RetrogeneDB ID: retro_vpac_63

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_1412:186917..187701(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP2R5A
• Ensembl ID: ENSVPAG00000011662
• Aliases: None
• Description: protein phosphatase 2, regulatory subunit B', alpha [Source:HGNC Symbol;Acc:9309]

Sequence

>retro_vpac_63
AACAGTGAGGACCCTTGAGAGCTGGACTTTCTCAAAACCATCTTGTATCGCATTTATGGCAAGATTTTAGGGCTCCGGAC
TGCCATCTGTAGGCAGATCAGCCACATCTTCTACAAGTTCATCTATAAGACGGAGCATCACAGTGGGATTGAGCACTTCT
GGAGCTCCTGGGCAGCATCAGCAATGGCTTTGCCTTCTCCCGAAGGAGGAGCGCAAGATGTTCCTCATCTGTGTCCTGCT
CCCCTTCACAAGGTCAAGTCCCTGAGTGTCTCACCCTCAGGTGGCATACTGCCTGGTACAGTTCCTGGAGAAGGAAAGTA
GCCTCACTGAGCTGGTGATTGTGGGACTTCTCAAGTTCTGGCCCAACACCCACAGCCCCAAGGAGGAGATGTTCCTGAAT
GAGCTAGAAGAGATTCTGGATGCCACTGAACATTCAGAGTCCAGCAAAGTGATAGAACCACTCTTCTGCCAGCTTGCCAA
GTGTGTCTCCAGTCCCCATTTCCAGGTGGCAGAATGTGCTGTTTATTATTAGAACAATGAGTACATCATGAGCCTGGTAA
GTGACAGTCCTGCCCAGGTCCTCCCCATCATTTTCCTTGTCCTCTACAGGAACTTCAAGAGCCACTGGAACAAGACAATC
TGTGGGCTGACCTACAACGTGCTGAAGCTGTTTATGGAGATGAGTCAGAAGCTGTTTCATGACTGTACCGATGAGTACAA
GGCAGAGAAACAGAAGGACCGGTTCTGAATGAAGGAAAGAGAACAGATGTGGCAAAATATTGAT

Alignment

ORF - retro_vpac_63 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.98 %
• Parental protein coverage: 68.49 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DSEDPRERDFLKTVLHRIYGKFLGLRAFIRKQINNIFLRFIYETEHFNGVAE-LLEILGSIINGFA-LPL
          .SEDP.E.DFLKT.L.RIYGK.LGLR..I..QI..IF..FIY.TEH..G....LLE.LGSI.NGFA.L..
Retrocopy NSEDP*ELDFLKTILYRIYGKILGLRTAICRQISHIFYKFIYKTEHHSGIEH<LLELLGSISNGFA<LLP

Parental  KAEHKQFLMKVLIPMHTAKGLALFHAQLAYCVVQFLEKDTTLTEPVIRGLLKFWPKTCSQKEVMFLGEIE
          K.E.K.FL..VL.P..T.......H.Q.AYC.VQFLEK...LTE.VI.GLLKFWP.T.S.KE.MFL.E.E
Retrocopy KEERKMFLICVLLPF-TRSSP*VSHPQVAYCLVQFLEKESSLTELVIVGLLKFWPNTHSPKEEMFLNELE

Parental  EILDVIEPTQFKKIEEPLFKQISKCVSSSHFQVAERALYFWNNEYILSLIEENIDKILPIMFGSLYKISK
          EILD..E.....K..EPLF.Q..KCVSS.HFQVAE.A.Y..NNEYI.SL........LPI.F..LY...K
Retrocopy EILDATEHSESSKVIEPLFCQLAKCVSSPHFQVAECAVYY*NNEYIMSLVSDSPAQVLPIIFLVLYRNFK

Parental  EHWNPTIVALVYNVLKTLMEMNGKLFDDLTSSYKAERQREKKKELEREELWKKLE
          .HWN.TI..L.YNVLK..MEM..KLF.D.T..YKAE.Q.......ERE..W....
Retrocopy SHWNKTICGLTYNVLKLFMEMSQKLFHDCTDEYKAEKQKDRF*MKEREQMWQNID

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_63 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_63 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000009549	1 retrocopy	retro_mluc_1768,
Mus musculus	ENSMUSG00000026626	5 retrocopies	retro_mmus_2410, retro_mmus_2415, retro_mmus_2417, retro_mmus_2421, retro_mmus_3390,
Pteropus vampyrus	ENSPVAG00000010468	1 retrocopy	retro_pvam_1209,
Rattus norvegicus	ENSRNOG00000000068	1 retrocopy	retro_rnor_2107,
Tarsius syrichta	ENSTSYG00000013786	1 retrocopy	retro_tsyr_1135,
Vicugna pacos	ENSVPAG00000011662	1 retrocopy	retro_vpac_63 ,