RetrogeneDB ID: retro_vpac_285

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_3670:103974..104537(+)
• Located in intron of: ENSVPAG00000009632

Retrocopy information

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

Parental gene information

• Parental gene symbol: NIPA2
• Ensembl ID: ENSVPAG00000000671
• Aliases: None
• Description: non imprinted in Prader-Willi/Angelman syndrome 2 [Source:HGNC Symbol;Acc:17044]

Sequence

>retro_vpac_285
ATGAGCCAGGGGCCTGGAAAGTATGACTTTTACATTGGTCTGGGATTGGCTATGAGCTCCTGCATTTTCATTGGAGGGTG
TTTCATTTTGAAAAAAAGAAAAAAAGGCCTTCTGCGGCTCGCCAGAAAAGGCTCCATGAGGGCAGGTCAGGGCGGCTGTG
CATATCTTAAAGAATGGCAGTGCTGGCTGGACTGCTGGCAGTGGGAGCTGGCCAGGTGGCCAACTTTGCTGCATATGCTT
TTGCACCAGCCACCTTAGTGACTCCGTTAGGAGCTCTCTGCATGCTAATTAAGTGCCATTCTTTCTTCATACTTTCTAAA
TGAAAGACGTAATCTTGATGGAAAAACTGAGTGTTTGCTAAGTGTTCTGGGATCTGCAGTTATGGTTATTCATGCTCCAA
AAGAAGAGGAGATTGAGACTTTAAATGAAATGTCTCACAAGCTATGGGATCTGGGTTTTGTGGCCTTTGCAACACTTGTG
TCATTGTGTCCTTGATACTAATCTTTGTGGCAGGGCCTCGCCATGGACAAACATTCTTGTTATATCACAGTCTCCTCTGT
AAT

Alignment

ORF - retro_vpac_285 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.1 %
• Parental protein coverage: 51.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSQGRGKYDFYIGLGLAMSSSIFIGGSFILKKK--GLLRLARKGSMRAGQGGHAYLKEWLWW-AGLLSMG
          MSQG.GKYDFYIGLGLAMSS.IFIGG.FIL.....GLLRLARKGSMRAGQGG.AYLKEW..W.AGLL..G
Retrocopy MSQGPGKYDFYIGLGLAMSSCIFIGGCFILXXXXXGLLRLARKGSMRAGQGGCAYLKEWQCW<AGLLAVG

Parental  AGEVANFAAYAFAPATLVTPLGALSVLV-SAILSSYFLNERLNLHGKIGCLLSILGSTVMVIHAPKEEEI
          AG.VANFAAYAFAPATLVTPLGAL..L..SAILSSYFLNER.NL.GK..CLLS.LGS.VMVIHAPKEEEI
Retrocopy AGQVANFAAYAFAPATLVTPLGALCMLI>SAILSSYFLNERRNLDGKTECLLSVLGSAVMVIHAPKEEEI

Parental  ETLNEMSHKLGDPGFVAFATLV-VIVSLILIFVVGPRHGQINILVYITICS
          ETLNEMSHKL.D.GFVAFATLV.VIVSLILIFV.GPRHGQ...L.....C.
Retrocopy ETLNEMSHKLWDLGFVAFATLV<VIVSLILIFVAGPRHGQTFLLYHSLLCN

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_285 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_285 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 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013824	1 retrocopy	retro_amel_1163,
Choloepus hoffmanni	ENSCHOG00000005553	1 retrocopy	retro_chof_9,
Callithrix jacchus	ENSCJAG00000005448	1 retrocopy	retro_cjac_1506,
Equus caballus	ENSECAG00000006379	1 retrocopy	retro_ecab_656,
Felis catus	ENSFCAG00000023073	1 retrocopy	retro_fcat_246,
Macaca mulatta	ENSMMUG00000003892	1 retrocopy	retro_mmul_1510,
Mus musculus	ENSMUSG00000030452	1 retrocopy	retro_mmus_3551,
Oryctolagus cuniculus	ENSOCUG00000010746	3 retrocopies	retro_ocun_1581, retro_ocun_773, retro_ocun_809,
Ictidomys tridecemlineatus	ENSSTOG00000004003	3 retrocopies	retro_itri_1847, retro_itri_347, retro_itri_388,
Vicugna pacos	ENSVPAG00000000671	1 retrocopy	retro_vpac_285 ,