RetrogeneDB ID: retro_vpac_216

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_2902:70226..70729(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSVPAG00000000013
• Aliases: None
• Description: None

Sequence

>retro_vpac_216
AGGAGGAGCCGAAGAGGAGATTGGCGAGGTTGTCAGCTAAAAGTGAAAAGAAGCCAAAAAGGCGAAAGGAAAGGATAATC
TCAGACAGAAAAGTGTAAACAAAAGGGAAAAAGGGAAACAGGCCGAAGTGGCTAACCAAGAAATTAAAGAAGATTTTCCT
GCAGAAAACGGAGAAACTAAAAATGAGGAGAGCCCAGCCTCTGATGAAACAGAAGAGAAAGGAGCCAAGTCTGATTAATA
GCACTCACCTGGTCTTATCAGTGGGCCCTGTCTCCCTTCTTGTACAATCCAGAGGAGTATATTTATCAACTATTTTGTAA
ATGCAAATTTTATAGTAGCTCTAGAAACATTTTTAAGAAGGAGGGAATCCCACCTCATCCTATTTTTTAAGTGTAAATGC
TTTTTTTAAAGACGTGAAATCATTTGCCGGTTGTTTATTTTTTGATACAACCAGAAAATAGCGGGATATTGAATATGGGA
GACTTTGATTGTCTTCGGTATCA

Alignment

ORF - retro_vpac_216 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.63 %
• Parental protein coverage: 73.08 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  REDRRGCQLNLLLQKWKRSQK-RRQERI-NL-QAKKCKQ-KGKGEQRENRLKWLTKSLKKIYLQKTEKLK
          R..RRG......L.K.KRSQK.RR.ERI.NL.Q..KCKQ.KGK.....NR.KWLTK.LKKI.LQKTEKLK
Retrocopy RRSRRGDWRGCQL-KVKRSQK<RRKERI<NL<QTEKCKQ<KGK---KGNRPKWLTKKLKKIFLQKTEKLK

Parental  MRRAQPLMKQERKKPSLINSTPGLIS-GP-CLPSCTIQRNIFINYFVNASFLVALETFLRRRESHLIPFF
          MRRAQPLMKQ.RK.PSLINST....S.GP.CLPSCTIQR.IFINYFVNA.F.VALETFLRRRESHLI.FF
Retrocopy MRRAQPLMKQKRKEPSLINSTHLVLSVGP<CLPSCTIQRSIFINYFVNANFIVALETFLRRRESHLILFF

Parental  KCKCFFLRGEIICWLFIF-YNQKI-WDIEWEALIVFSVS
          KCKCFF.R.EIIC.LFIF.YNQKI..DIE...L...SVS
Retrocopy KCKCFF*RREIICRLFIF*YNQKI>RDIEYGRL*LSSVS

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_216 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_216 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 6 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005727	4 retrocopies	retro_cjac_1105, retro_cjac_1412, retro_cjac_2018, retro_cjac_4230,
Gorilla gorilla	ENSGGOG00000013672	6 retrocopies	retro_ggor_107, retro_ggor_145, retro_ggor_16, retro_ggor_2248, retro_ggor_48, retro_ggor_49,
Otolemur garnettii	ENSOGAG00000033084	3 retrocopies	retro_ogar_1799, retro_ogar_2793, retro_ogar_3104,
Tarsius syrichta	ENSTSYG00000005812	15 retrocopies	retro_tsyr_1029, retro_tsyr_1109, retro_tsyr_1203, retro_tsyr_1209, retro_tsyr_1243, retro_tsyr_1318, retro_tsyr_1904, retro_tsyr_1956, retro_tsyr_310, retro_tsyr_399, retro_tsyr_652, retro_tsyr_664, retro_tsyr_680, retro_tsyr_728, retro_tsyr_913,
Tursiops truncatus	ENSTTRG00000015372	12 retrocopies	retro_ttru_1034, retro_ttru_129, retro_ttru_1511, retro_ttru_1682, retro_ttru_1714, retro_ttru_200, retro_ttru_337, retro_ttru_373, retro_ttru_558, retro_ttru_61, retro_ttru_680, retro_ttru_980,
Vicugna pacos	ENSVPAG00000000013	7 retrocopies	retro_vpac_146, retro_vpac_216 , retro_vpac_248, retro_vpac_371, retro_vpac_499, retro_vpac_557, retro_vpac_66,