RetrogeneDB ID: retro_rnor_93

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 17:58291612..58292800(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000032534
• Aliases: Nkapl, RGD1311667
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Nkap
• Ensembl ID: ENSRNOG00000031169
• Aliases: Nkap, 2610020o08rik
• Description: NF-kappa-B-activating protein [Source:UniProtKB/Swiss-Prot;Acc:Q4V7C9]

Sequence

>retro_rnor_93
ATGTCGCCTGTACCAGGATCCCGCCCTAATGAGGACACTCTGGGCTCTCAGAAACGACGACGAGGCTCGGAGAGCCCACC
GTCGGTGTTGCAGACTAGTCGATTCTCTCGGGGTTTTTGCTCTCACCTCAGCGGGCCTGAGGGGCTCCAGCCTCCGCGGG
GTGCGGACGGCGTCCGGCCGCTGCATCCGGTCAGCCGCCCCAGATCTGGAGAACGACCGCTATCGCTGGGAATCCGTACT
CTTGCCTCATCGTCCTCTCCCATCTGTGGTGGATACCGTTACCACCATAACTATGCGGGAGACTGTTCGTGGTCTGAGGA
CCAGGAGAAGGAAAAGGAGGAGAGCTATAGGCAAAGGAGGCTGAAGGAAAGGGAGAGGATTGGAGAACTGGGAGCGCCTG
AAGTATGGGGACTGTCACCCAAGATTCCTGAGCCAGATTCTGATGAACATACACCAGCTGAAGATGAGGTGAAGAATCAG
AAGAGCAGCAGTTCAGATTTAACCAACGAAGAAAAAAGGACCAAGACCAGTCATTCAACAAAGAAAAAAAGAAAGAAAAA
GCCTTCCAAAAAGAAGCATAAAAAATATGACAGCAATTCAGACTCAGACATTCATTCCAGCTCTGATAGTGATAAAAACA
AAGTTAAAATCAAGAAGAAAGAGAAGAAAAAGAAACATCGGGCGAAAGAACTCAAGAAGAAAAAGAGAACCAAAAAAGAA
TACAATGGCATAAGCTGCAAAGCTTCAGGAAGGGAATTGCCGGAAGATGTGTGGATGGAACAGTCGATGAGTGCAGATAG
CACAGATTTAATAGGTCCAGAAGCACCTGTTACACATACCTCACAAGATGAGAAACCTTTGAATTATGGCCACGCTCTAC
TTCCAGGTGAAGGTGCAGCAATGGCTGAATATGTAAAAGCTGGGAAGCGTATCCCACGAAGAGGTGAAATTGGGTTGACA
AGTGAAGAGATTGCCTCATTTGAATGTTCAGGTTATGTCATGAGTGGTAGCAGGCATCGCCGAATGGAGGCTGTAAGACT
GCGAAAAGAGAACCAGATTTACAGTGCGGATGAGAAACGAGCCCTGGCATCCTTTAACCAAGAAGAGAGGCGGAAGAGAG
AGAATAAGATCCTAGCCAGCTTTCGAGAAATGGTATACAGAAAGACAAAAGGGAAAGATGACAAGTGA

Alignment

ORF - retro_rnor_93 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.8 %
• Parental protein coverage: 82.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SRSRSRERPSAQRSAPFASSSSSAYYG-GYSRPYGGDKPWPSLLDKEREESLRQKRLSERERIGELGAPE
          SR.RS.ERP........ASSSS....G..Y...Y.GD..W.....KE.EES.RQ.RL.ERERIGELGAPE
Retrocopy SRPRSGERPLSLGIRTLASSSSPICGGYRYHHNYAGDCSWSEDQEKEKEESYRQRRLKERERIGELGAPE

Parental  VWGLSPKNPEPDSDEHTPVEDEEPKKSTTSASSSEDDKKKKRKSSRSKERAKKKRKKKSSKRKHKKYSED
          VWGLSPK.PEPDSDEHTP.EDE...K...S.SS......K..K.S.S....KKKRKKK.SK.KHKKY...
Retrocopy VWGLSPKIPEPDSDEHTPAEDEV--KNQKSSSSDLTNEEKRTKTSHS---TKKKRKKKPSKKKHKKY---

Parental  SDSDSESDTDSSDEDSKRRAKKAKKKEKKKKRRGKKYKKKKSKKNRKESSDSSSKESQEEFLENPWKDRS
          .DS.S.SD..SS....K...K..KKKEKKKK.R.K..KKKK.....KE....S.K.S..E..E..W...S
Retrocopy -DSNSDSDIHSSSDSDKNKVK-IKKKEKKKKHRAKELKKKK--RTKKEYNGISCKASGRELPEDVWMEQS

Parental  KTEEPSDLIGPEAPKTLASQDDKPLNYGHALLPGEGAAMAEYVKAGKRIPRRGEIGLTSEEIASFECSGY
          ......DLIGPEAP.T..SQD.KPLNYGHALLPGEGAAMAEYVKAGKRIPRRGEIGLTSEEIASFECSGY
Retrocopy MSADSTDLIGPEAPVTHTSQDEKPLNYGHALLPGEGAAMAEYVKAGKRIPRRGEIGLTSEEIASFECSGY

Parental  VMSGSRHRRMEAVRLRKENQIYSADEKRALASFNQEERRKRENKILASFREMVYRKTKGKDDK
          VMSGSRHRRMEAVRLRKENQIYSADEKRALASFNQEERRKRENKILASFREMVYRKTKGKDDK
Retrocopy VMSGSRHRRMEAVRLRKENQIYSADEKRALASFNQEERRKRENKILASFREMVYRKTKGKDDK

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
SRP017611_brain	0.29 RPM	14.02 RPM
SRP017611_kidney	0.14 RPM	15.49 RPM
SRP017611_liver	0.07 RPM	8.07 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_93 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_93 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_93 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
Mus musculus	retro_mmus_279

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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,