RetrogeneDB ID: retro_vpac_256

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_3383:163463..164411(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RIMKLB
• Ensembl ID: ENSVPAG00000003954
• Aliases: None
• Description: ribosomal modification protein rimK-like family member B [Source:HGNC Symbol;Acc:29228]

Sequence

>retro_vpac_256
GTGCTCCTGGACCAGATCGCCAACACCACAGTCGGCGGCAACCTCGGCCTGCAGCTGAGCCAGAAGGCGCTCACCACTTT
CCTAGACGTGGTGCTTGTCCGGGGTGCCCACACCCTCAGTGCAATCGGATAGTGACATCACAGTCCTGAGACACCTGGAG
AAGTTGGGTTGCCGCTTAGTCAACCGCCCACAGGGCATTTTAAACTGCATCAACAAATTCTGGATGTCCCAGGAGCTGGC
TGGACATGGGGGTCCCCATGCCAGACACCTTCTCCTATGGTGGGCATGAAGACTTTTCCAAAATGATCGATGAAGCCAAG
CCGCTGGGCTAGCCGGTGGTGATGAAGAGCACGCGCCGACATCAGGGAAAAGCTGTTCTTCTCGCAAGAGCTAAACACCA
CCTCTCAGACATCTGCCATCTGACCCGCCTTGACGTGTCCTACCTGTTCCTGAAGGAGTCCCGTGGAAAGGGTATCCGGG
TGGTGGCTGTTGGGGGCCAGGTGATGGGCTCCATGCTTTGCTGCTGCACAGACAGATGGACGCAGAACAACTGCTCTCTT
GGTGGCCTGAGCGTCATGTGCCCACTGACGGAACAAGGCAAGCAGCTGGCTATCCAGGTGTCCAACATCACGGACACGGA
CTTCTGTGGCATCGATCTCCTCATCATGGACGATGGCTCCTTTTGCGGTGTGTGAGGCAAACACCAACGTCAGTTTCCTA
GCCTTCGACCAGGCGTGCAACTTAGACATGAGTGGGATCATTGCAGACTATACCGTGTCCTTGCTGCCCACCAGGCAGAC
TGGGAGGATGGCCGTCCTCCCAGGACTGTCTAGTCCCAGGGAGAAGGAGCCAGATGGCTGTGCTTCAGCTCAGGGAGTAG
CAGAGAGCGTATACACCATCAACAGTGGGTCCACCTCTAGCGAGACGGAGCCTGAACCGAGAGAGCTG

Alignment

ORF - retro_vpac_256 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.63 %
• Parental protein coverage: 92.73 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VVMDEVVLTIEQGNLGLRINGELITAYPQVVVVR-VPTPWVQSDSDITVLRHLEKMGCRLMNRPQAILNC
          V..D....T...GNLGL.......T....VV.VR.VPTP.VQSDSDITVLRHLEK.GCRL.NRPQ.ILNC
Retrocopy VLLDQIANTTVGGNLGLQLSQKALTTFLDVVLVR>VPTPSVQSDSDITVLRHLEKLGCRLVNRPQGILNC

Parental  VNKFWTFQELAGHG-VPLPDTFSYGGHENFAKMIDEAEVLEFPMVVKNTRGHRGKAVFLARDKHHLADLS
          .NKFW..QELAGHG.VP.PDTFSYGGHE.F.KMIDEA..L..P.V.K.TR.H.GKAV.LAR.KHHL.D..
Retrocopy INKFWMSQELAGHG>VPMPDTFSYGGHEDFSKMIDEAKPLG*PVVMKSTRRHQGKAVLLARAKHHLSDIC

Parental  HLIRHEAPYLFQKYVKESHGRDVRVIVVGGRVVGTMLRCSTDGRMQSNCSLGGVGMMCSLSEQGKQLAIQ
          HL.R....YLF....KES.G...RV..VGG.V.G.ML.C.TD...Q.NCSLGG...MC.L.EQGKQLAIQ
Retrocopy HLTRLDVSYLF---LKESRGKGIRVVAVGGQVMGSMLCCCTDRWTQNNCSLGGLSVMCPLTEQGKQLAIQ

Parental  VSNILGMDVCGIDLLMKDDGSFC-VCEANANVGFIAFDKACNLDVAGIIADYAASLLPSGRLTRRMSLLS
          VSNI...D.CGIDLL..DDGSFC.VCEAN.NV.F.AFD.ACNLD..GIIADY..SLLP..R.T.RM..L.
Retrocopy VSNITDTDFCGIDLLIMDDGSFC>VCEANTNVSFLAFDQACNLDMSGIIADYTVSLLPT-RQTGRMAVLP

Parental  VVSTASETSEPELGPPASTAVDNMSASSSSVDSDPETTEREL
          ..S...E............A.......S.S..S..E...REL
Retrocopy GLSSPREKEPDGCASAQGVAESVYTINSGSTSSETEPEPREL

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_256 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_256 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 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000000332	1 retrocopy	retro_ggor_31,
Rattus norvegicus	ENSRNOG00000023814	1 retrocopy	retro_rnor_255,
Tursiops truncatus	ENSTTRG00000000699	3 retrocopies	retro_ttru_1672, retro_ttru_366, retro_ttru_460,
Vicugna pacos	ENSVPAG00000003954	1 retrocopy	retro_vpac_256 ,