RetrogeneDB ID: retro_vpac_555

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_4325:21873..22808(+)
• 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_555
GGGGCATCACAGCTGTCATGGTGAGCCAGCCTTCTGAGCCCCCTCAAGCTGGAGGTGGACCCCAACATCCAGGCTGTGAG
CACCCAGGAGAAGGAGCAGATCAAGACCCTCAACATAAGTTTGCCTCCTTCATCGACAAGCGACAAGGTGCGGCACCTGG
AGCAGCAGAACAAGATTCTGGAGAACAAATGGAACCTCCTGCAAAAGCAGAAGACAGCCCGGAGCAACACAGACAACATG
TTCAAGAGATACATCAATAACCTTCAGAGGCAGCTGGACACCCTGGCCCAGGAGAAACTGAAGCTGGAGGTGGAGCTTGG
CAACATACAGGGGCTGGTGGAGGACCTCAAGAACAAGTATGAGGAAGAGATCCAAAAGCGCATAGACGTGGAGAATGAAT
TTGTCATTATCAAGACGGATGTGGATGAAGCATACATGAACAAGGTAGAGCTGGAGTCCTGCCTGGAAGGGCTGACTGAC
GAGATCAACTTCTACAGGCAGCTGTATGAAGAGGAGATCCGTGAGATGCAGTCACAGATTTCAGACACGTCCGTGGTCCT
CTCCATGGTCAACCACTGCTCCCTGGACCTGGATGGCATCATCACCGAGGTCAAGGCCCAGTACGAGGAGATCACCAACT
GCAGCCCGGCCGAGGCCGAGGCCGAGACCATTTACCAGATCAAGTACGAGGAGCTGCAGACACAGGCTGGGAAGCACAGG
GATGGTCTCCATCACATGAAGATGGAGATTTCTGAGGTGAACCGGAACAACAGCTGACTCCAGGCTAAGATCGTGGGCCT
CAAAGGCCAGAGGCTTCCCTGGAGGCTGCCATTGCCGATGCTGAGCAGCATGGGGAGCTGGCCGTCAAGGATGCTCAAGC
CAAGCTGGCCGAGCTGGAGGCCGCTCTGAGAACCTCCAAGCAGGACACAGCCCAG

Alignment

ORF - retro_vpac_555 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.1 %
• Parental protein coverage: 63.27 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GIQEVTVNQSLLTPLNLQIDPAIQRVRTEEREQIKTLNNKF--ASFIDKVRFLEQQNKVLDTKWTLLQEQ
          G........SLL.PL.L..DP.IQ.V.T.E.EQIKTLN......S..DKVR.LEQQNK.L..KW.LLQ.Q
Retrocopy GASQLSW*ASLLSPLKLEVDPNIQAVSTQEKEQIKTLNISLPPSSTSDKVRHLEQQNKILENKWNLLQKQ

Parental  GTKTVRQNLEPLFEQYINNLRRQLDGILGERGRLDSELRNMQDLVEDFKNKYEDEINKRTTAENEFVMLK
          ..KT.R.N....F..YINNL.RQLD....E...L..EL.N.Q.LVED.KNKYE.EI.KR...ENEFV..K
Retrocopy --KTARSNTDNMFKRYINNLQRQLDTLAQEKLKLEVELGNIQGLVEDLKNKYEEEIQKRIDVENEFVIIK

Parental  KDVDAAYMNKVELEAKVDALMDEINFMKMFFDAELSQMQTHVSDTSVVLSMDNNRSLDLDSIIAEVKAQY
          .DVD.AYMNKVELE.....L.DEINF.......E...MQ...SDTSVVLSM.N..SLDLD.II.EVKAQY
Retrocopy TDVDEAYMNKVELESCLEGLTDEINFYRQLYEEEIREMQSQISDTSVVLSMVNHCSLDLDGIITEVKAQY

Parental  EEIANRS--RTEAESWYQTKYEELQQTAGRHGDDLRNTKHEISEMNRMIQRLRAEIDNVKKQC-ANLQNA
          EEI.N.S....EAE..YQ.KYEELQ..AG.H.D.L...K.EISE.NR....L.A.I...K.Q..A.L..A
Retrocopy EEITNCSPAEAEAETIYQIKYEELQTQAGKHRDGLHHMKMEISEVNRNNS*LQAKIVGLKGQR<ASLEAA

Parental  IADAEQRGELALKDARNKLAELEDALQKAKQDMAR
          IADAEQ.GELA.KDA..KLAELE.AL...KQD.A.
Retrocopy IADAEQHGELAVKDAQAKLAELEAALRTSKQDTAQ

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_555 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_555 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 ,