RetrogeneDB ID: retro_vpac_193

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_2669:928151..930320(-)
• Located in intron of: ENSVPAG00000006620

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUPT20H
• Ensembl ID: ENSVPAG00000007288
• Aliases: None
• Description: suppressor of Ty 20 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:20596]

Sequence

>retro_vpac_193
ATGCAACAGGCTTTAGAACAAGCTTTGGAGAGGGCTGAGTATGTCATTGAAAGTGCCCAACAGAGACCCCCTAAAAGGAA
ACACTCATCTAGTGGGCAAACGTCTCTCTATGAAAAACTTTATGACATTTACGTTGAAGAATGTGAAAAAGAGCCTGACA
CTCCGGAGGAATTACGAAGCAACGTGAACTTGTTAGAGAAGCTTGTTCAGAGAGAGTCGTTGCCGTGTTTGGTGGTCAAC
CTGTACCCAGGAAAGGAGGGCTATTCCCTGATGCTCAAGGGAAAAAATATTTCGGAGAACATTCGGCTGCCTTATGAGAA
AGCGGAACTGCTCGAATACTTGGATGCAGAAGAATTATCCCCTGTTTTGGTGGATCTGCTGGGAAAGTCTCAGGTTAACG
TTTTTCATGATGGGTGTGTCATAGCTGAAATCCGGGACTACAGGCAGTCCAGTAACAGGGAACCTCCCGGTTACCAAAGC
AGGCATATTCTCTTACGTCCTACGATGCAGACTTTAGCCTGTGATGTAGAGGCCATAGCCAGCGATAACCAGAAATGGAC
CCAAGAGGACAAACTTTTGCTTGAGAGCCAGCTGATCTTAGCCACAGCTGAACCACTGTGTCTAGACCCTTCCATATCAG
TAGCCTGCACTGCCAACAGAATGCTCTATAACAAGCAAAAGCTGAACACTCTCCCCATGAAAAGGAACTTCAAGAGGTTT
TCTTTGGCCTCTCTGAATCAGGAGCAAGAGCTTTCCCAGTGTCCACCTCCTCATGAGCTAGGAGTATTGGCTTCTTGCAA
AAAAATAAGAGAAACTAAAACAGGTGAACATCATGACCTCAAAATTTTTAAAGCAGGGAACTGTGCAGATATGTGGAAAC
AAATACCCTGTGACTTGGCTGTACCTTCTGAAGTGGATGTAGAGAAATACGCTAAAGGGAAGAATTCTGTCACATATGAT
GAATCACAACCAACAGTCTGGCCAACCCATGAGGTACAAGATGGTTCTGTATTTGGATGTGAAGATGGCGATCAGTCTCA
GACAACAATGCTCCCTTTCATGCAGTCACTTAATGATCCACTTATCTCTGGAAAAAGAAGGTCATGTAAAAAAGTCAGAC
ATACAAGACAACTGTCTCACCCCTATTCCTCCAGAGATGACCATTATAGTTTCATGCCCAGGCCAAAGACTGATGTCGGT
AAAGTGGTCAGTTGGTCTGAGAAAATGGTCCAGGACAGCATCCAATGTCCAGTCCAGATGTCAACCAGCTCCAGTGGCTC
AGCCAGTCTCAGGCAACCTTCTCCAGGGAAAGAACCAGAACAGCCTAAGACTGGGTATGTTCAGTCTTCAGTGCTAGGCA
AGGGAGCCAAACATCCACCTCCACCTACAAGACTTCCCTCAAGGTCAGCCAGGAGTTCCTCAGGTGACAGTTTTACTTCA
CAGCAGGCAAGCAGCTCTCATGCACCTCCATCTCCTGCCCCTGCTCCTAAGACACCAAGTCTTTCCAACAAATCCTCTGT
GGAGGTGAATCCAGCTAGCACGCCTCCTGCCACAGCCACGTCCAAGTCCACTGCAGGTTCACCACAAAGGACACAGGTTT
CGGGCAAATCCTCTGGCCTGAATGTCACCAAAGTGGCACGCCCTACATGCAGAGGCCAGGCCTTGAGGAGAGGCTCCAAG
CCTGTGCAGGACTCCACCAGGGGGGCCACAGCTCCTGTAAGAATCCAGTCCAGCCACCAGCCCACAGGAGCTTGGCCGCC
AAATGCACCACCCATGGCACCACAGGCTCCTTCTCAAGGAGGTGTTCAATTTATTTTTAAAAATGCTTCCAGTGTCCAGC
CCTTAGGTCTACTCCAGCTACCACCAGGTTCTCTCATTTTGAACACCCAGCAGCAGGCCCCACAGCAGCCATTGCTCTAC
CAGCTGATTCCACAGCAACAACTTCAACAACCCACCACTCTGCATCCTCAACAGCCAGTGCCACAGGCCACTGTACAAGG
TCCTGTCACCCAGAGTATGGCCTTACCTACTCAACAAGCCATGCTCCTTAACCTCAACAGAGTGGAGAGTTTTCTGCAGC
CCCAGGCAGTTATGCCGCCTCAGCTGGGCTCTGTCCAGAGCCAACCTGGGCCCAGCCTCCCTCAGCAGAGATTCCAGCTC
TTCTCTGCC

