RetrogeneDB ID: retro_mmul_1630

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:109251662..109253427(+)
• Located in intron of: ENSMMUG00000016017

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAD17
• Ensembl ID: ENSMMUG00000014881
• Aliases: None
• Description: None

Sequence

>retro_mmul_1630
ATGTCAAAAACTTTTCTTAGACCAAAGGTATCTTCCACAAAGGTAACAGACTGGATGACCCATCTTTCAATGATTTTCTA
GAGTGTAGAGTCATCTCTACTATTACTGCCACATCATTAGGTGTGAATAACTCAAGTCATAGAGAAAAAATTAGCCTTCT
ACATTAGAAAGTAGGATTATTTCCAGCTAGAAAAATAGGAAGTCTATCTTCCTTAGAACAGATTTATGGTTTAGAAAATT
CAAAAGACTATCTGTCTGAAAATGAATCATGGGTAGATAAATATAAACCAGAAATTTAGCATGCACTTGCTGTGCATAAA
AAGAAAACTGAAGAAGTTGAAACCTGGTAAAAAGCTCAAGTCTTAGAAAGGCAACCATAACAGGATGGATCTATTTTATT
AATAACAGGTCCTCCTGGATGTGAAACAATAACTACCAAAAAATACTATCAAATAAGCATGGTATTCAAGTACAAGAGTG
GATTAATCCAGTTTTACCAGACTTCCAAAAAGATGATTTCAAGGAAATGTTTCATACTGAATCAAGCTTCGGTACGTTTC
CCTATCAGTCTCAGATAGCAGTTTTCAAAGTTTCTACTAAGAGCAACAAAGTATAACAAGTTACACATGCTTACTGATCT
ATCTGAGAGCTGATAAAAAGATAATTCTGGCTGAAGATTTACCTAACCAGTTTTATCGGGATTCTCATACTTTACATGAA
GTTCTAAGGAAGTATGTGAAGATTGATGGATGTCCTCTTACATTTATAATCTCTGACAGTCTCAGTGGTGATAATAATCA
AAGTTTCTTGTTTCCCAAAGAAATCTAGGAAGAGTGTTCTATCTCAAATATTAGTTTCAACCCTGTGGCACCAACAATTA
TGATGAAATTTCTTAATCAAATAGTGAGTATAGAAGCTAACAAGAGTGGAAGAAAAATTACTGTCCCTGACAAAACTTCT
CTAGAGTTGCTCTGTCAAGGACGTTCTGGTGATATGAGAAGTGCAATAAACAGCCTCCAGATTTCTTCTTCAAAAGGGGA
AAACAACTTATGGCCAAGGAAAAAAAGAACGTCTTTAAAATTGAATGCTGTGCTGTCAAAATCAAAACGAAAAAAAAAAA
AACCTGATAGGGTTTTTGAAAATCAAGAGGTCCAAGCTATTGGTGGCAAAAATGTTTCTCTGTTTCTATTCCGATCTTTG
AGGAAAATCCTATACCATAAAAGAGCATCTTTAACAGAATTAGACTCACCTCGGTTGCCCTCTCATTTATCAGAATATGA
TCGGGATACATACTTGTTGAACCTGAGGAGGTAGTAGAAATGTCACATATGCCAGGAGACTTATTTAATTTATATCTTCA
CCAAAACTACATAGATTTCTTCATGAAATTGATGATATTGTGAGAGCCAGTGAATTTCTAAGTTTTGTAGATATCCTCAG
TGGTGACTGGAATACACACTCTTTACTCAGGAAATATAGGACAGCTATAGCTACGAGAGGTGTGATACATTCCAACAAAG
CCCGAGGATATGCTCATTGCCAAGGAGGAGGAGCAAGTTTTTGACCCTTGCACACAACCCAGTGGTTTCTAATAAATAAA
AAGTATCGGGAAAATTGCCTGGCAGCAAAAGCACTTTTTCCTGACTTCTGCGCACCAGCTTTATGCCTCCAAACTCAGCT
ACTGTCATACCTTGCTCTACTAACCATTCCGATGAGAAATCAAGCTCAGATTTCTTTTATCCAAGATATTGGAAGGCTCC
CTCTG

Alignment

ORF - retro_mmul_1630 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.11 %
• Parental protein coverage: 86.49 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  MSKTFLRPKVSSTKVTDWV-DPSFDDFLECRDISTITATSLGVNNSSHR-RKNGPSTLES-SKFPARKRG
          MSKTFLRPKVSSTKVTDW..DPSF.DFLECR.ISTITATSLGVNNSSHR.RKN.PSTLES...FPARK.G
Retrocopy MSKTFLRPKVSSTKVTDWM<DPSFNDFLECRVISTITATSLGVNNSSHR<RKN*PSTLES>GLFPARKIG

