RetrogeneDB ID: retro_vpac_334

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_962:782373..783299(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KRT5
• Ensembl ID: ENSVPAG00000011707
• Aliases: None
• Description: keratin 5 [Source:HGNC Symbol;Acc:6442]

Sequence

>retro_vpac_334
GGCATCTGTGAGGTCACCATCAATCAGAGCCTGCTGACCCCGCTGCAGGTGGACATCGACCCCTCCATCCAGCAGGTGCC
CCAGGAGGAGCGCGAGCAGATCAAGACCCTCAACAACACGTTCGCCTCCTTCACCTACAAGGTATGGTTCCTGGAGCTGC
AGAACAAGCTGCTGGAGACCAAGTGGGCGCTGCTTCAGGAGCAGAAGTCGACCGAGAGCAGCCGCCTCCCGGGCATCTTT
GAGGCCCACATTGCCTGCCTGCGGAAGCAGCTTGAGACGCTGCAGCTGGATGGGGGCCGCCTGGAGGTGGAGCTTCGGAA
CATGCAGGACATCGTGGAAGACTTCAAGAATAAGTATGAAGATGAAATTAACCATCGCATGGCTGCTCAGAATGAGTTCC
TGGGGTTGAAGAAGGGTGTAGATGTTGCCTACATGAACAAGGTGGAATTGGAGGCCAAGGTGGACCCCTTGAAAGACAAG
ATCAACTTCCTCAGGACTCTCTACGAGGAGGAGTTGAAAGAGCTGCAGTCCAAGGTCTCAGACATGTCCGTGGTCCTGTC
CATGGACAACAGCCGCTTCCTGGACCTGGAGGGCATCATCGCCGAGGTCAAGGCCCAGTATGAGGAGATCGCCAACCGCA
GCCGGGCCGAGGCCGAGACCTTGTACCAGACCAAGTTTGAGACCCCCAGGCCCAGGCTGGGAAGCACGGGGATGAACTCC
GGAATACCCGAAATGAGATTGCGGAGATGAACCGGGCTGTCCAGAGGCTGCAGGCTGAAATCGACAGCATCAAGAACCAG
CGTGCCAAGTTGGAGGCTGCCATCTCTGAGGCTGAGGAGCGTGGGGAGCTGGCACTCAAGGATGCACGCACCAAGCAGGA
AGACCTGGTGGCTGCCCTGCAACGAGCCAAGCAGGACATGGCCCGG

Alignment

ORF - retro_vpac_334 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.56 %
• Parental protein coverage: 63.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GIQEVTVNQSLLTPLNLQIDPAIQRVRTEEREQIKTLNNKFASFIDKVRFLEQQNKVLDTKWTLLQEQGT
          GI.EVT.NQSLLTPL...IDP.IQ.V..EEREQIKTLNN.FASF..KV.FLE.QNK.L.TKW.LLQEQ..
Retrocopy GICEVTINQSLLTPLQVDIDPSIQQVPQEEREQIKTLNNTFASFTYKVWFLELQNKLLETKWALLQEQKS

Parental  KTVRQNLEPLFEQYINNLRRQLDGILGERGRLDSELRNMQDLVEDFKNKYEDEINKRTTAENEFVMLKKD
          .T....L...FE..I..LR.QL.......GRL..ELRNMQD.VEDFKNKYEDEIN.R..A.NEF..LKK.
Retrocopy -TESSRLPGIFEAHIACLRKQLETLQLDGGRLEVELRNMQDIVEDFKNKYEDEINHRMAAQNEFLGLKKG

Parental  VDAAYMNKVELEAKVDALMDEINFMKMFFDAELSQMQTHVSDTSVVLSMDNNRSLDLDSIIAEVKAQYEE
          VD.AYMNKVELEAKVD.L.D.INF.......EL...Q..VSD.SVVLSMDN.R.LDL..IIAEVKAQYEE
Retrocopy VDVAYMNKVELEAKVDPLKDKINFLRTLYEEELKELQSKVSDMSVVLSMDNSRFLDLEGIIAEVKAQYEE

Parental  IANRSRTEAESWYQTKYE-ELQQTAGRHGDDLRNTKHEISEMNRMIQRLRAEIDNVKKQCANLQNAIADA
          IANRSR.EAE..YQTK.E...Q..AG.HGD.LRNT..EI.EMNR..QRL.AEID..K.Q.A.L..AI..A
Retrocopy IANRSRAEAETLYQTKFE<DPQAQAGKHGDELRNTRNEIAEMNRAVQRLQAEIDSIKNQRAKLEAAISEA

Parental  EQRGELALKDARNKLAELEDALQKAKQDMAR
          E.RGELALKDAR.K...L..ALQ.AKQDMAR
Retrocopy EERGELALKDARTKQEDLVAALQRAKQDMAR

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_334 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_334 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 6 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011913	4 retrocopies	retro_chof_1848, retro_chof_2381, retro_chof_2385, retro_chof_778,
Erinaceus europaeus	ENSEEUG00000009412	1 retrocopy	retro_eeur_521,
Echinops telfairi	ENSETEG00000007907	1 retrocopy	retro_etel_1586,
Nomascus leucogenys	ENSNLEG00000017746	5 retrocopies	retro_nleu_2270, retro_nleu_2596, retro_nleu_354, retro_nleu_457, retro_nleu_852,
Pongo abelii	ENSPPYG00000004548	1 retrocopy	retro_pabe_1103,
Vicugna pacos	ENSVPAG00000011707	3 retrocopies	retro_vpac_334 , retro_vpac_551, retro_vpac_555,