RetrogeneDB ID:

retro_vpac_424

Retrocopy
location
Organism:Alpaca (Vicugna pacos)
Coordinates:scaffold_1767:150397..150919(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:TPM1
Ensembl ID:ENSVPAG00000003277
Aliases:None
Description:tropomyosin 1 (alpha) [Source:HGNC Symbol;Acc:12010]


Retrocopy-Parental alignment summary:






>retro_vpac_424
CTGCAAAAGCTGGAGGAAGCCGAGAAATCTGCTAATGAGAGCAAGAGAGGTATGTAGGTTATTGAAAATTGAGCCTCAAA
AGATAAAGAAAATATGAAACTCCAGAAAATTCAACTCAAAGAAGCTAAGCACATTGCAGAAGAGGCAGATAGGAAATATG
AAGAGGTGGCTCGTAAGTTGGTGATCACTGAGGGAGACTTGAACACACAGAGGAATGGACTGAGCTGGTAGAGCCCTGTT
GCTGAGAGATGGATGAACAAACCAGACTGAAGGACCAGAACCTGAAGTGTCTTGAGTGCTGCTGAAGAAAAGTACTCTCA
AAAAGAAGACAAATACGAGGAAGAGAGAAAGATTCTTACTGATGAACTCAATTAGGCAGAGACCTGTGCTGAATTTGCTG
AGAGGTCAGTAGCCAAGCTGAAAAGACAACTGATGATTGAAGATAAACTGAAATACACCAAAGAGGAGCACCTCTGTACA
CACAGGATGCTGGACCAGACTCTGCTTGACCTGAATGAAATA

ORF - retro_vpac_424 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 63.84 %
Parental protein coverage: 85.78 %
Number of stop codons detected: 4
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalLQKLEEAEKAADESERGMKVIESRAQKDEEKMEIQEIQLKEAKHIAEDADRKYEEVARKLVIIESD-LER
LQKLEEAEK.A.ES.RGM.VIE..A.KD.E.M..Q.IQLKEAKHIAE.ADRKYEEVARKLVI.E.D.LE.
RetrocopyLQKLEEAEKSANESKRGM*VIEN*ASKDKENMKLQKIQLKEAKHIAEEADRKYEEVARKLVITEGD<LEH
ParentalAEERAELSEGKCAELEEELKTVTNNLKSLE-AQAEKYSQKEDKYEEEIKVLSDKLKEAETRAEFAERSVT
.EE..EL.E..C.E..E.......NLK.LE.A..EKYSQKEDKYEEE.K.L.D.L..AET.AEFAERSV.
RetrocopyTEEWTELVEPCC*EMDEQTRLKDQNLKCLE>AAEEKYSQKEDKYEEERKILTDELN*AETCAEFAERSVA
ParentalKLEKSIDDLEEKVAHAKEENLSMHQMLDQTLLELNNM
KL.......E.K....KEE.L..H.MLDQTLL.LN..
RetrocopyKLKRQL-MIEDKLKYTKEEHLCTHRMLDQTLLDLNEI

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






Vicugna pacos was not studied using RNA-Seq expression data.
Vicugna pacos was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_vpac_424 retrocopy.
Vicugna pacos was not studied using FANTOM5 data.
retro_vpac_424 was not experimentally validated.

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 9 parental genes, and 21 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000169661 retrocopy
Choloepus hoffmanni ENSCHOG0000001278811 retrocopies
Callithrix jacchus ENSCJAG000000043552 retrocopies
Macropus eugenii ENSMEUG000000145812 retrocopies
Pongo abelii ENSPPYG000000065341 retrocopy
Rattus norvegicus ENSRNOG000000181841 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000099551 retrocopy
Tursiops truncatus ENSTTRG000000037621 retrocopy
Vicugna pacos ENSVPAG00000003277 1 retrocopy
retro_vpac_424 ,



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