RetrogeneDB ID: retro_ogar_3217

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873743.1:1741157..1741809(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CAPZA1
• Ensembl ID: ENSOGAG00000014074
• Aliases: None
• Description: capping protein (actin filament) muscle Z-line, alpha 1 [Source:HGNC Symbol;Acc:1488]

Sequence

>retro_ogar_3217
ATAGAAGTATATGAAGATCAGGTCTTAATTATAGAACATGGTGACCCAGGTAATAGAATTTTAGATCCCAGAAAGAAAAT
TTCCTTTAGTTTGGTCATTTATGGAAAGGACCAAGTCACCTCCAGCCAGAGGAAGTAGATGGAGGTCAGAGGTCCTTTAG
AGAATCCTGTGATAGTGGTATAAGAGCCTGTGTGAAAAACTATTATTCTAATGGCTTCTCTATTGTTCATGCTAAAACTA
TAGTTGGGTAACAGACCACTACCGCATATATTGAAAGCCACTGGTTTCAGCCTAAAAATTTCTGGAATGGTGGTTGGTGA
TCAGATAGCAGTTCACCATTACACCACCTACAGCCCAGGTGGTTGGAGTGCTCAAGATTCAGGTTCACTATTATGAAGAT
GGCACTGTGGAATTGGTTAGTAATAAAGATGTATAGGATTCAATAACCATTTTGAATGAAGTTCAAACTGCCAAGGAGTT
TATCAAAATCATATAGCATGCAGAAAATGAGTATCAGTCAGCAATTAGTGAAAACTATAAAACAATGTCAGATTCAAGGG
CTTGTGCTGGCAGCTTCCAGTTACTTGCACCAAAATTGACTGGAGTAAGATTCTCAGCTATAAGATTGGCAAAGAAATAA
ATGCAGAATGCT

Alignment

ORF - retro_ogar_3217 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.44 %
• Parental protein coverage: 80.14 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IEGYEDQVLITEHGDLGNSRFLDPRNKISFK-FDHLRKEASDPQPEEIDGGLKSWRESCDSALRAYVKDH
          IE.YEDQVLI.EHGD.GN.R.LDPR.KISF..F.HL.K..S..QPEE.DGG..S.RESCDS..RA.VK..
Retrocopy IEVYEDQVLIIEHGDPGN-RILDPRKKISFS<FGHLWKGPSHLQPEEVDGGQRSFRESCDSGIRACVKNY

Parental  YSNGFCTVKVYAKTIDGQQTIIACIESHQFQPKNFWNGRWRSEW-KFTVTPPTAQVVGVLKIQVHYYEDG
          YSNGF..V...AKTI.G.QT..A.IESH.FQPKNFWNG.W.S....FT.TPPTAQVVGVLKIQVHYYEDG
Retrocopy YSNGFSIV--HAKTIVG*QTTTAYIESHWFQPKNFWNGGW*SDS<QFTITPPTAQVVGVLKIQVHYYEDG

Parental  NVQLVSHKDVQDSITVSSEVQTAKEFIKIIENAENEYQTAISENYQTMSDTTFKALRRQLPVTRTKIDWN
          .V.LVS.KDV.DSIT...EVQTAKEFIKII..AENEYQ.AISENY.TMSD....A..........K....
Retrocopy TVELVSNKDV*DSITILNEVQTAKEFIKII*HAENEYQSAISENYKTMSDS--RACAGSFQLLAPKLTGV

Parental  KILSYKIGKE-MQNA
          ........K..MQNA
Retrocopy RFSAIRLAKK*MQNA

Legend:

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

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_3217 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii 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 17 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003570	1 retrocopy	retro_amel_219,
Callithrix jacchus	ENSCJAG00000013548	3 retrocopies	retro_cjac_2259, retro_cjac_2850, retro_cjac_4125,
Cavia porcellus	ENSCPOG00000014532	1 retrocopy	retro_cpor_1155,
Dipodomys ordii	ENSDORG00000000671	3 retrocopies	retro_dord_224, retro_dord_265, retro_dord_44,
Felis catus	ENSFCAG00000013303	2 retrocopies	retro_fcat_700, retro_fcat_746,
Homo sapiens	ENSG00000116489	2 retrocopies	retro_hsap_2338, retro_hsap_4871,
Gorilla gorilla	ENSGGOG00000023677	1 retrocopy	retro_ggor_1216,
Latimeria chalumnae	ENSLACG00000017963	1 retrocopy	retro_lcha_20,
Macaca mulatta	ENSMMUG00000015668	2 retrocopies	retro_mmul_2612, retro_mmul_942,
Mus musculus	ENSMUSG00000070372	4 retrocopies	retro_mmus_179, retro_mmus_1828, retro_mmus_3370, retro_mmus_349,
Nomascus leucogenys	ENSNLEG00000004191	1 retrocopy	retro_nleu_1689,
Oryctolagus cuniculus	ENSOCUG00000000270	6 retrocopies	retro_ocun_1315, retro_ocun_1417, retro_ocun_1787, retro_ocun_301, retro_ocun_527, retro_ocun_555,
Otolemur garnettii	ENSOGAG00000014074	4 retrocopies	retro_ogar_1640, retro_ogar_2159, retro_ogar_3217 , retro_ogar_845,
Pongo abelii	ENSPPYG00000001021	2 retrocopies	retro_pabe_2116, retro_pabe_3789,
Pan troglodytes	ENSPTRG00000001110	2 retrocopies	retro_ptro_1710, retro_ptro_3245,
Rattus norvegicus	ENSRNOG00000013538	1 retrocopy	retro_rnor_77,
Tupaia belangeri	ENSTBEG00000001727	5 retrocopies	retro_tbel_1870, retro_tbel_3525, retro_tbel_4327, retro_tbel_638, retro_tbel_868,