RetrogeneDB ID: retro_vpac_579

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_5417:14485..14975(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CAPZA1
• Ensembl ID: ENSVPAG00000005361
• Aliases: None
• Description: capping protein (actin filament) muscle Z-line, alpha 1 [Source:HGNC Symbol;Acc:1488]

Sequence

>retro_vpac_579
ATGGCCAACTTGAAGAATCAGATGTTGAATAAAGAGAAGGTATACATAGCTGCTAAAATTTATCTCATGTCCCCCAAGGG
GAATTTAATAAAGTGTTTAATGATGGTAGGTTATTACTTAACAACAATGTTTTCTCAAGGAAGGGACAACTCATTCAATT
CCCAATAAAGCAGTGATCAGTCCTCACCAGTGAAGGTAGGAGGATAGAAAATCAGGTCTTAATTACAGAACATGACGACA
GAGGCAGTCAGAGTTGTTCAGCCAAAACCAAAATCTCTTTTATGTTTGCTCACCTAAAGAAAGAAAAAGCAACCCATAAT
GAAAGCGTACAGACGGGAGCTTGAGGTCTCTGAAACAGCCCTGTGGCAGCATGAGAAGGCTCCACATGAGAGATGCTTAT
CCCAATGTCTTCTGCCCTATTCATGCTATAACTATAGATGGACAGCAGATTACAATTATATTCATTGAAAGTTTCCAGTT
TCATCCAAAA

Alignment

ORF - retro_vpac_579 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.29 %
• Parental protein coverage: 58.04 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MADFEDRVSDEEKVRIAAKF-ITHAPPGEFNEVFNDVRLLLNNDNL-LREGAAHAF-AQYNMDQFTPVKI
          MA.........EKV.IAAK....H.P.GEFN.VFND.RLLLNN....L.EG..H....Q...DQ..PVK.
Retrocopy MANLKNQMLNKEKVYIAAKI<LSHVPQGEFNKVFNDGRLLLNNNVF<LKEGTTHSI<SQ*SSDQSSPVKV

Parental  EG-YEDQVLITEHGDLGNSRFLDPRNKISFKFDHLRKEA-SDPQPEEIDGSLKSWRESCDSALRAYVKDH
          .G..E.QVLITEH.D.G.S.......KISF.F.HL.KE..S.P.....DGSL.S....C.S..R....D.
Retrocopy GG<IENQVLITEHDDRG-SQSCSAKTKISFMFAHLKKEK<SNP**KRTDGSLRSLKQPCGSMRRLHMRDA

Parental  YSNGFCTVYAKTIDGQQTIIACIESHQFQPK
          Y.N.FC...A.TIDGQQ..I..IES.QF.PK
Retrocopy YPNVFCPIHAITIDGQQITIIFIESFQFHPK

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_579 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_579 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 11 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003570	1 retrocopy	retro_amel_219,
Latimeria chalumnae	ENSLACG00000017963	1 retrocopy	retro_lcha_20,
Myotis lucifugus	ENSMLUG00000009796	1 retrocopy	retro_mluc_2483,
Mustela putorius furo	ENSMPUG00000004977	1 retrocopy	retro_mputfur_616,
Mus musculus	ENSMUSG00000070372	4 retrocopies	retro_mmus_179, retro_mmus_1828, retro_mmus_3370, retro_mmus_349,
Oryctolagus cuniculus	ENSOCUG00000000270	6 retrocopies	retro_ocun_1315, retro_ocun_1417, retro_ocun_1787, retro_ocun_301, retro_ocun_527, retro_ocun_555,
Rattus norvegicus	ENSRNOG00000013538	1 retrocopy	retro_rnor_77,
Sorex araneus	ENSSARG00000001278	1 retrocopy	retro_sara_166,
Ictidomys tridecemlineatus	ENSSTOG00000015956	1 retrocopy	retro_itri_1044,
Tarsius syrichta	ENSTSYG00000006259	2 retrocopies	retro_tsyr_179, retro_tsyr_471,
Vicugna pacos	ENSVPAG00000005361	1 retrocopy	retro_vpac_579 ,