RetrogeneDB ID: retro_ptro_117

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:28507818..28509018(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000017872
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: NKAP
• Ensembl ID: ENSPTRG00000022233
• Aliases: None
• Description: NFKB activating protein [Source:UniProtKB/TrEMBL;Acc:K7CNN0]

Sequence

>retro_ptro_117
ATGCCCCCAGTATCCCGGTCCAGCTATTCCGAGGACATCGTGGGCTCTCGGAGAAGGCGACGCAGCTCCTCGGGGAGCCC
ACCATCCCCGCAGAGCAGATGTTCCTCTTGGGATGGCTGTTCCCGCTCTCACTCCCGCGGCCGTGAGGGCCTCAGGCCTC
CTTGGAGTGAGTCGGACGTGGGCGCTCTTTACCTCTTCAGTCGCTCTGGGTCGCGAGGGCGGCTCCCAAGATTCCGCAAC
TACGCCTTCGCGTCCTCCTGGTCGACCTCGTATAGTGGATATCGCCACCATCGTCACTGCTATGCAGAAGAACGGCAGTC
AGCAGAAGACTACGAGAAGGAAGAGAGCTATCGGCAGAGGAGGCTGAAGGAGAGAGAGAGGATTGGGGAGTTGGGAGCGC
CTGAAGTGTGGGGGCCGTCTCCAAAGTTCCCTCAGCCAGATTCTGACGAATATACCCCAGTTGAGGATGAAGAAGAGGTA
ACGCATCAGAAAAGCAGCAGTTCAGATTCCAACTCGGAAGAACATAGGAAAAAGAAGACCAGTCGTTCAAGAAACAAGAA
AAAAAGAAAGAATAAGTCGTCTAAAAGAAAGCATAGGAAATATTCTGATAGTGACAGTAACTCAGAGTCTGACACAAATT
CTAACTCTGATGATGATAAAAAGAGAGTTAAAGCCAAGAAGAAAAAGAAACACAAAACAAAGAAAAAGAAGAATAAGAAG
ACCAAAAAAGAATCCAGTGACTCAAGCTGTAAAGACTCAGAAGAGGACTTGTCAGAAGCTACCTGGATGGAGCAGCCAAA
TGTGGCAGATACTATGGATTTAATAGGGCCAGAAGCACCTATAATACATACCTCTCAAGATGAAAAACCTTTGAAGTATG
GCCATGCTTTGCTTCCCGGTGAAGGTGCAGCTATGGCTGAGTATGTAAAAGCTGGAAAGCGAATCCCACGAAGAGGTGAA
ATTGGGTTGACAAGTGAAGAGATCGGTTCTTTTGAATGCTCAGGTTATGTCATGAGTGGTAGCAGGCATCGCAGAATGGA
GGCTGTACGACTGCGTAAGGAGAACCAGATCTACAGTGCTGATGAGAAGAGAGCTCTTGCATCCTTTAACCAAGAAGAGA
GACGAAAGAGAGAAAATAAGATTTTAGCCAGTTTCCGAGAGATGGTGTACAAAAAGACAAAAGGGAAAGATGACAAGTAA

Alignment

ORF - retro_ptro_117 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.96 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RLSERERIGELGAPEVWGLSPKNPEPDSDEHTPVEDEEP---KKSTTSASTSEEEKKKKSSHSKERSKKR
          RL.ERERIGELGAPEVWG.SPK.P.PDSDE.TPVEDEE.....KS..S.S.SEE..KKK.S.S..R.KK.
Retrocopy RLKERERIGELGAPEVWGPSPKFPQPDSDEYTPVEDEEEVTHQKSSSSDSNSEEHRKKKTSRS--RNKKK

Parental  RKKKSSKRKHKKYSEDSDSDSDSETDSSDEDNKRRAKKAKKKEKKKKHRSKKYKKKRSKKSRKESSDSSS
          RK.KSSKRKH.KYS.DSDS.S.S.T.S...D.....KK..K..KKKKH.....KKK..KK..KESSDSS.
Retrocopy RKNKSSKRKHRKYS-DSDSNSESDTNSNSDDD----KKRVKAKKKKKHKT---KKKKNKKTKKESSDSSC

Parental  KESQEEFLENPWKDRTKAEEPSDLIGPEAPKTLTSQDDKPLNYGHALLPGEGAAMAEYVKAGKRIPRRGE
          K.S.E...E..W..........DLIGPEAP...TSQD.KPL.YGHALLPGEGAAMAEYVKAGKRIPRRGE
Retrocopy KDSEEDLSEATWMEQPNVADTMDLIGPEAPIIHTSQDEKPLKYGHALLPGEGAAMAEYVKAGKRIPRRGE

Parental  IGLTSEEIASFECSGYVMSGSRHRRMEAVRLRKENQIYSADEKRALASFNQEERRKRENKILASFREMVY
          IGLTSEEI.SFECSGYVMSGSRHRRMEAVRLRKENQIYSADEKRALASFNQEERRKRENKILASFREMVY
Retrocopy IGLTSEEIGSFECSGYVMSGSRHRRMEAVRLRKENQIYSADEKRALASFNQEERRKRENKILASFREMVY

Parental  RKTKGKDD
          .KTKGKDD
Retrocopy KKTKGKDD

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	0.57 RPM	2.84 RPM
SRP007412_cerebellum	0.47 RPM	4.91 RPM
SRP007412_heart	0.93 RPM	4.26 RPM
SRP007412_kidney	0.13 RPM	4.86 RPM
SRP007412_liver	0.10 RPM	4.26 RPM
SRP007412_testis	85.36 RPM	3.58 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_117 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_117 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_117 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_15
Pongo abelii	retro_pabe_198
Macaca mulatta	retro_mmul_121
Mus musculus	retro_mmus_279
Rattus norvegicus	retro_rnor_93

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018433	1 retrocopy	retro_cfam_172,
Dasypus novemcinctus	ENSDNOG00000000072	1 retrocopy	retro_dnov_50,
Echinops telfairi	ENSETEG00000001007	1 retrocopy	retro_etel_1882,
Felis catus	ENSFCAG00000004392	1 retrocopy	retro_fcat_10,
Homo sapiens	ENSG00000101882	1 retrocopy	retro_hsap_15,
Loxodonta africana	ENSLAFG00000002962	1 retrocopy	retro_lafr_37,
Macaca mulatta	ENSMMUG00000012382	1 retrocopy	retro_mmul_121,
Mus musculus	ENSMUSG00000016409	1 retrocopy	retro_mmus_279,
Nomascus leucogenys	ENSNLEG00000014922	1 retrocopy	retro_nleu_88,
Otolemur garnettii	ENSOGAG00000001004	1 retrocopy	retro_ogar_239,
Pongo abelii	ENSPPYG00000020679	1 retrocopy	retro_pabe_198,
Pan troglodytes	ENSPTRG00000022233	1 retrocopy	retro_ptro_117 ,
Rattus norvegicus	ENSRNOG00000031169	1 retrocopy	retro_rnor_93,
Sus scrofa	ENSSSCG00000012613	1 retrocopy	retro_sscr_13,
Ictidomys tridecemlineatus	ENSSTOG00000001134	1 retrocopy	retro_itri_73,