RetrogeneDB ID: retro_vpac_248

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_3303:474137..474610(-)
• Located in intron of: ENSVPAG00000001578

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_248
CGACGGAGCCCAAAAGGAGATCGGTGAGGTTGTCAGCTAAACCTGTTTCTGCAAAACTGGAAATGAAGCTAAAAAGGGTG
GCAGGAAAGGATAAGTCTTCAGACAAAAAATTGCAAACAAAAGGGAAAAGGGGAGCAAAAGGAAAACACGCCGCAGTGGC
TAACCAAGAGACTAAAGAAGCTTTACCTGCAGGAAACAGGAAACTGAAAACGAGGCGAGCACAGCCTCTGATGAAGCAGG
AGAGAAAGCCGCCAAGTCTGATTAATATCACACACTGGGTTTTATCACTGGCCCCCCTGTCTCCCTTCTTGTACAATCCG
GAGGAACATTTTTATCAACTATTTTGTAAATGCAAGTTTTTAAGCAGAAACATTTTTAAGAAGGAGGGAATCCCACTCAT
TCATTTTTTAAAGTGTAAATGTCTTTTTTTTTTTTTTTAAAGAGGTGAGATCATTTGCTGGTTGTTTATTTTT

Alignment

ORF - retro_vpac_248 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.8 %
• Parental protein coverage: 66.67 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RRSPREDRRGCQLNLLLQKWKRSQKRRQERINLQAKKCKQKGKGEQRENRLKWLTKSLKKIYLQKT-EKL
          RRSP..DR.GCQLNL.LQ.WK.S.K..QERI.LQ..................WLTK.LKK.YLQ.T..KL
Retrocopy RRSPKGDR*GCQLNLFLQNWK*S*KGWQERISLQXXXXXXXXXXXXXXXTPQWLTKRLKKLYLQET<RKL

Parental  KMRRAQPLMKQERKKPSLINSTPGLIS-GPCLP-SCTIQRNIFINYFVNASFLVALETFLRRRESH-LIP
          K.RRAQPLMKQERK.PSLIN.T....S..P..P.SCTI.RNIFINYFVNASF....ETFLRRRESH.LI.
Retrocopy KTRRAQPLMKQERKPPSLINITHWVLSLAPLSP>SCTIRRNIFINYFVNASF*A--ETFLRRRESH<LIH

Parental  FFKCKC---FFLRGEIICWLFIF
          F.KCKC......RGEIICWLFIF
Retrocopy FLKCKCXXXXXXRGEIICWLFIF

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_248 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_248 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,