RetrogeneDB ID: retro_mmus_279

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:21467253..21468441(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000059395
• Aliases: Nkapl, 4921504I05Rik
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Nkap
• Ensembl ID: ENSMUSG00000016409
• Aliases: Nkap, 2610020O08Rik, AA987160, AI849147, AL024236
• Description: NFKB activating protein [Source:MGI Symbol;Acc:MGI:1914300]

Sequence

>retro_mmus_279
ATGTCGCCTGTATCCCGATCTCGCCCTAATGAGGACACTCTGGGCTCTCAGAAACGACGACGTTTCTCGGAGAGCCCACC
GTCGGCGTTACAGACTAGCCGATCACCTCGGGGAGGCGGTTTCGGCTCTCTCCTCAGCGGTCCTGAGGGGCTCCAGCCTC
CGCGGGGTGCTCAGGGCGTCCGGCCACTGCATCCCATCAGCCGCCCCAGGTCTGGAGAACGACCGCTACCGCTGGGGATC
CGTACGCTTGCCTGCTCTTCCTCTCCCATCTGTGGTGGATACCGTTACCACCACAACTATGCGGGAGATCCTTCGTGGGC
TGAGGACCAGGAGAAGGAAAAGGAGGAGAGTTATAGGCAAAGGAGGCTGAAGGAAAGAGAGAGGATTGGAGAGCTGGGAG
CGCCTGAGGTATGGGGACTGTCACCCAAGATTCCTGAGCCAGATTCTGATGAACATACACCAGCTGAAGATGAGGTGAAG
AATCAGAAGAGTAGCAGTTCAGATTTCACCAATGAAGAAAAAAGGACAAAGACCAGTCATTCAACAAAGAAAAAAAGAAA
GAAAAAGCCTTCCAAAAGGAAGCATAAAAAATATTATGACAGCAGTTCAGACTGTCATTCTAGCTCTGATAGTGATAAAA
AGAAAGTTAAAACCAAGAAGAAAGAGAAGAAAAAGAAACATCGGGCAAAACAGCTCAAGAAGAAGAGGACTAAAAAAGAA
TACAATGACATAAGCTGCAAAGCTTCAGAAAGGGACTTGCCAGAAGATGCGTGGATGGAACAGTCGATGAGTGCAGAGAG
CATGGATTTAATAGGCCCAGAAGCACCTGTGATACACACCTCTCAAGATGAGAAACCTTTGAATTATGGCCATGCTCTGC
TTCCTGGTGAAGGTGCAGCAATGGCTGAATATGTAAAAGCCGGGAAGCGTATCCCACGAAGAGGTGAAATTGGGTTGACA
AGTGAAGAGATTGCCTCATTTGAATGTTCAGGTTACGTCATGAGTGGTAGCAGGCATCGCCGAATGGAGGCTGTAAGACT
GCGTAAAGAGAACCAGATTTACAGTGCTGATGAGAAACGAGCCCTTGCATCCTTTAACCAAGAAGAGAGGCGGAAGAGAG
AAAATAAGATCCTAGCCAGCTTTCGAGAAATGGTGTACAGAAAGACAAAAGGGAAAGATGACAAGTGA

Alignment

ORF - retro_mmus_279 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.79 %
• Parental protein coverage: 82.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SRSRSRSRERPSAQRSAPFASASSSAYYGGYS--RPYGGDKPWPSLLDKEREESLRQKRLSERERIGELG
          SR.RS..R..P...R.......SSS...GGY.....Y.GD..W.....KE.EES.RQ.RL.ERERIGELG
Retrocopy SRPRSGERPLPLGIRTL---ACSSSPICGGYRYHHNYAGDPSWAEDQEKEKEESYRQRRLKERERIGELG

Parental  APEVWGLSPKNPEPDSDEHTPVEDEEPKKSTTSASSSEDDKKKKRKSSHSKDRAKKKRKKKSSKRKHKKY
          APEVWGLSPK.PEPDSDEHTP.EDE...K...S.SS......K..K.SHS....KKKRKKK.SKRKHKKY
Retrocopy APEVWGLSPKIPEPDSDEHTPAEDE--VKNQKSSSSDFTNEEKRTKTSHS---TKKKRKKKPSKRKHKKY

Parental  SEDSDSDSESDTDSSDEDSKRRAKKAKKKDKKKKRRGKKYKKKKSKKNRKESSDSSSKESQEEFLENPWK
          ..DS.SD..S...SSD.D.K....K.KKK.KKKK.R.K..KKK..KK...E..D.S.K.S.....E..W.
Retrocopy -YDSSSDCHS---SSDSDKKK--VKTKKKEKKKKHRAKQLKKKRTKK---EYNDISCKASERDLPEDAWM

Parental  DRSKAEEPSDLIGPEAPKTLASQDDKPLNYGHALLPGEGAAMAEYVKAGKRIPRRGEIGLTSEEIASFEC
          ..S...E..DLIGPEAP....SQD.KPLNYGHALLPGEGAAMAEYVKAGKRIPRRGEIGLTSEEIASFEC
Retrocopy EQSMSAESMDLIGPEAPVIHTSQDEKPLNYGHALLPGEGAAMAEYVKAGKRIPRRGEIGLTSEEIASFEC

Parental  SGYVMSGSRHRRMEAVRLRKENQIYSADEKRALASFNQEERRKRENKILASFREMVYRKTKGKDDK
          SGYVMSGSRHRRMEAVRLRKENQIYSADEKRALASFNQEERRKRENKILASFREMVYRKTKGKDDK
Retrocopy SGYVMSGSRHRRMEAVRLRKENQIYSADEKRALASFNQEERRKRENKILASFREMVYRKTKGKDDK

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	0.14 RPM	12.27 RPM
SRP007412_cerebellum	0.35 RPM	13.98 RPM
SRP007412_heart	0.37 RPM	7.75 RPM
SRP007412_kidney	0.56 RPM	10.30 RPM
SRP007412_liver	0.14 RPM	6.28 RPM
SRP007412_testis	79.08 RPM	1.10 RPM

ChIP-Seq

RNA Polymerase II activity may be related with retro_mmus_279 in 3 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001YIJ	POLR2A	13:21468286..21468832
ENCFF001YJZ	POLR2A	13:21468277..21468891
ENCFF001YKA	POLR2A	13:21468316..21468790

EST

No EST(s) were mapped for retro_mmus_279 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_27723	1023 libraries	45 libraries	0 libraries	1 library	3 libraries
TSS #2	TSS_27724	570 libraries	428 libraries	68 libraries	2 libraries	4 libraries
TSS #3	TSS_27725	334 libraries	284 libraries	447 libraries	4 libraries	3 libraries

The graphical summary, for retro_mmus_279 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_279 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_279 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
Macaca mulatta	retro_mmul_121
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,