RetrogeneDB ID:

retro_xtro_11

Retrocopy
location
Organism:Xenopus (Xenopus tropicalis)
Coordinates:GL172701.1:305048..305987(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSXETG00000003833
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:hnrnpa3
Ensembl ID:ENSXETG00000001806
Aliases:None
Description:heterogeneous nuclear ribonucleoprotein A3 [Source:Jamboree;Acc:XB-GENE-5878765]


Retrocopy-Parental alignment summary:






>retro_xtro_11
GTTTCAATGAGTACCGGCGATATGGATACGACGCAACTCTGCAAACTGTTTATCGGGGGGCTTAACGTGCAGACCACCGA
AGAGGGCCTACGCCAGCATTTTGAGACCTACGGTCAACTGACGGACTGCGTGGTGGTTATCAACCCACAGACCAAGCGGT
CTCGATGTTTCGGTTTCGTAACCTACTCGAGTGCCGCGGAGGCCGACGCGGCGGTGGAGGCCTCGCCCCACGTGGTTGAC
GGTAACAACGTTGAGCTGAAGCGGGCCGTCTCCAGGGAAGATTCCGCCAAGCCGGGGGCACACGCTAAAGTGAAGAAGCT
CTTTGTTGGCGGCCTGAAAGAGGACGTCGGCGAGAGTGACTTGCTCGAACACTTCGCCCAGTTTGGCGCCGTGGAAAAAG
TGGAGATCATTGCCGATAAAGTGTCCGGCAAGAAACGCGGCTTCGGCTTTGTGTACTTTACCAACCACGATTCCGCCGAC
AAGGCCGCGGTGGTCAAGTTCCACTCCATCAACGGGCACCGCGTCGAGGTAAAGAAGGCCGTGCCCAAGGAGGAACTTTC
CCAGGGTTCCAATAGATCCTTCCGCGGCGGCAGGGGCGGGAGAGGCCGAGGTGGCGGCGGAGCGCCCCGGGACTACAATG
GCATCCCTGGAAGTGGCGGCAAAGCTGCTTTCGGTGGGGGCTACGGCGGCTATGGGGGCGGCAACCAGGGCTACGGCTCG
TACGGAGGCGGCTATGGCGAGCAGAGCGACTACGGCAATGGCTACAACAGTTTCGGGAGCTACAGCCAGCACCAGTCCTC
GTACGGGCCCATGAAGGGAGCGGGAAGCGGCAGCTGGAACCGGCCCAACACGTCAGGCCCCTACCGCGGAGGTTATAGCG
GCGGCGGCGGAGGAGGAGGTTATGGCGTCGGCAGCTCCTATGGCGGCGGCTCCTTCTGA

ORF - retro_xtro_11 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 53.44 %
Parental protein coverage: 79.37 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalQLRKLFIGGLSFETTDDSLREHFEQWGKLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAMSARPHKVDG
QL.KLFIGGL...TT...LR.HFE..G.LTDCVV...PQTKRSR.FGFVTYS...E.DAA..A.PH.VDG
RetrocopyQLCKLFIGGLNVQTTEEGLRQHFETYGQLTDCVVVINPQTKRSRCFGFVTYSSAAEADAAVEASPHVVDG
ParentalRVVEPKRAVSREDSARPGAHLTVKKIFVGGIKEDTEEYHLRDYFQSYGKIETIEVMEDRQSGKKRGFAFV
..VE.KRAVSREDSA.PGAH..VKK.FVGG.KED..E..L...F...G..E..E...D..SGKKRGF.FV
RetrocopyNNVELKRAVSREDSAKPGAHAKVKKLFVGGLKEDVGESDLLEHFAQFGAVEKVEIIADKVSGKKRGFGFV
ParentalTFDDHDTVDKIVVQKYHTINGHNCEVKKALSKQEMQTASAQRGRGGGGSNFMGRGG---NYGGGGGGGGN
.F..HD..DK..V.K.H.INGH..EVKKA..K.E....S....RGG.G....G.GG....Y.G..G.GG.
RetrocopyYFTNHDSADKAAVVKFHSINGHRVEVKKAVPKEELSQGSNRSFRGGRGGRGRGGGGAPRDYNGIPGSGGK
ParentalFGRGGGFGNRGGYGGGGGGGRGGGYGSGGD--GGYNGFGGEGGNYGGGPGYGGRGYGGSPGYGNQGGGYG
...GGG.G..GG.G..G.G..GGGYG...D...GYN.FG.............G.G..GS....N..G.Y.
RetrocopyAAFGGGYGGYGG-GNQGYGSYGGGYGEQSDYGNGYNSFGSYSQHQSSYGPMKGAG-SGSWNRPNTSGPYR
ParentalGGGSGGGGGGYDGYNEGGNFGGGNY
GG.SGGGGGG..GY..G...GGG..
RetrocopyGGYSGGGGGG--GYGVGSSYGGGSF

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






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP007412_brain 38 .63 RPM 277 .77 RPM
SRP007412_heart 23 .80 RPM 183 .56 RPM
SRP007412_kidney 23 .80 RPM 183 .56 RPM
SRP007412_liver 49 .18 RPM 243 .45 RPM
SRP007412_skeletal_muscle 7 .03 RPM 115 .15 RPM

ChIP-Seq - click to see more details

Xenopus tropicalis was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_xtro_11 retrocopy.

