RetrogeneDB ID:

retro_amel_909

Retrocopy
location
Organism:Panda (Ailuropoda melanoleuca)
Coordinates:GL192735.1:633278..634076(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSAMEG00000011235
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:YBX1
Ensembl ID:ENSAMEG00000000494
Aliases:None
Description:Y box binding protein 1 [Source:HGNC Symbol;Acc:8014]


Retrocopy-Parental alignment summary:






>retro_amel_909
GGGGACAAGAAGGTCATCACAAGGAAGGTTTTGGGAACAGTAAAATGGTTCAGTGTGAGAAACAGGTATGGCTTCATCAA
TAGGAATGACACCAAGGAAGATGCATTTGTACAGCAGACTGCCATCAAGAACAGTAGCCCGGGAAGCACCTTCACAGTGC
TGAGATGGAGAGACTGTGGAGCTGGATGTTGGTGAAGGAGAAAATGGGCCAGAGGCAGCAACTGTGACCCGCCCTGCTGG
AACTCCAGTGCAGGGCAGTAAATATGCAGCAGATCGGAACCATTCTAGAAACTCTCCGTGGTGCAGGGGTCCGCCACGCA
ATTCCCAGCAGAATTACCAGAATAGTGAGAGTGGGGAGAAGAGTGAGGGATTGGAAAGTGCCCGCAAAGTCCAGACCCAA
CAGCGCCAGCCCTTCCGTAGGCGACGGCTCCCACCTTACAACATGCGGAGACTGTCTGGGCATCGACCACAGTATGCCAT
CCGTCCTGTGCAGGGAGAAGTGATGGAAGGTGCTGACAACCAGGGTGCAGGAGAGCAGGGTAGGCCAGTGAGACAGAATA
TGTATTGGGGTTGTAGACCACCATTCCGTAGAGCCCTCCACCCCAAGGACAGCCTAGACAGGATGGCAATGAGGAAGGTG
AGGAAAATCAAGGAGATGAGATCCAAGGTCAGCAGCCCCGTCACTGTCGGTACCGCCACAACTTCAACTGCCAACACAGA
CACCCAGAAAACCCTAAATCACAAGATTGCAAAGAGACAAAAGCAGCTGATCCACCAGCTGAGAATTCCTCCACTCCT

ORF - retro_amel_909 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.96 %
Parental protein coverage: 86.41 %
Number of stop codons detected: 0
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalGGERLSATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPR-KYLRSVG-DGETVEFDVVEGE
G.......KVLGTVKWF.VRN.YGFINRNDTKED.FV.QTAIK...P..K.L.S...DGETVE.DV.EGE
RetrocopyGDKKVITRKVLGTVKWFSVRNRYGFINRNDTKEDAFVQQTAIKNSSPG<KHLHSAE<DGETVELDVGEGE
ParentalKGAEAANVTGPGGVPVQGSKYAADRNHYRRYPRRRGPPRNYQQNYQNSESGEKNEGSESAPEGQAQQRRP
.G.EAA.VT.P.G.PVQGSKYAADRNH.R..P..RGPPRN.QQNYQNSESGEK.EG.ESA...Q.QQR.P
RetrocopyNGPEAATVTRPAGTPVQGSKYAADRNHSRNSPWCRGPPRNSQQNYQNSESGEKSEGLESARKVQTQQRQP
ParentalYRRRRFPPYYMRRPYGRRPQYSNPPVQGEVMEGADNQGAGEQGRPVRQNMYRGYRPRFRR-GPPRQRQPR
.RRRR.PPY.MRR..G.RPQY...PVQGEVMEGADNQGAGEQGRPVRQNMY.G.RP.FRR..PP.Q.QPR
RetrocopyFRRRRLPPYNMRRLSGHRPQYAIRPVQGEVMEGADNQGAGEQGRPVRQNMYWGCRPPFRR<SPPPQGQPR
ParentalEDGNEEDKENQGDETQGQQPPQRRYRRNFNYRRRRPENPKPQDGKETKAADPPAENSSAP
.DGNEE..ENQGDE.QGQQP...RYR.NFN...R.PENPK.QD.KETKAADPPAENSS.P
RetrocopyQDGNEEGEENQGDEIQGQQPRHCRYRHNFNCQHRHPENPKSQDCKETKAADPPAENSSTP

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






RNA-Seq - click to see more details

Ailuropoda melanoleuca was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Ailuropoda melanoleuca was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_amel_909 retrocopy.

