RetrogeneDB ID: retro_mmul_1188

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 15:64687654..64688338(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.196
• Ensembl ID: ENSMMUG00000008715
• Aliases: JKAMP, C7H14orf100
• Description: JNK1/MAPK8-associated membrane protein [Source:RefSeq peptide;Acc:NP_001247922]

Sequence

>retro_mmul_1188
GCATGCCTTGAACTTTTTCATGGGAAGATCTTATGTAAAAATGGGTCAACTGAAATGTCTGGAGAATGTGACTTGTGCCA
AAGACGGACAGAGAACAAATGCACAGAAATACTGTCAGCCTTCCATGGTATCTCCAGAACTTCACAATTATCTCTACATT
GAATTTATTGGTATTCTTCCTCTTGTTTTAAGTTGGTTCTTTATTGAATGGTACTTGGGGGGAAAAAAAAGTTCTAGTGC
ATTTTTTCAACACATCACTGGATTATTTGAATCCAGTATGGCAGCCATTATCACCTTGCTTGTAAGTGATCCAGTTGGTG
TTCTTTATATCTGCTCATTCATGTTGAGTATTGACACTTTCAGATTGGTACACGATGCTTTACCACCCAAGTCCAGATTA
TGTTACCACAGTACTCAGGAAGCTGTCTACCCACTACATATCATTGTATTTATCTACTATGCATTCTGCTTGGTATTAAT
GATGCTGCTCCCAACTTTCCGGTGAAGAAGATTGCATGTGAGTTAGGGACGTCTGACTGATTTAAAAGTATTTATGCTGC
ACTTTACTTTTTCCTAATATTAATCATGCTTCAGGTGGTTGGTGGAGGCCTTTTACATTATGCCTTCCCATACCCTATAT
TAGTGTCATCTTTGGTTACTCTAGATGTGTATGTATCGGCTTCG

Alignment

ORF - retro_mmul_1188 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.95 %
• Parental protein coverage: 70.46 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ACLGLYCGKTLLFKNGSTEIYGECGVCPR-GQRTNAQKYCQPCTESPELYDWLYLGFMAMLPLVLHWFFI
          ACL.L..GK..L.KNGSTE..GEC..C.R.GQRTNAQKYCQP...SPEL...LY..F...LPLVL.WFFI
Retrocopy ACLELFHGK-ILCKNGSTEMSGECDLCQR>GQRTNAQKYCQPSMVSPELHNYLYIEFIGILPLVLSWFFI

Parental  EWYSGKKS-SSALFQHITALFECSMAAIITLLVSDPVGVLYIRSCRVLMLSDWYTMLYNP-SPDYVTTVH
          EWY.G....SSA.FQHIT.LFE.SMAAIITLLVSDPVGVLYI..C......D..........P......H
Retrocopy EWYLGXXXXSSAFFQHITGLFESSMAAIITLLVSDPVGVLYI--CSFMLSIDTFRLVHDALPPKSRLCYH

Parental  CTHEAVYPLYTIVFIYYAFCLVLMMLLRPLL-VKKIACGLGKSDRFKSIYAALYFFPILTVLQAVGGGLL
          .T.EAVYPL..IVFIYYAFCLVLMMLL.....VKKIAC.LG.SD.FKSIYAALYFF.IL..LQ.VGGGLL
Retrocopy STQEAVYPLHIIVFIYYAFCLVLMMLLPTFR<VKKIACELGTSD*FKSIYAALYFFLILIMLQVVGGGLL

Parental  YYAFPYIILVLSLVTLAVYMSAS
          .YAFPY.ILV.SLVTL.VY.SAS
Retrocopy HYAFPYPILVSSLVTLDVYVSAS

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	22.75 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	14.28 RPM
SRP007412_cerebellum	0.00 RPM	30.74 RPM
SRP007412_heart	0.00 RPM	9.77 RPM
SRP007412_kidney	0.00 RPM	18.54 RPM
SRP007412_liver	0.00 RPM	5.38 RPM
SRP007412_testis	0.00 RPM	21.18 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1188 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1188 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1188 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4132
Pan troglodytes	retro_ptro_2808

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000050130	1 retrocopy	retro_hsap_4132,
Macaca mulatta	ENSMMUG00000008715	1 retrocopy	retro_mmul_1188 ,
Mus musculus	ENSMUSG00000005078	1 retrocopy	retro_mmus_104,
Pan troglodytes	ENSPTRG00000006400	1 retrocopy	retro_ptro_2808,
Rattus norvegicus	ENSRNOG00000004751	1 retrocopy	retro_rnor_219,
Tupaia belangeri	ENSTBEG00000002820	1 retrocopy	retro_tbel_2109,