RetrogeneDB ID: retro_vpac_365

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_12523:71..761(+)
• 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_365
CCACTTTGGGAAACTGGAGCTTACATCAAGTTGGACAAGCTGGGAGAGGGTACATATGCCACCGTCTGCAAAGGCAAAAG
CAAGCTCCCAGACAACCTTGTGGCGCCCAGGGAGATCACACTGAACACGAAGAGGGGGCGCCCTGCACCGCCATCTGGGA
AGCGTCCCTGCTCAAGGACCTCAAACACGCCAGCATCATCCCACTACACGACATTATCCTCAGAGAAGTCGCTCACCCTT
GTCTTTGAGTACCTGGACAAGGACCTGACGCAGTACCTGGATGGCTGTGGCAACGTCATCAACATGCACAGTGCGAAACT
CTTCCTGTTCCAGCTGCTCCGCGGCCTGGTCTGCTGCCACCGGCAGTAGGTGCTACACCGAGACGTCAAGCCCCAGAACC
TGCTCATCAAGGAGAGAGGAGAGCTCAAGCTGGCCGTCTTCGGCCTGGCCCAGGCCGAGTCTGTTCCAATGAGGACCTAC
TCCAATTAGGTTGTAACGCTGTGTACCGGCCCCCAACATCCTGCTCAGGTCCACGGACTACTCCTCTCAGATTGGCATGT
CGGGTGTGGGCTGCATCTTCTATGAGATGGCCACGGGCCGGCCCCTCTTCCCGGGCTCCACGGTGGAGGAACAGCTGCAC
TTCATCTTCCGCGTCTTGGGAACCCAACTGAGGGGACGTGGCCAGACATC

Alignment

ORF - retro_vpac_365 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.3 %
• Parental protein coverage: 66.95 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  PFGAASSYLNLEKLGEGSYATVYKGISRINGQLVALKVISMNA-EEGVPFTAIREASLLKGLKHANIVLL
          P......Y..L.KLGEG.YATV.KG.S.....LVA...I..N..EEG.P.TAI.EASLLK.LKHA.I..L
Retrocopy PLWETGAYIKLDKLGEGTYATVCKGKSKLPDNLVAPREITLNT<EEGAPCTAIWEASLLKDLKHASIIPL

Parental  HDIIHTRE-TLTFVFEYMHTDLAQYMSQHPGGLHPYNVRLFMFQLLRGLAYIHHQHVLHRDLKPQNLLVS
          HDII..RE..LT.VFEY...DL.QY..............LF.FQLLRGL...H.Q.VLHRD.KPQNLL..
Retrocopy HDII-LRE>SLTLVFEYLDKDLTQYLDGCGNVINMHSAKLFLFQLLRGLVCCHRQ*VLHRDVKPQNLLIK

Parental  HLGELKLADFGLARAKSIPSQTYSSEVVTLW-YRP-PDALLGATEYSSELDIWGAGCIFIEMFQGQPLFP
          ..GELKLA.FGLA.A.S.P..TYS..VVTL..YRP.P..LL..T.YSS.....G.GCIF.EM..G.PLFP
Retrocopy ERGELKLAVFGLAQAESVPMRTYSN*VVTLC<YRP<PNILLRSTDYSSQIGMSGVGCIFYEMATGRPLFP

Parental  GVSNILEQLEKIWEVLGV-PTEDTWPGV
          G.S...EQL..I..VLG..PTE.TWP..
Retrocopy G-STVEEQLHFIFRVLGT<PTEGTWPDI

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_365 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_365 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,