TSS - click to see more details

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab - click to see more details

retro_amel_909 was not experimentally validated.

Retrocopy orthology:
Ailuropoda melanoleuca 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 18 parental genes, and 116 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG00000000494 9 retrocopies
retro_amel_1280, retro_amel_1358, retro_amel_141, retro_amel_1486, retro_amel_215, retro_amel_418, retro_amel_625, retro_amel_837, retro_amel_909 ,
Canis familiaris ENSCAFG000000025414 retrocopies
retro_cfam_1312, retro_cfam_2118, retro_cfam_758, retro_cfam_91,
Callithrix jacchus ENSCJAG000000031556 retrocopies
retro_cjac_1261, retro_cjac_1701, retro_cjac_2718, retro_cjac_3156, retro_cjac_4172, retro_cjac_817,
Cavia porcellus ENSCPOG000000108883 retrocopies
retro_cpor_654, retro_cpor_833, retro_cpor_905,
Felis catus ENSFCAG000000226046 retrocopies
retro_fcat_145, retro_fcat_1554, retro_fcat_1956, retro_fcat_241, retro_fcat_503, retro_fcat_631,
Homo sapiens ENSG000000659784 retrocopies
retro_hsap_1433, retro_hsap_3886, retro_hsap_4250, retro_hsap_4301,
Loxodonta africana ENSLAFG000000075971 retrocopy
retro_lafr_804,
Microcebus murinus ENSMICG0000001498419 retrocopies
retro_mmur_1098, retro_mmur_1285, retro_mmur_1326, retro_mmur_1435, retro_mmur_1437, retro_mmur_1445, retro_mmur_1621, retro_mmur_199, retro_mmur_315, retro_mmur_413, retro_mmur_581, retro_mmur_640, retro_mmur_676, retro_mmur_679, retro_mmur_726, retro_mmur_837, retro_mmur_900, retro_mmur_919, retro_mmur_942,
Macaca mulatta ENSMMUG000000131365 retrocopies
retro_mmul_1139, retro_mmul_1423, retro_mmul_2017, retro_mmul_423, retro_mmul_861,
Nomascus leucogenys ENSNLEG000000123247 retrocopies
retro_nleu_1053, retro_nleu_1188, retro_nleu_1312, retro_nleu_1601, retro_nleu_1749, retro_nleu_1888, retro_nleu_270,
Oryctolagus cuniculus ENSOCUG000000280472 retrocopies
retro_ocun_1519, retro_ocun_1953,
Otolemur garnettii ENSOGAG0000000678425 retrocopies
retro_ogar_1127, retro_ogar_1246, retro_ogar_1350, retro_ogar_1371, retro_ogar_1497, retro_ogar_2011, retro_ogar_2018, retro_ogar_2302, retro_ogar_2359, retro_ogar_2607, retro_ogar_2654, retro_ogar_3170, retro_ogar_3225, retro_ogar_324, retro_ogar_3303, retro_ogar_3316, retro_ogar_3317, retro_ogar_3366, retro_ogar_3416, retro_ogar_3474, retro_ogar_448, retro_ogar_572, retro_ogar_678, retro_ogar_690, retro_ogar_753,
Pongo abelii ENSPPYG000000014667 retrocopies
retro_pabe_1216, retro_pabe_1320, retro_pabe_2054, retro_pabe_2292, retro_pabe_3167, retro_pabe_3388, retro_pabe_3502,
Pteropus vampyrus ENSPVAG000000055047 retrocopies
retro_pvam_1255, retro_pvam_1348, retro_pvam_1391, retro_pvam_145, retro_pvam_405, retro_pvam_76, retro_pvam_971,
Sorex araneus ENSSARG000000078961 retrocopy
retro_sara_559,
Tarsius syrichta ENSTSYG000000069156 retrocopies
retro_tsyr_1030, retro_tsyr_173, retro_tsyr_2037, retro_tsyr_610, retro_tsyr_840, retro_tsyr_996,
Tursiops truncatus ENSTTRG000000013532 retrocopies
retro_ttru_461, retro_ttru_746,
Vicugna pacos ENSVPAG000000000682 retrocopies
retro_vpac_235, retro_vpac_647,


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