACTGAAGAACTCCTCCAAGACCTGGTTCAGTATAAAACACAC
AAGGATAAGAATGTAACGATGTCTGCTAGAACTTTGATTCAGCTCTTCCGAACACTGAATGCTCAGATGCTGCAGAAGAA
ATTCCGGGGTAAGCCTACAGAAGCCTCCGTAGAAGCAAGAGTACAAGAATATGGAGAATTAGATGCTAAAGTTTACATTC
CAGGAGCAGAAGTTCTGGAAGTTGAGAAAGAAGAGAATGCTGAAAATGATGAAGATGAATGGGAAAATACCAGTCTCAGT
GAGGAGGAGGATGCTGATGGTGAATAGATTGATATGCAACACTCTTCCGATGAAGAACAGCAAGAAATCTCCAAGAAGCT
GAACAGTATGTCCACGGAGGAGCGGAAAGCCAAAGCTGCAGCCATCAGCACCAGCTGAGTTTTAACTCAGGAAGACTTCC
AGAAAATCCTCATGGCCCAGATGAGAAAAGAACTTGATGCTGCCCCCGGGAAATCCCAGAAGAGGAAATACATTGAAAGA
GACAGTGATGAAGAGCCCAGGGGTGAATTACTTTCTCCTTGGGACATTGAACGCCTTCATTAAAAGCCAAAGTCTGACAA
AGAGACAAGACTAGCAACTGCAATGGCTGGAAAGACAGACCAAAAAGAATTTGTGAGGAAGAAGACCAAAATGAATCAAT
TTTCCAGTTCGACAAATAAAGAGAAGGAAAAACAGAAGAACTTTATGATAATGCGGTATAGCCAGAATGTCCGGTCAAAA
AAATAAGCATTCTTTCCAAGAAAAACAGTTGGCACTACAAGATGCACTTTTG

Alignment

ORF - retro_mmul_604 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.11 %
• Parental protein coverage: 57.56 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  IHDPQDFAEKLLKQLECCKERFEVKMMLMNLISRLVGIHELFLFNFYPF-LQRFLQPHQREVTKI-LLFA
          .HDPQDFAEKLLKQLECCKERFE.KMMLMNLISRLVGIHELFLFNFYPF.LQRFLQPHQREVTKI.LL..
Retrocopy MHDPQDFAEKLLKQLECCKERFEAKMMLMNLISRLVGIHELFLFNFYPF<LQRFLQPHQREVTKI<LLLD

Parental  AQASHHLVPPEIIQSLLMTVANNFVTDKNSGEVMTVGINAIKEITARCPLAMTEELLQDLAQYKTHKDKN
          AQASHHLVPPEIIQSL.M..A.NFVTDKNSGEVMTVGINAIKEIT..CPLA.TEELLQDL.QYKTHKDKN
Retrocopy AQASHHLVPPEIIQSLPMILAYNFVTDKNSGEVMTVGINAIKEITP*CPLAVTEELLQDLVQYKTHKDKN

Parental  VMMSARTLIQLFRTLNPQMLQKKFRGKPTEASMEARVQEYGELDAKDYIPGAEVLEVEKEENAENDEDGW
          V.MSARTLIQLFRTLN.QMLQKKFRGKPTEAS.EARVQEYGELDAK.YIPGAEVLEVEKEENAENDED.W
Retrocopy VTMSARTLIQLFRTLNAQMLQKKFRGKPTEASVEARVQEYGELDAKVYIPGAEVLEVEKEENAENDEDEW

Parental  ESTSLSEEEEDADGEWIDVQHSSDEEQQEISKKLNSMPMEERKAKAAAVSTSRVLTQEDFQKIRMAQMRK
          E.TSLSEEE.DADGE.ID.QHSSDEEQQEISKKLNSM..EERKAKAAA.STS.VLTQEDFQKI.MAQMRK
Retrocopy ENTSLSEEE-DADGE*IDMQHSSDEEQQEISKKLNSMSTEERKAKAAAISTS*VLTQEDFQKILMAQMRK

Parental  ELDAAPGKSQKRKYLEIDSDEEPRGELLSLRDIERLHKKPKSDKETRLATAMAGKTDRKEFARKKTKMNP
          ELDAAPGKSQKRKY.E.DSDEEPRGELLS..DIERLH.KPKSDKETRLATAMAGKTD.KEF.RKKTKMN.
Retrocopy ELDAAPGKSQKRKYIERDSDEEPRGELLSPWDIERLH*KPKSDKETRLATAMAGKTDQKEFVRKKTKMNQ

Parental  FSSSTNKEKKKQKNFMMMRYSQNVRS-KHKRSFREKQLALRDALL
          FSSSTNKEK.KQKNFM.MRYSQNVRS.K.K.SF.EKQLAL.DALL
Retrocopy FSSSTNKEKEKQKNFMIMRYSQNVRS>KNKHSFQEKQLALQDALL

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	28.46 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	19.99 RPM
SRP007412_cerebellum	0.00 RPM	17.69 RPM
SRP007412_heart	0.00 RPM	7.66 RPM
SRP007412_kidney	0.00 RPM	18.19 RPM
SRP007412_liver	0.00 RPM	5.42 RPM
SRP007412_testis	0.15 RPM	44.74 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_604 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_604 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_604 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2412
Pan troglodytes	retro_ptro_1388
Gorilla gorilla	retro_ggor_1498
Pongo abelii	retro_pabe_1777

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008521	2 retrocopies	retro_cfam_1211, retro_cfam_515,
Cavia porcellus	ENSCPOG00000008524	2 retrocopies	retro_cpor_510, retro_cpor_994,
Echinops telfairi	ENSETEG00000004811	2 retrocopies	retro_etel_1946, retro_etel_779,
Homo sapiens	ENSG00000198301	2 retrocopies	retro_hsap_2412, retro_hsap_4030,
Gorilla gorilla	ENSGGOG00000006441	1 retrocopy	retro_ggor_1498,
Loxodonta africana	ENSLAFG00000012217	1 retrocopy	retro_lafr_980,
Microcebus murinus	ENSMICG00000006682	1 retrocopy	retro_mmur_1204,
Macaca mulatta	ENSMMUG00000017503	1 retrocopy	retro_mmul_604 ,
Nomascus leucogenys	ENSNLEG00000027034	1 retrocopy	retro_nleu_2410,
Oryctolagus cuniculus	ENSOCUG00000026953	1 retrocopy	retro_ocun_547,
Pongo abelii	ENSPPYG00000014852	1 retrocopy	retro_pabe_1777,
Pan troglodytes	ENSPTRG00000024399	2 retrocopies	retro_ptro_1388, retro_ptro_2732,
Rattus norvegicus	ENSRNOG00000022229	2 retrocopies	retro_rnor_1381, retro_rnor_1967,
Sus scrofa	ENSSSCG00000008974	1 retrocopy	retro_sscr_571,
Tupaia belangeri	ENSTBEG00000005270	1 retrocopy	retro_tbel_2414,