RetrogeneDB ID: retro_vpac_151

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_2179:49135..51117(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MGEA5
• Ensembl ID: ENSVPAG00000003121
• Aliases: None
• Description: meningioma expressed antigen 5 (hyaluronidase) [Source:HGNC Symbol;Acc:7056]

Sequence

>retro_vpac_151
AGACCATGGGTATGGAACAGAGAAAAGAACTCTTTAGAAGGCTCCAGAAATGGGAACTAAATACATATTTGTATGCTCCA
AAAGATGACTACAAACATAGGATGTTTGGCGAGAGATGTATTCAGTGGAAGAAGCTGAGCAACTTATGACTCTCATCTCT
GCTGCACGGGAATATGAGATAGAGTTCATCTATGCTATCTCACCTGGATTGGATATTACCTTTTCTAACCCCAAGGAAGT
ATCTACCTTAAAACGCAAACTGGATCAGGTTTCTCAGTTTGGGTGCAGGTCATTTGCTTTCTTTTTGATGATATTGACCA
TAATATGTGTGCAGCTGACAAAGAGGTATTCAGTTCTTTTGCGCATGCCCAGGTCTCCATCACAAATGAAATTTATCAGT
ATCTAGGAGAGCCAGAAACGTTCCTCTTCTGTCCCACAGAATATCGTGGCACTTTCTGTTATCCAAATGTGTCTCAGTCT
CCTTACTTAAGGACTGTGGGTGAAAAGCTGCTACCTGGAATTGAGGTGCTTTGGACAGGTCCCAAAGTTGTATCTAAAGA
AATTCCAGTAGAGTCCATTGAAGAGGTTTCTAAGATTATTAAGAGAGCTCCGGTAATCTGGGATAACATTCATGCTAATG
ATTATGACCAGAAGAGACTATTTCTGGGCCCATACAAAGGAAGATCCACAGAACTCATCCCATGGTTAAAAGGAGTCCTG
GCTAATCCAAATTGTGAATTTGAAGCCAACTATGTTGCTATCCATACCCTTGCCACTTGGTACAAATCAAACATGAATGG
AGTGAGAAAAGATGTCGTAATGACTGACAGTGAAAGACAGTACAGTATCCATCCAGATAAAGTTAGAAAATGAAGGCAGT
GATGAAGATATTGAAACTGATGTACTCTATAGTCCACAGATGGCTCTAAAGTTAGCTTTAACAGAATGGCTGCAGGAGTT
TGGCGTACCTCATCAGTACAGCAGTAGGCAAGTTGCACACAGTGGCTCTAAAGCAAGTGTAGTTGATGGGACTCCTCTAG
TTGCAGCACCTTCTTTAAATGCCACAACTGTAGTTACAACAGTTTACCAGGAGCCCATTATGAGCCAAGGAGCAGCCTTG
AGTGGTGAGCCTACAGCTCTGACCAAGGAAGAAGAAAAGAAACAGCCCAGATGAGGAATCCATGGACATGGTAGTAGAAA
AACAGGAAGAAACAGACCACAAGAATGACAATCAAATACTGACTGAAATTGTCAAAGCTAAGATGGCAGAGGAATTGAAA
CCAATGGACACTGATAAAGAGAGCATAGCTGAATCAAAATCCCCAGAGATGTCTATGCAGGAAGATTGCATTAGTGATAT
TGCCCCTATGCAGACTGATGAACAGACAAACAAGGAGCAGTTTGTGCCTGGTCCAAATGAAAAGCCTTTGTACACTGCAG
AACCGGTGACTTTGGAGGATTTACAATTACTTGCTGACCTATTCTACCTTCCTTATGAACGTGGACCCAAAGGAGCACAG
ATGTTAAGGGAGTTCCAGTGGCTTCGAGCGAATAGCAGTGTTGTTAGCGTCAATTGCAAAGGGAAAGACTCTGAAAAAAT
TGAAGAATGGCGGTCACGAGCAGCCAAGTTTGAAGAGATGTGTGGACTAGTGATGGGAATGTTCACTCGGCTCTCCAGTT
GTGCCAACAGGACAATCCTTTATGACATGTACTCCTATGTTTGGGATATCAAGAGTATAATGTCTATGGTGAAGTCTTTT
GTACAGTGGTTAGGGTGTCGTAGTCATTCTTCAGCACAGTTCTTAATTGGAGACCAAGAAACCTGGGCCTTTAGAGGTGG
TCTAGCAGGAGAGTTCCAGCGTTTGCTGCCAATTGATGGGGCAAATGACCTCTTTTTTCAACCACCCCCACTGACTCCTA
CCTTCAAAGTTTATACTATCAGACCATATTTTCCTAAAGATGAGGCTTCCGTGTCCCAGATT

