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 symbol: TPM1
• Ensembl ID: ENSVPAG00000003277
• Aliases: None
• Description: tropomyosin 1 (alpha) [Source:HGNC Symbol;Acc:12010]

Sequence

>retro_vpac_424
CTGCAAAAGCTGGAGGAAGCCGAGAAATCTGCTAATGAGAGCAAGAGAGGTATGTAGGTTATTGAAAATTGAGCCTCAAA
AGATAAAGAAAATATGAAACTCCAGAAAATTCAACTCAAAGAAGCTAAGCACATTGCAGAAGAGGCAGATAGGAAATATG
AAGAGGTGGCTCGTAAGTTGGTGATCACTGAGGGAGACTTGAACACACAGAGGAATGGACTGAGCTGGTAGAGCCCTGTT
GCTGAGAGATGGATGAACAAACCAGACTGAAGGACCAGAACCTGAAGTGTCTTGAGTGCTGCTGAAGAAAAGTACTCTCA
AAAAGAAGACAAATACGAGGAAGAGAGAAAGATTCTTACTGATGAACTCAATTAGGCAGAGACCTGTGCTGAATTTGCTG
AGAGGTCAGTAGCCAAGCTGAAAAGACAACTGATGATTGAAGATAAACTGAAATACACCAAAGAGGAGCACCTCTGTACA
CACAGGATGCTGGACCAGACTCTGCTTGACCTGAATGAAATA

Alignment

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:

Parental  LQKLEEAEKAADESERGMKVIESRAQKDEEKMEIQEIQLKEAKHIAEDADRKYEEVARKLVIIESD-LER
          LQKLEEAEK.A.ES.RGM.VIE..A.KD.E.M..Q.IQLKEAKHIAE.ADRKYEEVARKLVI.E.D.LE.
Retrocopy LQKLEEAEKSANESKRGM*VIEN*ASKDKENMKLQKIQLKEAKHIAEEADRKYEEVARKLVITEGD<LEH

Parental  AEERAELSEGKCAELEEELKTVTNNLKSLE-AQAEKYSQKEDKYEEEIKVLSDKLKEAETRAEFAERSVT
          .EE..EL.E..C.E..E.......NLK.LE.A..EKYSQKEDKYEEE.K.L.D.L..AET.AEFAERSV.
Retrocopy TEEWTELVEPCC*EMDEQTRLKDQNLKCLE>AAEEKYSQKEDKYEEERKILTDELN*AETCAEFAERSVA

Parental  KLEKSIDDLEEKVAHAKEENLSMHQMLDQTLLELNNM
          KL.......E.K....KEE.L..H.MLDQTLL.LN..
Retrocopy KLKRQL-MIEDKLKYTKEEHLCTHRMLDQTLLDLNEI

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_424 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_424 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 9 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000016966	1 retrocopy	retro_cfam_2167,
Choloepus hoffmanni	ENSCHOG00000012788	11 retrocopies	retro_chof_1194, retro_chof_1272, retro_chof_1360, retro_chof_1789, retro_chof_1829, retro_chof_2309, retro_chof_346, retro_chof_399, retro_chof_412, retro_chof_770, retro_chof_967,
Callithrix jacchus	ENSCJAG00000004355	2 retrocopies	retro_cjac_2200, retro_cjac_691,
Macropus eugenii	ENSMEUG00000014581	2 retrocopies	retro_meug_1944, retro_meug_2161,
Pongo abelii	ENSPPYG00000006534	1 retrocopy	retro_pabe_624,
Rattus norvegicus	ENSRNOG00000018184	1 retrocopy	retro_rnor_734,
Ictidomys tridecemlineatus	ENSSTOG00000009955	1 retrocopy	retro_itri_166,
Tursiops truncatus	ENSTTRG00000003762	1 retrocopy	retro_ttru_446,
Vicugna pacos	ENSVPAG00000003277	1 retrocopy	retro_vpac_424 ,