RetrogeneDB ID: retro_mmul_1632

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:111128637..111129389(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.217
• Ensembl ID: ENSMMUG00000009029
• Aliases: None
• Description: None

Sequence

>retro_mmul_1632
CACACAAAATCCAACTGGAAGAAACATTTTGCATGCAAACATGAAAATCTGCAAAAGCAATATGTATGCAGTTTTGAAGG
ATGTAAGAAGACCTTTAAGAAGCATCAGCAGCTGAAAATCCATCAGTGCCAGCATGAAAATAAACCACTATTCAAGTTTA
ACCTTGAAGGATGTGGAAAACACTTTGTTTCACCCTGCAGGCTGAGAGGACAGATGCAGGTTCATCAGAAAAATATATAT
CAATAGGGATGTTCTTTTGTGGCAGAAACATGGACAGAGCTTCCAAAGCACATGAGAGAAATCCATAAAAAGGAAATAAC
ATATGATGTATGCCAGAAAACATTCAAATGTGAAGATTATCTCAAATAACCTGTGAAAACTCATGCCTCAGAATGAGATG
TATGTCAACATCCAAGAGACGGCTGCAGCAGAACTGTATTTAATCTCCAGAGCTGTCTTCTTTCTTTTCATACGGAGAAT
CACCCATTTATGTGTGAACATGCTGGCTGTGGCAAAAGGTTGGCTATGAAACAAAGTCTCACAAGACATGCTATTGTGTA
TGAGCTTGACAGGAAGAAAATGAAGACCAAAGTAAAGCTATCTTCTGAAAAATGAAATTTGTCTTCTCATCTCAGTAAAA
TATCCCTCATAAGAGGAAACAAGAACAAGGTTTATCTTTGCATGAAAATGGAGAGTCATTGAATCGTATTGATCTCGACC
GCTTCAATACTTATTGTTAGCTAAAAATCAGC

Alignment

ORF - retro_mmul_1632 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.14 %
• Parental protein coverage: 59.62 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NTKSNLKKHFERKHENQQKQYICSFEDCRKAFKKHQQLKIHQCQHTSEPLFKCTQEGCGKHFASPSKLKR
          .TKSN.KKHF..KHEN.QKQY.CSFE.C.K.FKKHQQLKIHQCQH...PLFK...EGCGKHF.SP..L..
Retrocopy HTKSNWKKHFACKHENLQKQYVCSFEGCKKTFKKHQQLKIHQCQHENKPLFKFNLEGCGKHFVSPCRLRG

Parental  HAKTHEGYVCQKGCSFVAKTWTELLKHVRETHKEEILCEVCQKTFKRKDYLKQHMKTHAPEREVCRCPRE
          ....H.....Q.GCSFVA.TWTEL.KH.RE.HK.EI...VCQKTFK..DYLK...KTHA.E..VC..PR.
Retrocopy QMQVHQKNIYQ*GCSFVAETWTELPKHMREIHKKEITYDVCQKTFKCEDYLK*PVKTHASE*DVCQHPRD

Parental  GCGRTYTTVFNLQSHILSFHEERRPFVCEHAGCGKTFAMKQSLTRHAVVHDPDKKKMKLKVKKSREKRSL
          GC.RT...VFNLQS..LSFH.E..PF.CEHAGCGK..AMKQSLTRHA.V...D.KKMK.KVK.S.EK..L
Retrocopy GCSRT---VFNLQSCLLSFHTENHPFMCEHAGCGKRLAMKQSLTRHAIVYELDRKKMKTKVKLSSEK*NL

Parental  ASHLSGY-IPPKRKQGQGLSLCQNGESPKCVEDKVLSTVAVLTLS
          .SHLS...IP.KRKQ.QGLSL..NGES..........T...L..S
Retrocopy SSHLSKI<IPHKRKQEQGLSLHENGESLNRIDLDRFNTYC*LKIS

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	48.85 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	49.26 RPM
SRP007412_cerebellum	0.00 RPM	31.64 RPM
SRP007412_heart	0.00 RPM	20.08 RPM
SRP007412_kidney	0.00 RPM	28.29 RPM
SRP007412_liver	0.00 RPM	32.26 RPM
SRP007412_testis	0.00 RPM	12.48 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1632 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1632 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1632 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
Callithrix jacchus	ENSCJAG00000019373	1 retrocopy	retro_cjac_3066,
Equus caballus	ENSECAG00000014803	1 retrocopy	retro_ecab_866,
Felis catus	ENSFCAG00000006982	1 retrocopy	retro_fcat_426,
Gasterosteus aculeatus	ENSGACG00000003107	1 retrocopy	retro_gacu_6,
Gorilla gorilla	ENSGGOG00000008407	1 retrocopy	retro_ggor_2622,
Microcebus murinus	ENSMICG00000014763	1 retrocopy	retro_mmur_368,
Macaca mulatta	ENSMMUG00000009029	1 retrocopy	retro_mmul_1632 ,
Nomascus leucogenys	ENSNLEG00000000331	2 retrocopies	retro_nleu_1134, retro_nleu_214,
Oreochromis niloticus	ENSONIG00000014134	1 retrocopy	retro_onil_8,
Vicugna pacos	ENSVPAG00000004995	1 retrocopy	retro_vpac_456,