RetrogeneDB ID: retro_ptro_2808

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 9:12513249..12513794(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: JKAMP
• Ensembl ID: ENSPTRG00000006400
• Aliases: JKAMP, C14orf100, JAMP
• Description: JNK1/MAPK8-associated membrane protein [Source:HGNC Symbol;Acc:20184]

Sequence

>retro_ptro_2808
ATGGCATGTCTTGGACTTTTTCATGGGAAGATCTTATTTAAAAATGGATCAACTGAAATATCTAGAGAATGTGACTTGTG
CCAAAGAGGGACAGAGAAGAAAAGCACAGAAATATTGTCAGCTTTGCATGGTGTCTCCAGAACTTCACAATTATCTCTAC
GTTGAATTTATTGCTACTCTTCCTCTTGTTTTACGTTGGTTCTTTATTTAATGGTAAATGGGGAAAAAAAAGTTCTAGTG
TACTTTTTCAACACATCATTAGATTATTTGAATCCAGTATGGCAGCTGTTGTGACCCTACTTGTGAGTAATGCAATTGGT
GTTCTTTATATCTGTTCGTTCATGTCGAGTATTGACACTTTCAGATTGGTACATGATGCTTTGCAACCCAAGTCCAGATT
GTGTTACCGCGGTGCACAGTACTCAGGAAGCTGGCTACCCACTACATATCATTGTATTTATCTATTATGCATTCTGCTTG
GTATTAATGATGCTGCTCCCAACTTTCTGGTGAAGAAGATTGCATGTGAGTTAGGGAAGTCTGAT

Alignment

ORF - retro_ptro_2808 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.52 %
• Parental protein coverage: 56.74 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LTCLGLYCGKTLLFKNGSTEIYGECGVCPRG-QRTNAQKYCQPCTESPELYDWLYLGFMAMLPLVLHWFF
          ..CLGL..GK..LFKNGSTEI..EC..C.RG.QR..AQKYCQ.C..SPEL...LY..F.A.LPLVL.WFF
Retrocopy MACLGLFHGK-ILFKNGSTEISRECDLCQRG>QRRKAQKYCQLCMVSPELHNYLYVEFIATLPLVLRWFF

Parental  IEWYSGKKS-SSALFQHITALFECSM-AAIITLL-VSDPVGVLYIRSCRVLMLSDWYTMLYNPSPDYVTT
          I.W..G....SS.LFQHI..LFE.SM.A....L..V...V.....RSCRVL.LSDWY.ML.NPSPD.VT.
Retrocopy I*W*MGXXX>SSVLFQHIIRLFESSMAAVVTLLV>VMQLVFFISVRSCRVLTLSDWYMMLCNPSPDCVTA

Parental  VHCTHEAVYPLYTIVFIYYAFCLVLMMLLRP-LLVKKIACGLGKSD
          VH.T.EA.YPL..IVFIYYAFCLVLMMLL....LVKKIAC.LGKSD
Retrocopy VHSTQEAGYPLHIIVFIYYAFCLVLMMLLPT<FLVKKIACELGKSD

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_prefrontal_cortex	0.00 RPM	19.75 RPM
SRP007412_cerebellum	0.00 RPM	18.93 RPM
SRP007412_heart	0.00 RPM	9.79 RPM
SRP007412_kidney	0.00 RPM	33.71 RPM
SRP007412_liver	0.00 RPM	14.24 RPM
SRP007412_testis	0.00 RPM	54.17 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2808 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2808 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2808 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4132
Macaca mulatta	retro_mmul_1188

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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,