RetrogeneDB ID: retro_sscr_13

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 7:24052584..24053802(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000001205
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: NKAP
• Ensembl ID: ENSSSCG00000012613
• Aliases: None
• Description: NFKB activating protein [Source:HGNC Symbol;Acc:29873]

Sequence

>retro_sscr_13
ATGGCTCCGGTGTCTCGGTCCCGCTACCCCGAGGACACCGTAGGCTCTAGGAGACGGCGATGCAGCTCGTCCGGGAGCCC
GCCTTCCGCGCAGGCCAGACGCTCCCCTTTGGGCGGCCGTTCCCACTTTTACTCCCGCGGCCGCGAGGGCCTCAGGCCTC
CGTGGGGTGGGTCGGGCGTTGGCGCTCTTTATTCCCTTAGCGGTTCTGGGTCTCGGGAGCGGTCCCCAGGGCTCCGCAAC
TTCTCATCCTCGTCCTCTTCTGTCTATTATGGGGGATACCGCTACCATCACCATCACTATGTGGGCGACAGGCAATGGGC
AGAAGACTACGAGAAGGAGAAGGAGGAGAACTATCGCCAGAGAAGGCTGAAAGAGAGAGAAAGAATTGGGGAGTTGGGAG
CTCCTGAGGTGTGGGGACTGTCTCCAAAGCTTCCTGAGCCGGATTCAGATGAACACACCCCAGTTGAGGATGACGAGGTA
AAGACTAAGAAGACCAGCAGTTCAGATTCCAGCTCCGAAGAAAAAAGGAAAAAGAAGACCAGTCATTCAAAAAAGAAGAG
GAAGAAAAAGTCCAAAAGAAAATATAGGAAGTATTCTGATAACAGTGACAGTAATTCAGATTCCAACACTGATTCTAGCT
CTGATGATGATGATAAAAAGAGACCCAAAAAAGCCAAGAAGAAAGAGAAGAAAAAGAAACACAGAGCTAAAAAGCCCAAG
AAAAAGAAGACCAAGAAGACTAGAAAAGAATCCAGTGACTCAAACTATAAGGATTCAGAAGGGGAGTTGCCAGAAGGTAT
CTGGATTGAGCAGTCAAAGATTGCAGATAACATGGATCTAATAGGTCCGGAAGCACCTATAACACAGATCTCTCAAGATG
AGAAGCCTTTGAACTATGGCCATGCTCTGCTTCCAGGTGAAGGTGCAGCTATGGCTGAATATGTAAAAGCTGGAAAGCGT
ATCCCTCGAAGAGGTGAAATTGGGTTGACAAGTGAAGAGATTGCTTCTTTTGAATACTCAGGTTATGTTATGAGTGGTAG
CAGGCATCGCAGAATGGAGGCTGTTCGACTGCGCAAAGAGAACCAGATCTATAGTGCTGATGAGAAGAGAGCCCTTGCAT
CCTTTAACCAAGAAGAGAGACGGAAGAGAGAGAATAAGATTCTAGCCAGTTTCCGAGAGATGGTGTATCGAAAGACAAAA
GGGAAAGAGGACAAATAA

Alignment

ORF - retro_sscr_13 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.29 %
• Parental protein coverage: 92.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CSKSSRSPRGRRSRSHSCSRSGDRNGLSHQSSGPSQGSRNQSYRSRSRSRSRERPSAPRGAPFASASSAY
          CS.S...P.....RS....RS............P..GS......S.S.S.SRER....R.....S.SS.Y
Retrocopy CSSSGSPPSAQARRSPLGGRSHFYSRGREGLRPPWGGSGVGALYSLSGSGSRERSPGLRNFS-SSSSSVY

Parental  YGGYS---RPYGSDKPWPSLLDKEREESLRQKRLSERERIGELGAPEVWGLSPKNPEPDSDEHTPVEDEE
          YGGY......Y..D..W.....KE.EE..RQ.RL.ERERIGELGAPEVWGLSPK.PEPDSDEHTPVED.E
Retrocopy YGGYRYHHHHYVGDRQWAEDYEKEKEENYRQRRLKERERIGELGAPEVWGLSPKLPEPDSDEHTPVEDDE

Parental  PKKSTTSASTSEEEKKRKKKSGHSKERSKKRRKKKSSKRKHKKYSDDSDSDSDSDTDSS-DEDTKRRAKK
          .K...TS.S.S..E.KRKKK..H....SKK.RKKKS.KRK..KYSD.SDS.SDS.TDSS.D.D.K.R.KK
Retrocopy VKTKKTSSSDSSSEEKRKKKTSH----SKKKRKKKS-KRKYRKYSDNSDSNSDSNTDSSSDDDDKKRPKK

Parental  SKKKEKKKKRRSKKYKKKKSKKSRKDSSDSSSKESQEELLENPWKDRSKPEEPSDLIGPEAPKTLASQDD
          .KKKEKKKK.R.KK.KKKK.KK.RK.SSDS..K.S..EL.E..W...SK.....DLIGPEAP.T..SQD.
Retrocopy AKKKEKKKKHRAKKPKKKKTKKTRKESSDSNYKDSEGELPEGIWIEQSKIADNMDLIGPEAPITQISQDE

Parental  KPLNYGHALLPGEGAAMAEYVKAGKRIPRRGEIGLTSEEIASFECSGYVMSGSRHRRMEAVRLRKENQIY
          KPLNYGHALLPGEGAAMAEYVKAGKRIPRRGEIGLTSEEIASFE.SGYVMSGSRHRRMEAVRLRKENQIY
Retrocopy KPLNYGHALLPGEGAAMAEYVKAGKRIPRRGEIGLTSEEIASFEYSGYVMSGSRHRRMEAVRLRKENQIY

Parental  SADEKRALASFNQEERRKRENKILASFREMVYRKTKGKEDK
          SADEKRALASFNQEERRKRENKILASFREMVYRKTKGKEDK
Retrocopy SADEKRALASFNQEERRKRENKILASFREMVYRKTKGKEDK

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
SRP014902_placenta	0.13 RPM	9.42 RPM
SRP014902_testis	0.99 RPM	12.02 RPM
SRP018288_heart	0.73 RPM	9.04 RPM
SRP018288_kidney	0.39 RPM	15.27 RPM
SRP018288_liver	0.16 RPM	8.16 RPM
SRP018288_lung	0.51 RPM	14.15 RPM
SRP018856_adipose	0.14 RPM	17.13 RPM
SRP035408_brain	10.58 RPM	55.74 RPM
SRP035408_liver	0.47 RPM	27.33 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

1 EST(s) were mapped to retro_sscr_13 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
EW567141	24053223	24053509	99.7	285	1	284

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_13 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_13 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Canis familiaris	retro_cfam_172

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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,