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


Retrocopy-Parental alignment summary:






>retro_ogar_3217
ATAGAAGTATATGAAGATCAGGTCTTAATTATAGAACATGGTGACCCAGGTAATAGAATTTTAGATCCCAGAAAGAAAAT
TTCCTTTAGTTTGGTCATTTATGGAAAGGACCAAGTCACCTCCAGCCAGAGGAAGTAGATGGAGGTCAGAGGTCCTTTAG
AGAATCCTGTGATAGTGGTATAAGAGCCTGTGTGAAAAACTATTATTCTAATGGCTTCTCTATTGTTCATGCTAAAACTA
TAGTTGGGTAACAGACCACTACCGCATATATTGAAAGCCACTGGTTTCAGCCTAAAAATTTCTGGAATGGTGGTTGGTGA
TCAGATAGCAGTTCACCATTACACCACCTACAGCCCAGGTGGTTGGAGTGCTCAAGATTCAGGTTCACTATTATGAAGAT
GGCACTGTGGAATTGGTTAGTAATAAAGATGTATAGGATTCAATAACCATTTTGAATGAAGTTCAAACTGCCAAGGAGTT
TATCAAAATCATATAGCATGCAGAAAATGAGTATCAGTCAGCAATTAGTGAAAACTATAAAACAATGTCAGATTCAAGGG
CTTGTGCTGGCAGCTTCCAGTTACTTGCACCAAAATTGACTGGAGTAAGATTCTCAGCTATAAGATTGGCAAAGAAATAA
ATGCAGAATGCT

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:

ParentalIEGYEDQVLITEHGDLGNSRFLDPRNKISFK-FDHLRKEASDPQPEEIDGGLKSWRESCDSALRAYVKDH
IE.YEDQVLI.EHGD.GN.R.LDPR.KISF..F.HL.K..S..QPEE.DGG..S.RESCDS..RA.VK..
RetrocopyIEVYEDQVLIIEHGDPGN-RILDPRKKISFS<FGHLWKGPSHLQPEEVDGGQRSFRESCDSGIRACVKNY
ParentalYSNGFCTVKVYAKTIDGQQTIIACIESHQFQPKNFWNGRWRSEW-KFTVTPPTAQVVGVLKIQVHYYEDG
YSNGF..V...AKTI.G.QT..A.IESH.FQPKNFWNG.W.S....FT.TPPTAQVVGVLKIQVHYYEDG
RetrocopyYSNGFSIV--HAKTIVG*QTTTAYIESHWFQPKNFWNGGW*SDS<QFTITPPTAQVVGVLKIQVHYYEDG
ParentalNVQLVSHKDVQDSITVSSEVQTAKEFIKIIENAENEYQTAISENYQTMSDTTFKALRRQLPVTRTKIDWN
.V.LVS.KDV.DSIT...EVQTAKEFIKII..AENEYQ.AISENY.TMSD....A..........K....
RetrocopyTVELVSNKDV*DSITILNEVQTAKEFIKII*HAENEYQSAISENYKTMSDS--RACAGSFQLLAPKLTGV
ParentalKILSYKIGKE-MQNA
........K..MQNA
RetrocopyRFSAIRLAKK*MQNA

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






RNA-Seq - click to see more details

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

ChIP-Seq - click to see more details

Otolemur garnettii was not studied using ChIP-Seq data.

EST - click to see more details

Otolemur garnettii was not studied using EST data.

TSS - click to see more details

Otolemur garnettii was not studied using FANTOM5 data.

Lab - click to see more details

retro_ogar_3217 was not experimentally validated.

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.
Parental genes homology:
Parental genes homology involve 17 parental genes, and 41 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000035701 retrocopy
retro_amel_219,
Callithrix jacchus ENSCJAG000000135483 retrocopies
retro_cjac_2259, retro_cjac_2850, retro_cjac_4125,
Cavia porcellus ENSCPOG000000145321 retrocopy
retro_cpor_1155,
Dipodomys ordii ENSDORG000000006713 retrocopies
retro_dord_224, retro_dord_265, retro_dord_44,
Felis catus ENSFCAG000000133032 retrocopies
retro_fcat_700, retro_fcat_746,
Homo sapiens ENSG000001164892 retrocopies
retro_hsap_2338, retro_hsap_4871,
Gorilla gorilla ENSGGOG000000236771 retrocopy
retro_ggor_1216,
Latimeria chalumnae ENSLACG000000179631 retrocopy
retro_lcha_20,
Macaca mulatta ENSMMUG000000156682 retrocopies
retro_mmul_2612, retro_mmul_942,
Mus musculus ENSMUSG000000703724 retrocopies
retro_mmus_179, retro_mmus_1828, retro_mmus_3370, retro_mmus_349,
Nomascus leucogenys ENSNLEG000000041911 retrocopy
retro_nleu_1689,
Oryctolagus cuniculus ENSOCUG000000002706 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 ENSPPYG000000010212 retrocopies
retro_pabe_2116, retro_pabe_3789,
Pan troglodytes ENSPTRG000000011102 retrocopies
retro_ptro_1710, retro_ptro_3245,
Rattus norvegicus ENSRNOG000000135381 retrocopy
retro_rnor_77,
Tupaia belangeri ENSTBEG000000017275 retrocopies
retro_tbel_1870, retro_tbel_3525, retro_tbel_4327, retro_tbel_638, retro_tbel_868,


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