RetrogeneDB ID: retro_vpac_44

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_1191:10311..11449(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMC2
• Ensembl ID: ENSVPAG00000008921
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, ATPase, 2 [Source:HGNC Symbol;Acc:9548]

Sequence

>retro_vpac_44
ATGCTGGATGACCTCGGTGCTGATCAGTGGAAAACCAAAGAAGACAAGCCCATCTGAGCTCAGGATAAGGGGGATACTGC
CTTGCTGAAAACTTACGGTCAGAGCACTTACTCTAGGCAGATCAAACAGTTTGAAGATGACATTTAACAACTTCTCAAGA
AAATTAATGAGCTCACTGATATTAAAGAGTCTGACACTGGCCTGGCCCCACCAGCACTTTGGGATTTGGCAGCCAGTAAG
GAAAACACTCCAGGGTGAACAGTCTTTGCAAGCTGCAAATGTATAAAGATCATCCACGCTGATTCCGAGGACCCGAAGTA
CATTATCAATGTGAAGCAGTATGCCAAGTTTGTGAAGGACCTCAGTGATCAGGTAGCACCCACCAACATTGAAGAAGGGA
TGAGAGTTGGTGTGGATAGAAATAAGTATTAAATTCACATTCCACTGCCTCCTAAGATTGACCCAACAGTTACTGTGATG
CAGGTGGAGGAAAAACCTGGTGTTACATACAGTGATGTGGGTGGCTGTAAGGAAGAGATCGAGAAACTTCAAGAAGTAGT
TAAAACCCCACTACTTCATCCAGAGAGGTTTGCTGACCTTGGCATTGAGCCTCCCAAGGGTGTGCTGCTCTTTGCTTCCA
CTAGGTAGAGGCAAGACATTCTGTGCTCTGGCAGTTGCTAATAGGAGTGATGCTTGCTTCAATCGAGTTATTGGATTTGA
ACTTGTATAGAAATACGTCGGTGAGGGGGCTCCAAATGGTTCGAGAGCTCTTAGAAATGGCCAGAACAACAACAGCAAAA
AAAGCCTGCTTTATTTTCTGTGATGAGGTTGATGCTATTGGAGGGGTTTGTTTTGACGATGGTGCTGGAGGTGACAATAA
AGTGTGCAGAGAAGGATGTTGGAATTGATCCATCAGCTGGATGGGTTTGATCCTTGAGGCAACATTAAAGTGCTGATGGC
CACAAACAGACCTGACACTCTAGACCCAGTGCTGATGAGGCTGGAGGGACTGGACAGGAAGACTGAGTTGAGTAGCTTAG
CTGATCTACAGGGTCAGACTCACATTTTTAAGATTCATGCTCATTCAGTGAGTGTTGAAAGCGATATCAGATTTGAATTG
TTAGCATGACTGTGTCCA

Alignment

ORF - retro_vpac_44 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.84 %
• Parental protein coverage: 87.3 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MPDYLGADQRKTKEDEKDDKPIRALDEGDIALLKTYGQSTYSRQIKQVEDDIQQLLKKINELTGIKESDT
          M.D.LGADQ.KT....K.DKPI.A.D.GD.ALLKTYGQSTYSRQIKQ.EDDI.QLLKKINELT.IKESDT
Retrocopy MLDDLGADQWKT----KEDKPI*AQDKGDTALLKTYGQSTYSRQIKQFEDDI*QLLKKINELTDIKESDT

Parental  GLAPPALWDLAADKQ-TLQSEQPLQVA-RCTKIINADSEDPKYIINVKQFAKFVVDLSDQVAPYDMEEGM
          GLAPPALWDLAA.K..TLQ.EQ.LQ.A..C.KII.ADSEDPKYIINVKQ.AKFV.DLSDQVAP...EEGM
Retrocopy GLAPPALWDLAASKE>TLQGEQSLQAA<KCIKIIHADSEDPKYIINVKQYAKFVKDLSDQVAPTNIEEGM

Parental  RIGVDRNKYQIHIPLPPKIDPTVTMMQVEEKPDVTYSDVGGCKEQIEKLREVVETPLLHPERFVNLGIEP
          R.GVDRNKY.IHIPLPPKIDPTVT.MQVEEKP.VTYSDVGGCKE.IEKL.EVV.TPLLHPERF..LGIEP
Retrocopy RVGVDRNKY*IHIPLPPKIDPTVTVMQVEEKPGVTYSDVGGCKEEIEKLQEVVKTPLLHPERFADLGIEP

Parental  PKGVLLFG-PPGTGKTLCARAVANRTDACFIRVIGSELVQKYVGEGA-RMVRELFEMART---KKACLIF
          PKGVLLF..P.G.GKT.CA.AVANR.DACF.RVIG.ELV.KYVGEGA..MVREL.EMART...KKAC.IF
Retrocopy PKGVLLFA>PLGRGKTFCALAVANRSDACFNRVIGFELV*KYVGEGA>QMVRELLEMARTTTAKKACFIF

Parental  FDEIDAIGGARF-DDGAGGDN-EVQRTMLELINQLDGFDPRGNIKVLMATNRPDTLDPALMRPGRLDRKI
          .DE.DAIGG..F.D...G.....VQR.MLELI.QLDGFDP.GNIKVLMATNRPDTLDP.LMR...LDRK.
Retrocopy CDEVDAIGGVCFDDGAGGDNK<SVQRRMLELIHQLDGFDP*GNIKVLMATNRPDTLDPVLMRLEGLDRKT

Parental  EF-SLPDLEGRTHIFKIHARSMSVERDIRFELLARLCP
          E..SL.DL.G.THIFKIHA.S.SVE.DIRFELLA.LCP
Retrocopy ELSSLADLQGQTHIFKIHAHSVSVESDIRFELLA*LCP

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_44 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_44 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 13 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000005729	1 retrocopy	retro_etel_1316,
Homo sapiens	ENSG00000161057	2 retrocopies	retro_hsap_2705, retro_hsap_3980,
Gorilla gorilla	ENSGGOG00000009167	3 retrocopies	retro_ggor_1885, retro_ggor_2672, retro_ggor_2673,
Myotis lucifugus	ENSMLUG00000008853	1 retrocopy	retro_mluc_1642,
Macaca mulatta	ENSMMUG00000003432	2 retrocopies	retro_mmul_1538, retro_mmul_2299,
Monodelphis domestica	ENSMODG00000017238	1 retrocopy	retro_mdom_868,
Mustela putorius furo	ENSMPUG00000018268	3 retrocopies	retro_mputfur_1025, retro_mputfur_232, retro_mputfur_387,
Nomascus leucogenys	ENSNLEG00000009274	2 retrocopies	retro_nleu_1578, retro_nleu_2042,
Otolemur garnettii	ENSOGAG00000005164	2 retrocopies	retro_ogar_2198, retro_ogar_2309,
Pongo abelii	ENSPPYG00000017883	2 retrocopies	retro_pabe_2257, retro_pabe_2412,
Pan troglodytes	ENSPTRG00000019553	2 retrocopies	retro_ptro_1826, retro_ptro_2702,
Tarsius syrichta	ENSTSYG00000000666	4 retrocopies	retro_tsyr_1031, retro_tsyr_1272, retro_tsyr_1857, retro_tsyr_2178,
Vicugna pacos	ENSVPAG00000008921	1 retrocopy	retro_vpac_44 ,