Alignment

ORF - retro_vpac_193 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.45 %
• Parental protein coverage: 93.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQQALELALDRAEYVIESARQRPPKRKYLSSGRKSIFQKLYDLYIEECEKEPEV-KKLRRNVNLLEKLVM
          MQQALE.AL.RAEYVIESA.QRPPKRK..SSG..S...KLYD.Y.EECEKEP.....LR.NVNLLEKLV.
Retrocopy MQQALEQALERAEYVIESAQQRPPKRKHSSSGQTSLYEKLYDIYVEECEKEPDTPEELRSNVNLLEKLVQ

Parental  QETLSCLVVNLYPGNEGYSLMLRGKNGSDSETIRLPYEEGELLEYLDAEELPPILVDLLEKSQVNIFHCG
          .E.L.CLVVNLYPG.EGYSLML.GKN...SE.IRLPYE..ELLEYLDAEEL.P.LVDLL.KSQVN.FH.G
Retrocopy RESLPCLVVNLYPGKEGYSLMLKGKN--ISENIRLPYEKAELLEYLDAEELSPVLVDLLGKSQVNVFHDG

Parental  CVIAEIRDYRQSSNMKSPGYQSRHILLRPTMQTLICDVHSITSDNHKWTQEDKLLLESQLILATAEPLCL
          CVIAEIRDYRQSSN...PGYQSRHILLRPTMQTL.CDV..I.SDN.KWTQEDKLLLESQLILATAEPLCL
Retrocopy CVIAEIRDYRQSSNREPPGYQSRHILLRPTMQTLACDVEAIASDNQKWTQEDKLLLESQLILATAEPLCL

Parental  DPSIAVTCTANRLLYNKQKMNTRPMKRCFKRYSRSSLNRQQDLSNCPPPPQLKLLDFLQKRKERKAGQHY
          DPSI.V.CTANR.LYNKQK.NT.PMKR.FKR.S..SLN..Q.LS.CPPP..L..L....K..E.K.G.H.
Retrocopy DPSISVACTANRMLYNKQKLNTLPMKRNFKRFSLASLNQEQELSQCPPPHELGVLASCKKIRETKTGEHH

Parental  DLKISKAGNCVDMWKRSPCNLAIPSEVDVEKYAKVEKSIKSDDSQPTVWPAHDIKDDYVFECEAGNQYQK
          DLKI.KAGNC.DMWK..PC.LA.PSEVDVEKYAK...S...D.SQPTVWP.H...D..VF.CE.G.Q.Q.
Retrocopy DLKIFKAGNCADMWKQIPCDLAVPSEVDVEKYAKGKNSVTYDESQPTVWPTHEVQDGSVFGCEDGDQSQT

