RetrogeneDB ID: retro_vpac_448

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_20349:2567..3215(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSVPAG00000012148
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NUP62CL
• Ensembl ID: ENSVPAG00000003649
• Aliases: None
• Description: nucleoporin 62kDa C-terminal like [Source:HGNC Symbol;Acc:25960]

Sequence

>retro_vpac_448
CCAGCCACCGGGGCCGCCGCATCCGGTCCTGGTGCAGCTGCTGGGGTGACGGCCAGTCCCGCCATGACCTATGCCCAGCT
GGAGAGTCTGATCAACACGTGGAGCCTGTAGCTGGAGGACCAGGAGCGGCACTTCCTGCAGCAGGCCACGCAGGTCAACG
CTTGGGATCGCACACTGATCGAGAACGGGGAGAAGATCACCACCCTCCATCGTGAGGTGGAGAAGGTGAAATTGGACCAG
AAGAGGCTGGACCAAGAGCTCGACTTCATCAAAAATCAGCAGAAGGAGCTGGAGGACCTGCTGAGCCCGCTGGAGGAGTT
GGTCAAGGAGCAGAGTGGGACGGTGTACCTGCAGCACGCCGACGAGGAGCGCGAGAAGACCTACAAGCTGGCCGAGAACA
TCGACGCGCAGCTGAAGCGCATGGCCCAGGACCTCAAGGACATCATCGAGCACCTGAACACATCCGGGGGTCCCGCCGAC
ACCAGCGACCCGCTGCAGCAGATCTGCAAGATCCTCAATGCGCACATGGACTCGCTGCAGTGGATTGACCAGAACTCAGC
ACTGCTGCAGCGGAAGGTGGAGGAGGTGACCAGGGTGTGCGAGGGGCGGCGCAAAGAGCAGGAGCGCAGCTTTCGCATCA
CGTTCGAC

Alignment

ORF - retro_vpac_448 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.73 %
• Parental protein coverage: 82.71 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PVTSSGISNPVPFTSTVDAIVTPVMTYGQLDALLNNWSLELEDQEKHFLHQATQINAWDHMLIENGEKIT
          P.T....S.P............P.MTY.QL..L.N.WSL.LEDQE.HFL.QATQ.NAWD..LIENGEKIT
Retrocopy PATGAAASGP---GAAAGVTASPAMTYAQLESLINTWSL*LEDQERHFLQQATQVNAWDRTLIENGEKIT

Parental  ALHGEVEKVKLNQKRLEQELDFILSQQKELEDLLIPLEGSVKGESGSAYPQHTDEEHERTYNVAENIDAQ
          .LH.EVEKVKL.QKRL.QELDFI..QQKELEDLL.PLE..VK..SG..Y.QH.DEE.E.TY..AENIDAQ
Retrocopy TLHREVEKVKLDQKRLDQELDFIKNQQKELEDLLSPLEELVKEQSGTVYLQHADEEREKTYKLAENIDAQ

Parental  LKQMAQDFKDIIEHLNTFGSPADPTDPLQQICKILNVQVDSLQWINQTSDMLQRKVEEVTEVFEHPCRKE
          LK.MAQD.KDIIEHLNT.G.PAD..DPLQQICKILN...DSLQWI.Q.S..LQRKVEEVT.V.E...RKE
Retrocopy LKRMAQDLKDIIEHLNTSGGPADTSDPLQQICKILNAHMDSLQWIDQNSALLQRKVEEVTRVCEGR-RKE

Parental  QERNVVIAFD
          QER...I.FD
Retrocopy QERSFRITFD

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_448 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_448 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017963	1 retrocopy	retro_cfam_218,
Dasypus novemcinctus	ENSDNOG00000001467	1 retrocopy	retro_dnov_1108,
Felis catus	ENSFCAG00000001984	1 retrocopy	retro_fcat_120,
Macropus eugenii	ENSMEUG00000001005	1 retrocopy	retro_meug_1130,
Nomascus leucogenys	ENSNLEG00000013865	1 retrocopy	retro_nleu_2076,
Pteropus vampyrus	ENSPVAG00000001787	1 retrocopy	retro_pvam_694,
Vicugna pacos	ENSVPAG00000003649	1 retrocopy	retro_vpac_448 ,