RetrogeneDB ID: retro_drer_17

Retrocopy location

• Organism: Zebrafish (Danio rerio)
• Coordinates: 1:15202018..15203293(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDARG00000091657
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: vrk1
• Ensembl ID: ENSDARG00000018006
• Aliases: vrk1, wu:fe16f06, zgc:56266
• Description: vaccinia related kinase 1 [Source:ZFIN;Acc:ZDB-GENE-040426-2709]

Sequence

>retro_drer_17
ATGCCACCAAAGAAGGCAGACGGGGTGAAGAAAGCAAGAGCTCCAGCTAAGAGGAAACTGGCTGAAGAATTCCCGTCTGG
AGAAGTCCTGACAGATAACGCAAAGAAAAAATGGAAGCTTGGATCAGCTGTTGGACAAGGAGGTTTTGGCCTGCTGTATC
TTGCAAATGAAGACTCTTCAGGACCTGTCACCGCTGATGCACCTTATGTCATTAAAGTGGAACCAAGTGACAACGACCCT
CTCTTCTCTGAACTGAAGTTTTACATGCGAGCTGCCAAACCTGATCTAATCGGGGCTGGGATGAAGTCAAAGAAAATAGA
GTATTTGGGAGTTCCAAAATATTGGGGTTCTGGTTTTCATGAGAAAAATGGAAAGAGGTACAGATTTATGGTGATGGATC
GATTTGGAACAGATCGACAGAAATTGTTTAAAGGAAATGGGAAGAAGTTTTCAAGGAAGCTGGTTCTTCAGCTGGGCCTT
CGACTTCTTGACATTCTGGAGTACATCCATGACCATGAATATGTGCATGCAGACATCAAAGCCTACAACGTCCTCCTGTC
CTACACCAACCCCAATCAGGTATTTTTAGTAGATTATGGACTGGCCTATAGATATGCTCCTGAGGGAGTGCCAAAGGAGT
ATAAGGAAGACCCAAAGAGGTGTCATGACGGTACCATTGAGTTCACAAGTATTGACGCACACAAAGGAGTCTCTCCTTCA
AGGCGAGCAGACCTGGAAATCATGGGCTACTGCATGATCCAGTGGTTATGTAGCCGTCTGCCCTGGGAAGACAAACTTCA
GGACCCACTCTACGTCAGAGACTCCAAGCTCAGGTGTAGAGACAATATTGATGAGTTCTTGAAAAGCTGTTTCGCTTCAG
GAAATATACCAGCTGAAATGGGAAAGTTCATGCAAGAGGTCAAGGTTCTGGGATACACAGACAGGCCAGATTACGACAAA
TTGCGAGGTATTTTGCAGCAAGGCCTAAAGTCCATAGGGTCAACAGATGACAAAAAGCTGGACTTTGGAGTGGCGACCAA
CAGCACAAGTTTGCCCTCTGTCAAGACTCCCAAGCGAAAGAAAGCAGAGGAAAAAGGCCAGTCTGCTGACGAAACCGATA
GCACCCCAGCAAAGAAGAGGCGAGCTCCTCAGAAGAAGGAAGTGAATGGGGCTAAAAAGACAGCAAGTCCTGCAAAGCGT
CCAGTGAAGAAAGAAGCTCAGGCCTCCTCTGAGCCAGCGGTGAAAAAAAGCCGAGGAAGGCCTAAGAAGAACTCT

Alignment

ORF - retro_drer_17 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.35 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPPKKADGVKKARAPAKRKLAEEFPSGEVLTDNAKKKWKLGSAVGQGGFGLLYLANEDSSGPVTADAPYV
          MPPKKADGVKKARAPAKRKLAEEFPSGEVLTDNAKKKWKLGSAVGQGGFGLLYLANEDSSGPVTADAPYV
Retrocopy MPPKKADGVKKARAPAKRKLAEEFPSGEVLTDNAKKKWKLGSAVGQGGFGLLYLANEDSSGPVTADAPYV

Parental  IKVEPSDNGPLFSELKFYMRAAKPDLIGAWMKSKKMEYLGVPKYWGSGFHEKNGKRYRFMVMDRFGTDLQ
          IKVEPSDN.PLFSELKFYMRAAKPDLIGA.MKSKK.EYLGVPKYWGSGFHEKNGKRYRFMVMDRFGTD.Q
Retrocopy IKVEPSDNDPLFSELKFYMRAAKPDLIGAGMKSKKIEYLGVPKYWGSGFHEKNGKRYRFMVMDRFGTDRQ

Parental  KLFEGNGKKFSRKLVLQLGLRLLDILEYIHDHEYVHADIKASNLLLSYTNPNQVFLVDYGLAYRYAPEGV
          KLF.GNGKKFSRKLVLQLGLRLLDILEYIHDHEYVHADIKA.N.LLSYTNPNQVFLVDYGLAYRYAPEGV
Retrocopy KLFKGNGKKFSRKLVLQLGLRLLDILEYIHDHEYVHADIKAYNVLLSYTNPNQVFLVDYGLAYRYAPEGV

Parental  PKEYKEDPKRCHDGTIEFTSIDAHKGVSPSRRADLEIMGYCMIQWLCSRLPWEDKLQDPLYVRDSKLRCR
          PKEYKEDPKRCHDGTIEFTSIDAHKGVSPSRRADLEIMGYCMIQWLCSRLPWEDKLQDPLYVRDSKLRCR
Retrocopy PKEYKEDPKRCHDGTIEFTSIDAHKGVSPSRRADLEIMGYCMIQWLCSRLPWEDKLQDPLYVRDSKLRCR

Parental  DNIDEFLKSCFASGNIPAEMGKFMQEVKVLGYTDRPDYDKLRGILQQGLKSIGSTDDKKLDFGVATNSTS
          DNIDEFLKSCFASGNIPAEMGKFMQEVKVLGYTDRPDYDKLRGILQQGLKSIGSTDDKKLDFGVATNSTS
Retrocopy DNIDEFLKSCFASGNIPAEMGKFMQEVKVLGYTDRPDYDKLRGILQQGLKSIGSTDDKKLDFGVATNSTS

Parental  LPSVKTPKRKKAEEKGQSADETDSTPAKKRRAPQKKEVNGAKKTASPAKRPVKKEAQASSEPAVKKSRGR
          LPSVKTPKRKKAEEKGQSADETDSTPAKKRRAPQKKEVNGAKKTASPAKRPVKKEAQASSEPAVKKSRGR
Retrocopy LPSVKTPKRKKAEEKGQSADETDSTPAKKRRAPQKKEVNGAKKTASPAKRPVKKEAQASSEPAVKKSRGR

Parental  PKKNS
          PKKNS
Retrocopy PKKNS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Danio rerio was not studied using RNA-Seq expression data.

ChIP-Seq

Danio rerio was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_drer_17 retrocopy.

TSS

Danio rerio was not studied using FANTOM5 data.

Lab

retro_drer_17 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_drer_17 has 0 orthologous retrocopies within teleost group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000001772	1 retrocopy	retro_cpor_1214,
Danio rerio	ENSDARG00000018006	1 retrocopy	retro_drer_17 ,
Macropus eugenii	ENSMEUG00000012543	1 retrocopy	retro_meug_186,
Otolemur garnettii	ENSOGAG00000016785	1 retrocopy	retro_ogar_2000,
Sorex araneus	ENSSARG00000009110	2 retrocopies	retro_sara_287, retro_sara_337,
Ictidomys tridecemlineatus	ENSSTOG00000011492	1 retrocopy	retro_itri_1674,