Parental  TKLTILQSLGDPLYYGKIQPCKEDEESDSQMSPSHFSTDDHSNWFIIGSKTDAERVVNQYQELVQNEAKC
          T.L...QSL.DPL..GK...CK.......Q.S....S.DDH...F....KTD...VV......VQ....C
Retrocopy TMLPFMQSLNDPLISGKRRSCKKVRHT-RQLSHPYSSRDDHYS-FMPRPKTDVGKVVSWSEKMVQDSIQC

Parental  PVKMSHSSSGSASLSQPSPGKEAEQPETVSVQPSVLGKGVKHRPPPIKLPSGSGSSSSGNYFTPQQASSF
          PV.MS.SSSGSASL.QPSPGKE.EQP.T..VQ.SVLGKG.KH.PPP..LPS.S..SSSG..FT.QQASS.
Retrocopy PVQMSTSSSGSASLRQPSPGKEPEQPKTGYVQSSVLGKGAKHPPPPTRLPSRSARSSSGDSFTSQQASSS

Parental  LKSPTPPPTSKPPSLSRKSSVDLSQVSMLSPAALSPASSSQRSTATQVMANSAGLNFINVVGSVCGAQAL
          ...P.P.P..K.PSLS.KSSV.....S...PA.....S.......TQV...S.GLN...V....C..QAL
Retrocopy HAPPSPAPAPKTPSLSNKSSVEVNPAS-TPPATATSKSTAGSPQRTQVSGKSSGLNVTKVARPTCRGQAL

Parental  MSGSNPMLGCNTGAITPAGINLSGLLPSGGLLPSALPGAMQAASQAGVPFGLKNTSSLRPLNLLQLPGGS
          ..GS.P......GA..P..I..S...P.G...P.A.P.A.QA.SQ.GV.F..KN.SS..PL.LLQLP.GS
Retrocopy RRGSKPVQDSTRGATAPVRIQ-SSHQPTGAWPPNAPPMAPQAPSQGGVQFIFKNASSVQPLGLLQLPPGS

Parental  LIFNTLQQQQQQ--LPQFTQQQP-QQPTASSPQQPGEQAAEQSSSSQEQALPAQHTAVINLAGVGSFMQS
          LI.NT.QQ..QQ..L.Q...QQ..QQPT...PQQP..QA..Q....Q..ALP.Q.....NL..V.SF.Q.
Retrocopy LILNTQQQAPQQPLLYQLIPQQQLQQPTTLHPQQPVPQATVQGPVTQSMALPTQQAMLLNLNRVESFLQP

Parental  QAAVLSQLGSAENRPEQSLPQQRFQLSSA
          QA....QLGS....P..SLPQQRFQL.SA
Retrocopy QAVMPPQLGSVQSQPGPSLPQQRFQLFSA

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_193 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_193 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.

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000000116	2 retrocopies	retro_ecab_1052, retro_ecab_1101,
Homo sapiens	ENSG00000102710	2 retrocopies	retro_hsap_4659, retro_hsap_4794,
Loxodonta africana	ENSLAFG00000027507	1 retrocopy	retro_lafr_1199,
Macaca mulatta	ENSMMUG00000003590	2 retrocopies	retro_mmul_2479, retro_mmul_2555,
Pongo abelii	ENSPPYG00000005288	2 retrocopies	retro_pabe_3619, retro_pabe_3729,
Pan troglodytes	ENSPTRG00000005791	2 retrocopies	retro_ptro_3095, retro_ptro_3189,
Pteropus vampyrus	ENSPVAG00000014609	1 retrocopy	retro_pvam_401,
Tarsius syrichta	ENSTSYG00000013227	1 retrocopy	retro_tsyr_2160,
Vicugna pacos	ENSVPAG00000007288	1 retrocopy	retro_vpac_193 ,