TSS - click to see more details

Xenopus tropicalis was not studied using FANTOM5 data.

Lab - click to see more details

retro_xtro_11 was not experimentally validated.

Retrocopy orthology:
Xenopus tropicalis 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 30 parental genes, and 127 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000119204 retrocopies
retro_amel_1407, retro_amel_557, retro_amel_715, retro_amel_765,
Bos taurus ENSBTAG000000215808 retrocopies
retro_btau_1029, retro_btau_1310, retro_btau_1587, retro_btau_212, retro_btau_277, retro_btau_370, retro_btau_811, retro_btau_90,
Canis familiaris ENSCAFG0000001349712 retrocopies
retro_cfam_1214, retro_cfam_1326, retro_cfam_1388, retro_cfam_1548, retro_cfam_1690, retro_cfam_1816, retro_cfam_265, retro_cfam_272, retro_cfam_400, retro_cfam_625, retro_cfam_65, retro_cfam_836,
Cavia porcellus ENSCPOG000000042513 retrocopies
retro_cpor_1516, retro_cpor_1543, retro_cpor_65,
Dasypus novemcinctus ENSDNOG000000190223 retrocopies
retro_dnov_540, retro_dnov_711, retro_dnov_959,
Ficedula albicollis ENSFALG000000032151 retrocopy
retro_falb_15,
Felis catus ENSFCAG000000121465 retrocopies
retro_fcat_1231, retro_fcat_572, retro_fcat_662, retro_fcat_677, retro_fcat_842,
Homo sapiens ENSG0000017014411 retrocopies
retro_hsap_1117, retro_hsap_1274, retro_hsap_1572, retro_hsap_209, retro_hsap_2194, retro_hsap_2664, retro_hsap_2951, retro_hsap_34, retro_hsap_4764, retro_hsap_665, retro_hsap_862,
Gallus gallus ENSGALG000000092501 retrocopy
retro_ggal_10,
Gorilla gorilla ENSGGOG000000061306 retrocopies
retro_ggor_1001, retro_ggor_1197, retro_ggor_14, retro_ggor_1736, retro_ggor_576, retro_ggor_702,
Macropus eugenii ENSMEUG000000136226 retrocopies
retro_meug_1264, retro_meug_1760, retro_meug_1913, retro_meug_238, retro_meug_470, retro_meug_56,
Macaca mulatta ENSMMUG000000018584 retrocopies
retro_mmul_1945, retro_mmul_2442, retro_mmul_386, retro_mmul_801,
Monodelphis domestica ENSMODG000000198031 retrocopy
retro_mdom_1590,
Mustela putorius furoENSMPUG000000141036 retrocopies
retro_mputfur_1141, retro_mputfur_1336, retro_mputfur_1545, retro_mputfur_603, retro_mputfur_674, retro_mputfur_779,
Mus musculus ENSMUSG000000590056 retrocopies
retro_mmus_133, retro_mmus_1359, retro_mmus_1409, retro_mmus_210, retro_mmus_3635, retro_mmus_60,
Oryctolagus cuniculus ENSOCUG000000027432 retrocopies
retro_ocun_994, retro_ocun_995,
Otolemur garnettii ENSOGAG000000259483 retrocopies
retro_ogar_1685, retro_ogar_3010, retro_ogar_3175,
Otolemur garnettii ENSOGAG000000281327 retrocopies
retro_ogar_1869, retro_ogar_1924, retro_ogar_2222, retro_ogar_2590, retro_ogar_3215, retro_ogar_600, retro_ogar_814,
Pongo abelii ENSPPYG000000129671 retrocopy
retro_pabe_450,
Pelodiscus sinensis ENSPSIG000000030111 retrocopy
retro_psin_16,
Pan troglodytes ENSPTRG000000126765 retrocopies
retro_ptro_1059, retro_ptro_2430, retro_ptro_2966, retro_ptro_683, retro_ptro_872,
Pteropus vampyrus ENSPVAG000000103802 retrocopies
retro_pvam_1077, retro_pvam_326,
Rattus norvegicus ENSRNOG0000000155611 retrocopies
retro_rnor_1510, retro_rnor_1665, retro_rnor_1869, retro_rnor_2053, retro_rnor_2659, retro_rnor_2669, retro_rnor_2713, retro_rnor_2776, retro_rnor_2809, retro_rnor_348, retro_rnor_959,
Sarcophilus harrisii ENSSHAG000000182551 retrocopy
retro_shar_518,
Sus scrofa ENSSSCG000000159886 retrocopies
retro_sscr_1110, retro_sscr_1152, retro_sscr_391, retro_sscr_621, retro_sscr_764, retro_sscr_927,
Ictidomys tridecemlineatus ENSSTOG000000251254 retrocopies
retro_itri_1444, retro_itri_1878, retro_itri_952, retro_itri_98,
Tarsius syrichta ENSTSYG000000129492 retrocopies
retro_tsyr_1480, retro_tsyr_2122,
Tursiops truncatus ENSTTRG000000142253 retrocopies
retro_ttru_1459, retro_ttru_675, retro_ttru_9,
Xenopus tropicalis ENSXETG00000001806 1 retrocopy
retro_xtro_11 ,
Xiphophorus maculatus ENSXMAG000000004391 retrocopy
retro_xmac_2,


Copyright © RetrogeneDB 2014-2017