RetrogeneDB ID: retro_pabe_198

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:29159524..29160733(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000016368
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: NKAP
• Ensembl ID: ENSPPYG00000020679
• Aliases: None
• Description: NFKB activating protein [Source:HGNC Symbol;Acc:29873]

Sequence

>retro_pabe_198
TTGCTCCCAGTATCCCGGTCCAGCTATTCTGAGGACATCATGGGCTCTCGGAGAAGGCGACGGAGCTCCTCGGGGAGCCC
ACCATCCCCGCAGAGCAGATGTTCCTCTTGGGATGGCCGTTCCCGCTCTCACTCCCGCGGCCGTGAGGGCCGCAGGCCTC
CTTGGAGTGAGTCGGACGTGGGCGCTCTTTACCCCCTTAGTCGCTCTGGGTCGCGAGGGCGGCCCCCAAGATTCCGCAAC
TACGCCTTCGCGTCCTCTTGGTCGACCTCGTATAGTGGATATCGCTACCATCATCACTGCTATGCAGAAGAACGGCAGTC
AGCGGAAGACTACGAGAAGGAGGAGAGCTATCGGCAGAGGCGGCTGAAGGAGAGAGAGAGGATTGGGGAGTTGGGAGCGC
CTGAAGTGTGGGGGCCGTCTCCAAAGTTCCCTGAGCCAGATTCTGACGAACATACCCCAGTTGAGGATGAAGAAGAGGTA
ACGCATCAGAAAAGCAGCAGTTCAGATTCCAACTCGGAAGAACATAGGAAAAAGAAGACCAGTCGTTCAACAAACAAGAA
AAAAAGAAAGAATAAGTCGTCTAAAAGAAAGCATAGGAAATATTCTGATAGTGACAGTAACTCAGAGTCTGACACAAATT
CTAACTCTGATGATGATAAAAAGAGAGTTAAAGCCAAGAAGAAAAAGAAGAAAAAGAAACACAAAACAAAGAAAAAGAAG
AATAAGAAGACCAAAAAAGAATCCAGTGACTCAAGCTGTAAAGACTCAGAAGAGGAGTTGTCAGAAGCCACCTGGGTGGA
GCAGCCAAATGTGGCAGATACTATGGATTTAATAGGGCCAGAAGCACCTATAATACATACCTCTCAAGATGAAAAACCTT
TGAACTATGGCCATGCTTTGCTCCCCGGTGAAGGTGCAGCTATGGCTGAGTATGTAAAAGCTGGAAAGCGAATCCCACGA
AGAGGTGAGATTGGGTTGACAAGTGAAGAGATCGCTTCTTTTGAATGCTCAGGTTATGTCATGAGTGGTAGCAGGCATCG
CAGAATGGAGGCTGTACGACTGCGTAAGGAGAACCAGATCTACAGTGCTGATGAGAAGAGAGCTCTTGCATCCTTTAACC
AGGAAGAGAGACGAAAGAGAGAAAATAAGATTTTAGCCAGTTTCCGAGAGATGGTGTACAAAAAGACAAAAGGGAAAGAT
GACAAGTAA

Alignment

ORF - retro_pabe_198 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.88 %
• Parental protein coverage: 81.97 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SRSRSRERPSAPRGIPFASASSSVYYGSYSRPYGSDKPWPSLLDKEREESLRQKRLSERERIGELGAPEV
          SRS.SR.RP...R...FAS..S..Y.G.............S..D.E.EES.RQ.RL.ERERIGELGAPEV
Retrocopy SRSGSRGRPPRFRNYAFASSWSTSYSGYRYHHHCYAEERQSAEDYEKEESYRQRRLKERERIGELGAPEV

Parental  WGLSPKNPEPDSDEHTPVEDEEP-KKSTTSASTSEEEKKKKKKSSRSKERSKKRRKKKSSKRKHKYSEDS
          WG.SPK.PEPDSDEHTPVEDEE.......S.S.S..E...KKK.SRS....KK.RK.KSSKRKH....DS
Retrocopy WGPSPKFPEPDSDEHTPVEDEEEVTHQKSSSSDSNSEEHRKKKTSRST--NKKKRKNKSSKRKHRKYSDS

Parental  DSDSDSETDSSDEDNKRRAKKAKKKEKKKKHRSKKYKKKRSKKSRKESSDSSSKESQEEFLENPWKDRTK
          DS.S.S.T.S...D.K.R.K.AKKK.KKKKH.....KKK..KK..KESSDSS.K.S.EE..E..W.....
Retrocopy DSNSESDTNSNSDDDKKRVK-AKKKKKKKKHKT---KKKKNKKTKKESSDSSCKDSEEELSEATWVEQPN

Parental  AEEPSDLIGPEAPKTLTSQDDKPLNYGHALLPGEGAAMAEYVKAGKRIPRRGEIGLTSEEIASFECSGYV
          .....DLIGPEAP...TSQD.KPLNYGHALLPGEGAAMAEYVKAGKRIPRRGEIGLTSEEIASFECSGYV
Retrocopy VADTMDLIGPEAPIIHTSQDEKPLNYGHALLPGEGAAMAEYVKAGKRIPRRGEIGLTSEEIASFECSGYV

Parental  MSGSRHRRMEAVRLRKENQIYSADEKRALASFNQEERRKRENKILASFREMVYRKTKGKDDK
          MSGSRHRRMEAVRLRKENQIYSADEKRALASFNQEERRKRENKILASFREMVY.KTKGKDDK
Retrocopy MSGSRHRRMEAVRLRKENQIYSADEKRALASFNQEERRKRENKILASFREMVYKKTKGKDDK

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	0.44 RPM	9.12 RPM
SRP007412_cerebellum	1.34 RPM	9.73 RPM
SRP007412_heart	0.51 RPM	5.33 RPM
SRP007412_kidney	0.30 RPM	7.79 RPM
SRP007412_liver	0.49 RPM	6.06 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_198 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_198 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_198 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_15
Pan troglodytes	retro_ptro_117
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,