RetrogeneDB ID: retro_cfam_172

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 35:25399160..25400378(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000025009
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: NKAP
• Ensembl ID: ENSCAFG00000018433
• Aliases: None
• Description: NFKB activating protein [Source:HGNC Symbol;Acc:29873]

Sequence

>retro_cfam_172
ATGGCCCCGGTGTCCCGGTCCCGCTACTCCAAGGAAGCTGTGGGCTCTCGGAGGTGGCGACGCCGCTCGTCGGGGAGCCC
GCCTTTGGCGCAGGCCAGACGCTCCCCGTGGGGAGGCCTCGTCCGTTCTTACTCCTGCGGCCGCGAGGCCCTCAGACCTC
CGTGGGGAGGGTCGGGCGTTGGCGCCCGTTACCCGCTCGGCCGCTCTGAGTTTCGAGAACCACCGCCGGGGCCCTGCGAC
TATGCGTTCTCGTCGTCCTCCGTCTATTACGGCAGCGGCAGCGGGTACCACTGCCATCACCGCCACTCCCCGAGGGACCG
GCAGTGGGCGGAGGAGTACCAGGAGGAGGAGGAGAGCTATCGTCAGAGGAGGCTGAAGGAGAGAGAAAGGATTGGGGAGT
TGGGCGCCCCTGAGGTGTGGGGGCTGTCTCCGAAGTTTCCTGAGCTGGATTCTGATGAGCACACCCCCGTGGAGGATGAC
CGGGCGAAGGCTCAGAAGACCGCCGGTTCAGAATCCAGCTCCGAGGGAAAGAGGAAAAAGGCCAGTCGTTCAAAAAGCAA
GAAAAAGAGAAAGAAAAAGTCCAAAAAGAAACACAGGAAATATTCTAATGATAGTGATGGTAATTCAGACTCCGACATGG
ATTCTAGCTCTGATGATGATAAAAAGAGAGCCAAAAAAGCCAGGAAGAAGGAGAAGAAAAAGAAACACAGGGCAAGAAAA
AACAAGAAAAAGAAGAAGACTAAAAAAGAATCCAGTGACTCAAGCTTTAAAGATTCAGAAGGGGAGTTGCTGGAAGATAT
TTGGATTAAGCAGTCAAAGATTGCAGATACCATGGATCTGATAGGTCCAGAAGCACCCATAATACACACGTCTCAAGAGG
AGAAACCTTTGAACTATGGCCATGCTCTGCTCCCAGGTGAAGGTGCAGCAATGGCTGAGTATGTAAAAGCTGGAAAGCGA
ATCCCACGAAGAGGTGAAATTGGGCTGACAAGTGAAGAGATTGCTTCATTTGAATGCTCAGGTTATGTTATGAGTGGTAG
CAGGCATCGTAGGATGGAGGCTGTGCGACTGCGTAAAGAGAACCAGATCTACAGTGCTGATGAGAAGAGAGCGCTTGCAT
CCTTTAACCAGGAAGAGAGGCGGAAGAGAGAGAATAAGATTCTAGCCAGTTTCCGAGAGATGGTGTACAGGAAGACAAAA
GGGAAAGATGACAAGTAA

Alignment

ORF - retro_cfam_172 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.78 %
• Parental protein coverage: 93.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RLSERERIGELGAPEVWGLSPKNPEPDSDEHTPVEDDEPKKSSTSASTSEEEKKKKKKSGHSKERSKKRR
          RL.ERERIGELGAPEVWGLSPK.PE.DSDEHTPVEDD..K...T..S.S..E.K.KK....S...SKK.R
Retrocopy RLKERERIGELGAPEVWGLSPKFPELDSDEHTPVEDDRAKAQKTAGSESSSEGKRKKA---SRSKSKKKR

Parental  KKKSSKRKHKKYSDDSDSDSDSDTDSSDEDTKRRSKKAKKKEKKKKHRSKKYKKKKSKKSRKDSSDSSSK
          KKKS.K.KH.KYS.DSD..SDSD.DSS..D.K.R.KKA.KKEKKKKHR..K.KKKK..K..K.SSDSS.K
Retrocopy KKKS-KKKHRKYSNDSDGNSDSDMDSSSDDDKKRAKKARKKEKKKKHRARKNKKKK--KTKKESSDSSFK

Parental  DSQEEFLENPWKDRSKPEEPSDLIGPEAPKTLASQDDKPLNYGHALLPGEGAAMAEYVKAGKRIPRRGEI
          DS..E.LE..W...SK.....DLIGPEAP....SQ..KPLNYGHALLPGEGAAMAEYVKAGKRIPRRGEI
Retrocopy DSEGELLEDIWIKQSKIADTMDLIGPEAPIIHTSQEEKPLNYGHALLPGEGAAMAEYVKAGKRIPRRGEI

Parental  GLTSEEIASFECSGYVMSGSRHRRMEAVRLRKENQIYSADEKRALASFNQEERRKRENKILASFREMVYR
          GLTSEEIASFECSGYVMSGSRHRRMEAVRLRKENQIYSADEKRALASFNQEERRKRENKILASFREMVYR
Retrocopy GLTSEEIASFECSGYVMSGSRHRRMEAVRLRKENQIYSADEKRALASFNQEERRKRENKILASFREMVYR

Parental  KTKGKDDK
          KTKGKDDK
Retrocopy KTKGKDDK

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
SRP012049_cerebellum	0.17 RPM	11.00 RPM
SRP017611_brain	0.40 RPM	9.53 RPM
SRP017611_kidney	0.00 RPM	11.69 RPM
SRP017611_liver	0.00 RPM	6.67 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

1 EST(s) were mapped to retro_cfam_172 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BM537189	25399452	25399882	100	430	0	430

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_172 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_172 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Sus scrofa	retro_sscr_13

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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,