Parental  NLSSLEQIYGLENSKESLSENEPWVDKYKPETQHELAVHKKKIEEVETWLKAQVLERQPKQGGSILLITG
          .LSSLEQIYGLENSK..LSENE.WVDKYKPE..H.LAVHKKK.EEVETW.KAQVLERQP.Q.GSILLITG
Retrocopy SLSSLEQIYGLENSKDYLSENESWVDKYKPEI*HALAVHKKKTEEVETW*KAQVLERQP*QDGSILLITG

Parental  PPGCGKTTTIK-VLSKEHGIQVQEWINPVLPDFQKDDF-REIFNTESSFHMFPYQSQIAVFKEFLLRATK
          PPGC...TT.K..LS..HGIQVQEWINPVLPDFQKDDF.R..F........FP.......F..FLLRATK
Retrocopy PPGCETITTKK<ILSNKHGIQVQEWINPVLPDFQKDDF>RKCFILNQASVRFPISLR*Q-FSKFLLRATK

Parental  YNKLQMLGD-DLRTDKKIILVEDLPNQFYRDSHTLHEVLRKYVRIGRCPLIFVISDSLSGDNNQRLLFPK
          YNKL.ML.D..LR.DKKIIL.EDLPNQFYRDSHTLHEVLRKYV.I..CPL.F.ISDSLSGDNNQ..LFPK
Retrocopy YNKLHMLTD>YLRADKKIILAEDLPNQFYRDSHTLHEVLRKYVKIDGCPLTFIISDSLSGDNNQSFLFPK

Parental  EIQEECSISNISFNPVAPTIMMKFLNRIVTIEANKNGGKITVPDKTSLELLCQGCSGDIRSAINSLQFSS
          EI.EECSISNISFNPVAPTIMMKFLN.IV.IEANK.G.KITVPDKTSLELLCQG.SGD.RSAINSLQ.SS
Retrocopy EI*EECSISNISFNPVAPTIMMKFLNQIVSIEANKSGRKITVPDKTSLELLCQGRSGDMRSAINSLQISS

Parental  SKGENNLWPRKKGMSLKSDAVLSKSK-RRKKPDRVFENQEVQAIGGKDVSLFLFRALGKILYCKRASLTE
          SKGENNLWPRKK..SLK..AVLSKSK.....PDRVFENQEVQAIGGK.VSLFLFR.L.KILY.KRASLTE
Retrocopy SKGENNLWPRKKRTSLKLNAVLSKSKXXXXXPDRVFENQEVQAIGGKNVSLFLFRSLRKILYHKRASLTE

Parental  LDSPRLPSHLSEYERDT-LLVEPEEIVEMSHMPGDLFNLYLHQNYIDFFM-DIDDIVRASEFLSFADILS
          LDSPRLPSHLSEY.RDT..LVEPEE.VEMSHMPGDLFNLYLHQNYIDFFM..IDDIVRASEFLSF.DILS
Retrocopy LDSPRLPSHLSEYDRDT<ILVEPEEVVEMSHMPGDLFNLYLHQNYIDFFM<EIDDIVRASEFLSFVDILS

Parental  GDWNTCSLLREYSTSIATRGVIHSNKARGYAHCQGGGSSFRPLHKPQWFLIYKKYRENCLAAKALFPDFC
          GDWNT.SLLR.Y.T.IATRGVIHSNKARGYAHCQGGG.SF.PLH..QWFLI.KKYRENCLAAKALFPDFC
Retrocopy GDWNTHSLLRKYRTAIATRGVIHSNKARGYAHCQGGGASF*PLHTTQWFLINKKYRENCLAAKALFPDFC

Parental  LPALCLQTQLLPYLALLTIPMRNQAQISFIQDIGRLPL
          .PALCLQTQLL.YLALLTIPMRNQAQISFIQDIGRLPL
Retrocopy APALCLQTQLLSYLALLTIPMRNQAQISFIQDIGRLPL

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	14.01 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	6.03 RPM
SRP007412_cerebellum	0.00 RPM	15.11 RPM
SRP007412_heart	0.00 RPM	6.95 RPM
SRP007412_kidney	0.00 RPM	10.80 RPM
SRP007412_liver	0.04 RPM	2.85 RPM
SRP007412_testis	0.00 RPM	35.09 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1630 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1630 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1630 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3821

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000152942	1 retrocopy	retro_hsap_3821,
Macaca mulatta	ENSMMUG00000014881	1 retrocopy	retro_mmul_1630 ,
Nomascus leucogenys	ENSNLEG00000004118	1 retrocopy	retro_nleu_215,
Pan troglodytes	ENSPTRG00000016950	1 retrocopy	retro_ptro_2599,