RetrogeneDB ID: retro_vpac_551

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_41912:434..1471(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSVPAG00000011802
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_vpac_551
GGCATCCGCGAGGTCGCCATCAATCAGAGCCTGCTGACTCGGCTGCAGGTGGACGTCGACGTCTCCATCCAGCAGGTGCG
CCAGGAGGAGCGCGAGCAGATGAAGACTCTCATCAACAAGCTCGCCTCCTTCATCAACAAGGTCCGGTTCCTGGCGCAGC
AGAACAAGCTGCTGGAGGCCACGTGGGCGCTGCGGCAGGAGCAGAAGTCGACCGAGAGCTGCCGCCTCCCGGGCATCTCT
GAGGCCCGCATTGCCGGCCTGCGGAAGCAGCTTGAGACAATACAGCTGGATGGGGGCCGCCTGGAGGTGGAGCTTCGGAA
CATGCAGGAAGTCGTGGACGACTTCAAGAGTAAGTACGAAGATGAAAGTAACCGTCGCACGGCTGCCGAGAATGAGATCG
CGGTGTTGAAGAAGGATGCAGATGTTGCCTACATGAATAAGGTGGAATTGGAGGCCAAGGTGGATGCCTTGAATGACGAG
ATCAACTTCCTCAGGGCTCTCTACCAGGAGTTGAAAGAGCTGCAGTCCGAGGTCTCAGACACGTCCGTGGACAACAGCCG
CTCCCTGGACCTGGATGGCATCATCGCTGAGGTCAAGGCCCAGTACGAGGAGATCGCCAACCGCAGCCGGGCCGAGGCCG
AGACCATGTACAAGACCAAGTTTAAGACCCTCCAGGCCCAGGCTGGGAAGCAGGGGGATGAACTCCGGAATACCGGAAAT
GAGATTGCGGAGATGAACCCGGCCGTCCAGGGGCTGCATGCGGAGATCGACAGCATCGAGAACCAGCGTGCCAATTTGGA
GGCTGCCATCGCTGAGCTGAGGAGCGTGGGGAGCTGGCACTCAAGAGGCACGCGCCAAGCAGAAGAGCTGGAGCTGCTCT
GCAACAAGCCAAGCAGGCCATGGCCTGGCAGCTCCAGGAGTACCAGGAGTTGATGAATATCAAGCTGGCCCTGGACATCG
AGATCGCCACCTACCACAAGCTGCTGGAGGGCGAGGAGAGCAGGTTGACCGGAGATGGAGTGGAAACCGTGAACATC

Alignment

ORF - retro_vpac_551 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.75 %
• Parental protein coverage: 71.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GIQEVTVNQSLLTPLNLQIDPAIQRVRTEEREQIKTLNNKFASFIDKVRFLEQQNKVLDTKWTLLQEQGT
          GI.EV..NQSLLT.L....D..IQ.VR.EEREQ.KTL.NK.ASFI.KVRFL.QQNK.L...W.L.QEQ..
Retrocopy GIREVAINQSLLTRLQVDVDVSIQQVRQEEREQMKTLINKLASFINKVRFLAQQNKLLEATWALRQEQKS

Parental  KTVRQNLEPLFEQYINNLRRQLDGILGERGRLDSELRNMQDLVEDFKNKYEDEINKRTTAENEFVMLKKD
          .T....L....E..I..LR.QL..I....GRL..ELRNMQ..V.DFK.KYEDE.N.RT.AENE...LKKD
Retrocopy -TESCRLPGISEARIAGLRKQLETIQLDGGRLEVELRNMQEVVDDFKSKYEDESNRRTAAENEIAVLKKD

Parental  VDAAYMNKVELEAKVDALMDEINFMKMFFDAELSQMQTHVSDTSVVLSMDNNRSLDLDSIIAEVKAQYEE
          .D.AYMNKVELEAKVDAL.DEINF.......EL...Q..VSDTSV....DN.RSLDLD.IIAEVKAQYEE
Retrocopy ADVAYMNKVELEAKVDALNDEINFLRALYQ-ELKELQSEVSDTSV----DNSRSLDLDGIIAEVKAQYEE

Parental  IANRSRTEAESWYQTKYEELQQTAGRHGDDLRNTKHEISEMNRMIQRLRAEIDNVKKQCANLQNAIAD-A
          IANRSR.EAE..Y.TK...LQ..AG..GD.LRNT..EI.EMN...Q.L.AEID....Q.ANL..AIA..A
Retrocopy IANRSRAEAETMYKTKFKTLQAQAGKQGDELRNTGNEIAEMNPAVQGLHAEIDSIENQRANLEAAIAE<A

Parental  EQRGELALK-DARNK-LAELEDALQK-AKQDMARLLREYQELMT-KLALDVEIATYRKLLEAEECRLSGE
          E.RGELALK..AR.K...ELE....K.AKQ.MA..L.EYQELM..KLALD.EIATY.KLLE.EE.RL.G.
Retrocopy EERGELALK<EARAK<AEELELLCNK<AKQAMAWQLQEYQELMNIKLALDIEIATYHKLLEGEESRLTGD

Parental  GVGPVNI
          GV..VNI
Retrocopy GVETVNI

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_551 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_551 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,