RetrogeneDB ID: retro_vpac_580

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_5533:19168..19860(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: CDK15
• Ensembl ID: ENSVPAG00000006704
• Aliases: None
• Description: cyclin-dependent kinase 15 [Source:HGNC Symbol;Acc:14434]

Sequence

>retro_vpac_580
ATCGACTTTGGGAAACTGGAGACCTATATCAAGTTGGACAAGCTGGGAGAGGGTACATATGCCACCGTCTGCAAAGGCAA
AAACAAGCTCACAGACAACCTTGTGGCGCCCAGGGAGATCAGACTGAACACGAAGAGGGGGCGCCCTGCACCGCCATCTG
GGAAGCGTCCCTGCTCAAGGACCTCAAACATGCCAGCATCATCCCACCACACGACATTATCCTCAGAGAAGTCGCTCACC
CTTGTCTTTGAGTACCTGGACAAGGACCTGACGCAGCACCCGGATGGCTGTGGGAACGTCATCAACATGCACAATGCGAA
ACTCTTCCTGTTCCAGCTGCTCCGCGGCCTGGTCTGCTGCCACCGGCAGTAGGTGCTACACCGAGACGTCAAGCCCCAGA
ACCTGCTCATCAACGAGAGAGGAGAGCTCAAGCTGGCCGTCTTCGGCCTGGCCCAGGCCGAGTCTGTTCCAATGAGGACC
TACTCCAATTAGGTTGTAACGCTGTGTACCGGCCCCCAACATCCTGCTTGGGTCCACGGACTACCCTCTCAGATTGGCAT
GTGGGGTGTGGGCTGCAACTTCTATGAGATGGCCACGGGCCGGCCCCTCTTCCCGGGATCCACGGTGGAGGAACAGCTGC
ACTTCATCTTCCGCGTCTTGGGAACCCAACTGAGGGGACGTGGCCAGGCATC

Alignment

ORF - retro_vpac_580 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.83 %
• Parental protein coverage: 67.24 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  LPFGAASSYLNLEKLGEGSYATVYKGISRINGQLVALKVISMNA-EEGVPFTAIREASLLKGLKHANIVL
          ..FG....Y..L.KLGEG.YATV.KG.......LVA...I..N..EEG.P.TAI.EASLLK.LKHA.I..
Retrocopy IDFGKLETYIKLDKLGEGTYATVCKGKNKLTDNLVAPREIRLNT<EEGAPCTAIWEASLLKDLKHASIIP

Parental  LHDIIHTRE-TLTFVFEYMHTDLAQYMSQHPGGLHPYNVRLFMFQLLRGLAYIHHQHVLHRDLKPQNLLV
          .HDII..RE..LT.VFEY...DL.Q............N..LF.FQLLRGL...H.Q.VLHRD.KPQNLL.
Retrocopy PHDII-LRE>SLTLVFEYLDKDLTQHPDGCGNVINMHNAKLFLFQLLRGLVCCHRQ*VLHRDVKPQNLLI

Parental  SHLGELKLADFGLARAKSIPSQTYSSEVVTLW-YRP-PDALLGATEY-SSELDIWGAGCIFIEMFQGQPL
          ...GELKLA.FGLA.A.S.P..TYS..VVTL..YRP.P..LLG.T.Y..S....WG.GC.F.EM..G.PL
Retrocopy NERGELKLAVFGLAQAESVPMRTYSN*VVTLC<YRP<PNILLGSTDY<PSQIGMWGVGCNFYEMATGRPL

Parental  FPGVSNILEQLEKIWEVLGV-PTEDTWPGV
          FPG.S...EQL..I..VLG..PTE.TWPG.
Retrocopy FPG-STVEEQLHFIFRVLGT<PTEGTWPGI

Legend:

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

Expression

RNA-Seq

Vicugna pacos was not studied using RNA-Seq expression data.

ChIP-Seq

Vicugna pacos was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_vpac_580 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_580 was not experimentally validated.

Homology

Retrocopy orthology:

Vicugna pacos does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Vicugna pacos	ENSVPAG00000002256	1 retrocopy	retro_vpac_179,
Vicugna pacos	ENSVPAG00000006704	4 retrocopies	retro_vpac_365, retro_vpac_437, retro_vpac_488, retro_vpac_580 ,