RetrogeneDB ID: retro_vpac_279

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_360:562465..562717(-)
• Located in intron of: ENSVPAG00000011374

Retrocopy information

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

Parental gene information

• Parental gene symbol: SKP1
• Ensembl ID: ENSVPAG00000001583
• Aliases: None
• Description: S-phase kinase-associated protein 1 [Source:HGNC Symbol;Acc:10899]

Sequence

>retro_vpac_279
AAGCAAAGGGATGAGATTCTTGTCTGGGACTAAGAATTCCTGAAAGTTTCCCAAGGAGTACTTTTTGAACTTACTCTGCC
TGCAAACTATTTAGACATCAAAGATTTGGTTGATAGTATGCGCAAGTCTGTTGCCAATATGATCAGGGGGAAAGCTCATG
AGGAGATTCCCAAGACTTTCAATATCAAAAATGACTTTACTGAAGAAGAGGAAGCCCAGGCAAACAAAGAGAACCAGTGG
TGAGAAGAGAAG

Alignment

ORF - retro_vpac_279 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.81 %
• Parental protein coverage: 51.22 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KRTDDIPVWDQEFLKVDQGTLFELILAANYLDIKGLLDVTCKTVANMIKGKTPEEIRKTFNIKNDFTEEE
          K..D.I.VWD.EFLKV.QG.LFEL.L.ANYLDIK.L.D...K.VANMI.GK..EEI.KTFNIKNDFTEEE
Retrocopy KQRDEILVWD*EFLKVSQGVLFELTLPANYLDIKDLVDSMRKSVANMIRGKAHEEIPKTFNIKNDFTEEE

Parental  EAQVRKENQWCEEK
          EAQ..KENQW.EEK
Retrocopy EAQANKENQW*EEK

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_279 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_279 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 13 parental genes, and 67 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017810	1 retrocopy	retro_amel_897,
Canis familiaris	ENSCAFG00000000994	5 retrocopies	retro_cfam_1613, retro_cfam_779, retro_cfam_813, retro_cfam_889, retro_cfam_965,
Callithrix jacchus	ENSCJAG00000013613	1 retrocopy	retro_cjac_112,
Dasypus novemcinctus	ENSDNOG00000012999	9 retrocopies	retro_dnov_1216, retro_dnov_1338, retro_dnov_2433, retro_dnov_2526, retro_dnov_2647, retro_dnov_281, retro_dnov_286, retro_dnov_389, retro_dnov_776,
Echinops telfairi	ENSETEG00000007560	5 retrocopies	retro_etel_1730, retro_etel_515, retro_etel_758, retro_etel_762, retro_etel_811,
Felis catus	ENSFCAG00000031140	1 retrocopy	retro_fcat_653,
Gorilla gorilla	ENSGGOG00000022930	7 retrocopies	retro_ggor_1288, retro_ggor_1300, retro_ggor_2601, retro_ggor_2602, retro_ggor_2796, retro_ggor_2797, retro_ggor_778,
Microcebus murinus	ENSMICG00000017588	3 retrocopies	retro_mmur_270, retro_mmur_803, retro_mmur_997,
Myotis lucifugus	ENSMLUG00000022919	13 retrocopies	retro_mluc_1455, retro_mluc_1738, retro_mluc_1895, retro_mluc_2009, retro_mluc_2260, retro_mluc_2261, retro_mluc_2520, retro_mluc_2527, retro_mluc_2557, retro_mluc_267, retro_mluc_383, retro_mluc_841, retro_mluc_944,
Monodelphis domestica	ENSMODG00000014168	4 retrocopies	retro_mdom_1173, retro_mdom_155, retro_mdom_1648, retro_mdom_929,
Oryctolagus cuniculus	ENSOCUG00000022505	10 retrocopies	retro_ocun_1119, retro_ocun_1228, retro_ocun_1242, retro_ocun_1420, retro_ocun_1453, retro_ocun_1572, retro_ocun_1784, retro_ocun_397, retro_ocun_448, retro_ocun_553,
Pongo abelii	ENSPPYG00000015783	7 retrocopies	retro_pabe_1915, retro_pabe_199, retro_pabe_2072, retro_pabe_2736, retro_pabe_2756, retro_pabe_626, retro_pabe_824,
Vicugna pacos	ENSVPAG00000001583	1 retrocopy	retro_vpac_279 ,