RetrogeneDB ID: retro_vpac_437

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_19108:1919..2612(-)
• 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_437
ATCGACTTTGGGAAACTGGAGACCTACATCAAGTTGGACAAGCTGGGAGAGGGTACATATGCCACCGTCTGCAAAGGCAA
AAGCAAGCTCACAGACAACCTTGTGGCGCCCAGGGAGATCAGACTGAACACGAAGAGGGGGCGCCCTGCACCGCCATCTG
GGAAGCGTCCCTGCTCAAGGACCTCAAACACGCCAGCATCATCCCACTACACGACATTATCCTCAGAGAAGTCGCTCACC
CTTGTCTTTGAGTACCTGGACAAGGACCTGACGCAGCACCCGGATGGCTGTGGGAACGTCATCAACATGCACAATGCGAA
ACTCTTCCTGTTCCAGCTGCTCCGCGGCCTGGTCTGCTGCCACCGGCAGTAGGTGCTACACCGAGACGTCAAGCCCCAGA
ACCTGCTCATCAACGAGAGAGGAGAGCTCAAGCTGGCCGTCTTCGGCCTGGCCCAGGCCGAGTCTGTTCCAATGAGGACC
TACTCCAATTAGGTTGTAACGCTGTGTACCGGCCCCCAACATCCTGCTCGGGTCCACGGACTGCTCCTCTCAGATTGGCA
TGTCGGGTGTGGGCTGCATCTTCTATGAGATGGCCACAGGCCGGCCCCTCTTCCCGGGCTCCACGGTGGAGGAACAGTTG
CACTTCATCTTCCGCGTCTTGGGAACCCAACTGAGGGGACGTGGCCAGACATC

Alignment

ORF - retro_vpac_437 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.49 %
• Parental protein coverage: 67.24 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

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

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

Parental  SHLGELKLADFGLARAKSIPSQTYSSEVVTLW-YRP-PDALLGATEYSSELDIWGAGCIFIEMFQGQPLF
          ...GELKLA.FGLA.A.S.P..TYS..VVTL..YRP.P..LLG.T..SS.....G.GCIF.EM..G.PLF
Retrocopy NERGELKLAVFGLAQAESVPMRTYSN*VVTLC<YRP<PNILLGSTDCSSQIGMSGVGCIFYEMATGRPLF

Parental  PGVSNILEQLEKIWEVLGV-PTEDTWPGV
          PG.S...EQL..I..VLG..PTE.TWP..
Retrocopy PG-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_437 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_437 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,