Alignment

ORF - retro_vpac_151 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.45 %
• Parental protein coverage: 77.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  RPWV-MEQRKELFRRLQKWELNTYLYAPKDDYKHRMF-WREMYSVEEAEQLMTLISAAREYEIEFIYAIS
          RPWV.MEQRKELFRRLQKWELNTYLYAPKDDYKHRMF.WREMYSVEEAEQLMTLISAAREYEIEFIYAIS
Retrocopy RPWV<MEQRKELFRRLQKWELNTYLYAPKDDYKHRMF<WREMYSVEEAEQLMTLISAAREYEIEFIYAIS

Parental  PGLDITFSNPKEVSTLKRKLDQVSQFGCRSFAL-LFDDIDHNMCAADKEVFSSFAHAQVSITNEIYQYLG
          PGLDITFSNPKEVSTLKRKLDQVSQFGCRSFA..LFDDIDHNMCAADKEVFSSFAHAQVSITNEIYQYLG
Retrocopy PGLDITFSNPKEVSTLKRKLDQVSQFGCRSFAF<LFDDIDHNMCAADKEVFSSFAHAQVSITNEIYQYLG

Parental  EPETFLFCPTEYCGTFCYPNVSQSPYLRTVGEKLLPGIEVLWTGPKVVSKEIPVESIEEVSKIIKRAPVI
          EPETFLFCPTEY.GTFCYPNVSQSPYLRTVGEKLLPGIEVLWTGPKVVSKEIPVESIEEVSKIIKRAPVI
Retrocopy EPETFLFCPTEYRGTFCYPNVSQSPYLRTVGEKLLPGIEVLWTGPKVVSKEIPVESIEEVSKIIKRAPVI

Parental  WDNIHANDYDQKRLFLGPYKGRSTELIPRLKGVLTNPNCEFEANYVAIHTLATWYKSNMNGVRKDVVMTD
          WDNIHANDYDQKRLFLGPYKGRSTELIP.LKGVL.NPNCEFEANYVAIHTLATWYKSNMNGVRKDVVMTD
Retrocopy WDNIHANDYDQKRLFLGPYKGRSTELIPWLKGVLANPNCEFEANYVAIHTLATWYKSNMNGVRKDVVMTD

Parental  SE-DSTVSIQIKLENEGSDEDIETDVLYSPQMALKLALTEWLQEFGVPHQYSSRQVAHSGSKASVVDGTP
          SE.DSTVSIQIKLENEGSDEDIETDVLYSPQMALKLALTEWLQEFGVPHQYSSRQVAHSGSKASVVDGTP
Retrocopy SE>DSTVSIQIKLENEGSDEDIETDVLYSPQMALKLALTEWLQEFGVPHQYSSRQVAHSGSKASVVDGTP

Parental  LVAAPSLNATTVVTTVYQEPIMSQGAALSGEPTALTKEEEKKQP-DEEPMDMVVEKQEETDHKNDNQILT
          LVAAPSLNATTVVTTVYQEPIMSQGAALSGEPTALTKEEEKKQP.DEE.MDMVVEKQEETDHKNDNQILT
Retrocopy LVAAPSLNATTVVTTVYQEPIMSQGAALSGEPTALTKEEEKKQP>DEESMDMVVEKQEETDHKNDNQILT

Parental  EIVEAKMAEELKPMDTDKESIAESKSPEMSMQEDCISDIAPMQTDEQTNKEQFVPGPNEKPLYTAEPVTL
          EIV.AKMAEELKPMDTDKESIAESKSPEMSMQEDCISDIAPMQTDEQTNKEQFVPGPNEKPLYTAEPVTL
Retrocopy EIVKAKMAEELKPMDTDKESIAESKSPEMSMQEDCISDIAPMQTDEQTNKEQFVPGPNEKPLYTAEPVTL

Parental  EDLQLLADLFYLPYEHGPKGAQMLREFQWLRANSSVVSVNCKGKDSEKIEEWRSRAAKFEEMCGLVMGMF
          EDLQLLADLFYLPYE.GPKGAQMLREFQWLRANSSVVSVNCKGKDSEKIEEWRSRAAKFEEMCGLVMGMF
Retrocopy EDLQLLADLFYLPYERGPKGAQMLREFQWLRANSSVVSVNCKGKDSEKIEEWRSRAAKFEEMCGLVMGMF

Parental  TRLSNCANRTILYDMYSYVWDIKSIMSMVKSFVQWLGCRSHSSAQFLIGDQEPWAFRGGLAGEFQRLLPI
          TRLS.CANRTILYDMYSYVWDIKSIMSMVKSFVQWLGCRSHSSAQFLIGDQE.WAFRGGLAGEFQRLLPI
Retrocopy TRLSSCANRTILYDMYSYVWDIKSIMSMVKSFVQWLGCRSHSSAQFLIGDQETWAFRGGLAGEFQRLLPI

Parental  DGANDLFFQPPPLTPTSKVYTIRPYFPKDEASVYKI
          DGANDLFFQPPPLTPT.KVYTIRPYFPKDEASV..I
Retrocopy DGANDLFFQPPPLTPTFKVYTIRPYFPKDEASVSQI

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_151 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_151 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000010002	1 retrocopy	retro_ogar_119,
Vicugna pacos	ENSVPAG00000003121	1 retrocopy	retro_vpac_151 ,