RetrogeneDB ID: retro_vpac_425

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_178411:431..1014(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2E2
• Ensembl ID: ENSVPAG00000007007
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2E 2 [Source:HGNC Symbol;Acc:12478]

Sequence

>retro_vpac_425
GAGCGCCCCAGCACCAGCAGTAGTTCAGACGCCGACCAGGGAGACCCAGCTGCTCCACAGCCTGAAGAAGAAGAAAGAAA
ACCTTCTGCCGCCCAGCAGAAGAAAAACACCAAACTCTCTAGCAAAACCGCTGCTAAATTATCCACTAGTGCTAAAAGAA
TTCAGAAGGAACTAGCTGAAATAACCCTTGATCTTCCTCCTAACTGCAGTGCTGGGTCTAAAGGAGGTAACATTTCCGAA
TGGAGATCGACTATATTCGGCTCACTAGGTTCTATATATGAAGGTGCTGTGCTTTTTCCTGGATATCACATTTCCATCCA
ATTACCCATTTAAGCCACCAAAGGTTAATTTCCGCACCAGACTCTCTCTCCACAACATCAACAGTTAGGGAGTCATCTGC
CTGGACATCCTTAAAGACAACTGGAGTCCTGCTCTGACTGGTGCAAAGGTTTTGCTGTCTATTTGTTCTCTTTGGACAGA
CTGCAACCCTGTGGATCCTCTGGTTGGAAGCATAGCCACTCAGTATTTGACCAACAGAGCAGAACATGACAGGATAGCCA
GACAGTGGACCAAGAGGTACGCA

Alignment

ORF - retro_vpac_425 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.47 %
• Parental protein coverage: 94.97 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DSPSTSGGSSDGDQRESVQQEPEREQVQP----KKKEGKISSKTAAKLSTSAKR-QKE-AEITLDPLPNC
          ..PSTS..SSD.DQ.......PE.E...P.....KK..K.SSKTAAKLSTSAKR.QKE.AEITLD..PNC
Retrocopy ERPSTSS-SSDADQGDPAAPQPEEEERKPSAAQQKKNTKLSSKTAAKLSTSAKRIQKELAEITLDLPPNC

Parental  SAGPKGDNIYEWRSTILGPPGSVYEGGV-FFLDITFSPDYPFKPPKVTFRTRIYHCNINSQGVICLDILK
          SAG.KG.NI.EWRSTI.G..GS.YEG.V.FFLDITF...YPFKPPKV.FRTR....NINS.GVICLDILK
Retrocopy SAGSKGGNISEWRSTIFGSLGSIYEGAV>FFLDITFPSNYPFKPPKVNFRTRLSLHNINS*GVICLDILK

Parental  DNWSPALTISKVLLSICSLLTDCNPADPLVGSIATQYMTNRAEHDRMARQWTKRYA
          DNWSPALT..KVLLSICSL.TDCNP.DPLVGSIATQY.TNRAEHDR.ARQWTKRYA
Retrocopy DNWSPALTGAKVLLSICSLWTDCNPVDPLVGSIATQYLTNRAEHDRIARQWTKRYA

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_425 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_425 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 10 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010341	2 retrocopies	retro_chof_1304, retro_chof_674,
Ciona intestinalis	ENSCING00000006860	1 retrocopy	retro_cint_33,
Dasypus novemcinctus	ENSDNOG00000005448	7 retrocopies	retro_dnov_1217, retro_dnov_1281, retro_dnov_1360, retro_dnov_156, retro_dnov_2026, retro_dnov_2508, retro_dnov_424,
Felis catus	ENSFCAG00000007748	2 retrocopies	retro_fcat_1582, retro_fcat_913,
Microcebus murinus	ENSMICG00000016799	3 retrocopies	retro_mmur_1075, retro_mmur_15, retro_mmur_419,
Myotis lucifugus	ENSMLUG00000025144	1 retrocopy	retro_mluc_712,
Ochotona princeps	ENSOPRG00000010615	2 retrocopies	retro_opri_329, retro_opri_788,
Tursiops truncatus	ENSTTRG00000005156	1 retrocopy	retro_ttru_1075,
Vicugna pacos	ENSVPAG00000006944	5 retrocopies	retro_vpac_343, retro_vpac_513, retro_vpac_561, retro_vpac_585, retro_vpac_587,
Vicugna pacos	ENSVPAG00000007007	3 retrocopies	retro_vpac_108, retro_vpac_315, retro_vpac_425 ,