RetrogeneDB ID: retro_mmul_121

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:27988531..27989749(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000007226
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: NKAP
• Ensembl ID: ENSMMUG00000012382
• Aliases: None
• Description: NF-kappa-B-activating protein [Source:RefSeq peptide;Acc:NP_001248014]

Sequence

>retro_mmul_121
ATGCCCCCAGTATCCCGGTCCAGCTATTCCGAGGACATTCTGGGCTCTCGGAGGCGGCGACGCAGCTCCTCAGGGAGCCC
ACCATCCCCGCGGAGCAGATGTTCTTCTGGGGATGGTCGTTCCCGTTCTCACTCCCGCGGCCGTGAGGGCCTCAGGCCTC
CTTGGAGTGAATCGGACGTGGGCGCTCTTTACCCCTTTAGTCGCTCTGGGTCGCGAGAGCTGCCCCCAGGGCTCCGCAAC
TACGCCTACCCGTCTTCTTCGTCGACCTCGTATAGCGGATATCGCTACCATCACCACTACTATGCAGAAGAACGGCAGTG
GGCGGAAGACTATGAGAAGGAGAAGGAAGAGAACTATCGGCAGAGGAGGCTGAAGGAGAGAGAGAGGATTGGGGAATTGG
GAGCGCCTGAGGTGTGGGGGCCGTCTCCAAAGTTCCCTGAGCCAGATTCTGACGAACATAACCCAAGTGAGGATGAAGAA
GAGATAATGCATCAGAAAAGGAGCGGTTCAGATTCCAATTCGGAAGAACATAGGAAAAAGAAGACCAGTCGTTCAAGAAA
CAAGAAAACAAGAAATAAAAAGTCGTCTAAAAGAAAACATAGGAAGTATTCTGTTAGTGACAGTAACTCAGACTCTGACA
CAAATTCTAACTCTGTTGATGATAAGAGAGTTAAAGCCAAGAAGAAAGAGAAGAAAAAGAAACACAAAACAAAAAAATAC
AAGAAAATGAAGAATAAGAAGACCAAAAAAGAATCCAGTGACTCAAGCTGTAAAGACTCAGAAGAGTTGTCAGAAGATAC
CTGGATGGAGCAGCCAAATATGGCAGATACTATGGATTTAATAGGGCCAGAAGTACCTATAATACCTACCTCTCAAGATG
AGAAACCTTTAAACTATGGCCATGCTTTGCTCCCCGGTGAAGGTGCAGCTATGGCTGAGTATGTAAAAGCTGGAAAGCGA
ATCCCACGAAGAGGTGAAATTGGGTTGACAAGTGAAGAGATCGCTTCTTTTGAATGCTCAGGTTATGTCATGAGTGGCAG
CAGGCATCGCAGAATGGAGGCTGTACGTCTGCGTAAGGAGAACCAGATCTACAGTGCTGATGAGAAGAGAGCTCTTGCAT
CCTTTAACCAAGAAGAGAGACGAAAGAGAGAAAATAAGATTTTAGCCAGTTTCCGAGAGATGGTGTACAAAAAGACAAAA
GGGAAAGATGACAAGTAA

Alignment

ORF - retro_mmul_121 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.23 %
• Parental protein coverage: 81.97 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SRSRSRERPSAPRGIPFASASSSVY--YGSYSRPYGSDKPWPSLLDKEREESLRQKRLSERERIGELGAP
          SRS.SRE.P...R.....S.SS..Y..Y......Y.....W.....KE.EE..RQ.RL.ERERIGELGAP
Retrocopy SRSGSRELPPGLRNYAYPSSSSTSYSGYRYHHHYYAEERQWAEDYEKEKEENYRQRRLKERERIGELGAP

Parental  EVWGLSPKNPEPDSDEHTPVEDEEP---KKSTTSASTSEEKKKKKKSSHSKERSKKRRKKKSSKRKHKKY
          EVWG.SPK.PEPDSDEH.P.EDEE.....K...S.S.SEE..KKK....S..R.KK.R.KKSSKRKH.KY
Retrocopy EVWGPSPKFPEPDSDEHNPSEDEEEIMHQKRSGSDSNSEEHRKKKT---SRSRNKKTRNKKSSKRKHRKY

Parental  SEDSDSDSDSETDSSDEDNKRRAKKAKKKEKKKKHRSKKYKKKKSKKSRKESSDSSSKESQEEFLENPWK
          S..SDS.SDS.T.S...D.KR...KAKKKEKKKKH..KKYKK.K.KK..KESSDSS.K.S.EE..E..W.
Retrocopy SV-SDSNSDSDTNSNSVDDKR--VKAKKKEKKKKHKTKKYKKMKNKKTKKESSDSSCKDS-EELSEDTWM

Parental  DRTKAEEPSDLIGPEAPKTLTSQDDKPLNYGHALLPGEGAAMAEYVKAGKRIPRRGEIGLTSEEIASFEC
          .........DLIGPE.P...TSQD.KPLNYGHALLPGEGAAMAEYVKAGKRIPRRGEIGLTSEEIASFEC
Retrocopy EQPNMADTMDLIGPEVPIIPTSQDEKPLNYGHALLPGEGAAMAEYVKAGKRIPRRGEIGLTSEEIASFEC

Parental  SGYVMSGSRHRRMEAVRLRKENQIYSADEKRALASFNQEERRKRENKILASFREMVYRKTKGKDDK
          SGYVMSGSRHRRMEAVRLRKENQIYSADEKRALASFNQEERRKRENKILASFREMVY.KTKGKDDK
Retrocopy SGYVMSGSRHRRMEAVRLRKENQIYSADEKRALASFNQEERRKRENKILASFREMVYKKTKGKDDK

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	0.45 RPM	6.27 RPM
SRP007412_brain_prefrontal_cortex	0.56 RPM	6.11 RPM
SRP007412_cerebellum	0.90 RPM	7.04 RPM
SRP007412_heart	1.06 RPM	5.36 RPM
SRP007412_kidney	0.00 RPM	6.57 RPM
SRP007412_liver	0.04 RPM	2.18 RPM
SRP007412_testis	173.99 RPM	10.03 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_121 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_121 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_121 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_15
Pan troglodytes	retro_ptro_117
Pongo abelii	retro_pabe_198
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,