RetrogeneDB ID: retro_vpac_232

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_3075:98899..99599(+)
• Located in intron of: ENSVPAG00000012221

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP6V1D
• Ensembl ID: ENSVPAG00000005696
• Aliases: None
• Description: ATPase, H+ transporting, lysosomal 34kDa, V1 subunit D [Source:HGNC Symbol;Acc:13527]

Sequence

>retro_vpac_232
CGAATGGCCCAGACTATGTGAAAGATCAGTTAAAAGGAGGCAGACAGGTCGAAACCTCCGAAGATAAAACATGATGTGTT
AGCTCTTCGATTTTGACAGATCCTTAAGTAGATAACACAGACTCAAATACTGCTGGGTGCAGTGAAGATGGAAGCTGTCT
CTTCCCTTGCTGAAGCCAAGTTCACAGAAGGAGACTTCAGCATCACAGTTATCCAACACGTAAATAAAGCCCAAGTGAAG
ATTAGAGCAAAGAAAGAAAATGTAGCATTGTCACTTTGCCTGTATTTGAACATTACCATGAAGGACTTGGCAGTTATGAA
CTGACTGGTTTAGCCAGAGGTGACACACAGTTGGATAAATTGAAGAGGAATTATGCCAAAGAAGTGGGCCTACTGGTGGA
ACTATCTTTGCAACAGACATCCTTTGTTACTATGGATGAAGCTATTAAGATAACCAGCAGGTGTGTAAATGCCATTGACC
ATGTCATCATTCCCCGGACTGAACATACCCTTGCTTATATCATCACAAAGCTGGATGGGAGAGAGTGAGAAGAGTTCTAC
AGGTTAAAGAAAATACAAGAGAAGGAAAAGATTCTCAAGGAAAAGTCTGAGAAGGGCTTGGAGCAATGGAGGGCAGCTGG
AGAGTGATGGAGCCTGCTAATCTTCTGGCTGAAGAGAAGGATGAGGATCTACTATTTGAA

Alignment

ORF - retro_vpac_232 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.5 %
• Parental protein coverage: 95.14 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  RMAQTI-MKARLKGA-QTGRNLL-KKKSDALTLRFRQILKKIIETKMLMGEVMREAAFSLAEAKFTAGDF
          RMAQT...K..LKG..QTGRNL..K.K.D.L.LRF.QILK.I..T..L.G.V..EA..SLAEAKFT.GDF
Retrocopy RMAQTM<VKDQLKGG<QTGRNLR<KIKHDVLALRF*QILK*ITQTQILLGAVKMEAVSSLAEAKFTEGDF

Parental  STTVIQNVNKAQVKIRAKKDNVAG-VTLPVFEHYHEGTDSYELTGLARGGEQLAKLKRNYAKAVELLVEL
          S.TVIQ.VNKAQVKIRAKK.NVA..VTLPVFEHYHEG..SYELTGLARG..QL.KLKRNYAK.V.LLVEL
Retrocopy SITVIQHVNKAQVKIRAKKENVAL<VTLPVFEHYHEGLGSYELTGLARGDTQLDKLKRNYAKEVGLLVEL

Parental  ASLQTSFVTLDEAIKITNRRVNAIEHVIIPRIERTLAYIITELDEREREEFYRLKKIQEKKKILKEKSEK
          ...QTSFVT.DEAIKIT.R.VNAI.HVIIPR.E.TLAYIIT.LD.RE.EEFYRLKKIQEK.KILKEKSEK
Retrocopy SLQQTSFVTMDEAIKITSRCVNAIDHVIIPRTEHTLAYIITKLDGRE*EEFYRLKKIQEKEKILKEKSEK

Parental  DLEQRRAAGE-VMEPANLLAEEKDEDLLFE
          .LEQ.RAAGE.VMEPANLLAEEKDEDLLFE
Retrocopy GLEQWRAAGE<VMEPANLLAEEKDEDLLFE

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_232 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_232 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 15 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008240	1 retrocopy	retro_amel_332,
Bos taurus	ENSBTAG00000016309	2 retrocopies	retro_btau_1757, retro_btau_408,
Canis familiaris	ENSCAFG00000016369	2 retrocopies	retro_cfam_1186, retro_cfam_999,
Choloepus hoffmanni	ENSCHOG00000003733	5 retrocopies	retro_chof_1229, retro_chof_2711, retro_chof_54, retro_chof_926, retro_chof_938,
Cavia porcellus	ENSCPOG00000009085	1 retrocopy	retro_cpor_36,
Felis catus	ENSFCAG00000011078	1 retrocopy	retro_fcat_632,
Myotis lucifugus	ENSMLUG00000006244	5 retrocopies	retro_mluc_2345, retro_mluc_442, retro_mluc_540, retro_mluc_666, retro_mluc_94,
Macaca mulatta	ENSMMUG00000021418	1 retrocopy	retro_mmul_1159,
Monodelphis domestica	ENSMODG00000009896	5 retrocopies	retro_mdom_1196, retro_mdom_1522, retro_mdom_1730, retro_mdom_390, retro_mdom_594,
Mustela putorius furo	ENSMPUG00000007002	2 retrocopies	retro_mputfur_1381, retro_mputfur_748,
Otolemur garnettii	ENSOGAG00000015052	1 retrocopy	retro_ogar_966,
Sus scrofa	ENSSSCG00000002288	1 retrocopy	retro_sscr_357,
Ictidomys tridecemlineatus	ENSSTOG00000027710	1 retrocopy	retro_itri_383,
Vicugna pacos	ENSVPAG00000005696	1 retrocopy	retro_vpac_232 ,
Drosophila melanogaster	FBgn0040377	1 retrocopy	retro_dmel_70,