RetrogeneDB ID:

retro_amel_1485

Retrocopy
location
Organism:Panda (Ailuropoda melanoleuca)
Coordinates:GL193482.1:647183..647564(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSAMEG00000017548
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_amel_1485
ATGGGAAATAAGCCAATCTGGGGGCAGACCGGATCCAGGTTCATTCAACATTACTGCCAGTTCTTTAATAATGACAGAAT
GCAAAGAGGTGCCATTTATATTGACATTACATCATGCCTCAGGTGGGAAGGACAGCAATTCCAGGGGAAAGCTACCATTG
TGGAGAGATTGTTCAGCCTTCTGTTCCAGAAAATCTAGCACAGCATCATGGCGCAGGATCATTAGCCCATGCTAGATAGC
TGCATCATCACCAGGGTCGTGGACCAGCTCAAGGCTGATGAAAACCCCATGATGGGATTCCCCCAGATATTCCTATTAAA
GAACATCAAGGATGCTTGAGTTTGCACCAATGACATGCTCAGGCTTGCCCTGCACAACTTC

ORF - retro_amel_1485 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.59 %
Parental protein coverage: 99.21 %
Number of stop codons detected: 3
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMGDKPIWEQIGSSFIQHYYQLFDNDRTQLGAIYID-ASCLTWEGQQFQGKAAIVEKLSSLPFQKIQHSIT
MG.KPIW.Q.GS.FIQHY.Q.F.NDR.Q.GAIYID..SCL.WEGQQFQGKA.IVE.L.SL.FQKI.HSI.
RetrocopyMGNKPIWGQTGSRFIQHYCQFFNNDRMQRGAIYIDITSCLRWEGQQFQGKATIVERLFSLLFQKI*HSIM
ParentalAQDHQPTPDSCIISMVVGQLKADEDPIMGFHQMFLLKNINDAWVCTNDMFRLALHNF
AQDH.P..DSCII..VV.QLKADE.P.MGF.Q.FLLKNI.DA.VCTNDM.RLALHNF
RetrocopyAQDH*PMLDSCIITRVVDQLKADENPMMGFPQIFLLKNIKDA*VCTNDMLRLALHNF

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_1485 retrocopy.

TSS - click to see more details

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab - click to see more details

retro_amel_1485 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 35 parental genes, and 131 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG00000017548 5 retrocopies
retro_amel_1225, retro_amel_134, retro_amel_1485 , retro_amel_415, retro_amel_445,
Bos taurus ENSBTAG000000064142 retrocopies
retro_btau_1573, retro_btau_881,
Choloepus hoffmanni ENSCHOG000000030593 retrocopies
retro_chof_1386, retro_chof_1619, retro_chof_2488,
Callithrix jacchus ENSCJAG0000001601514 retrocopies
retro_cjac_1328, retro_cjac_2247, retro_cjac_2562, retro_cjac_2864, retro_cjac_2913, retro_cjac_2953, retro_cjac_2978, retro_cjac_3126, retro_cjac_3299, retro_cjac_4044, retro_cjac_4173, retro_cjac_587, retro_cjac_777, retro_cjac_924,
Cavia porcellus ENSCPOG000000035211 retrocopy
retro_cpor_1368,
Equus caballus ENSECAG000000215301 retrocopy
retro_ecab_151,
Erinaceus europaeus ENSEEUG000000034702 retrocopies
retro_eeur_149, retro_eeur_571,
Echinops telfairi ENSETEG000000163549 retrocopies
retro_etel_1700, retro_etel_1737, retro_etel_1909, retro_etel_1925, retro_etel_245, retro_etel_281, retro_etel_301, retro_etel_399, retro_etel_746,
Felis catus ENSFCAG000000081673 retrocopies
retro_fcat_154, retro_fcat_743, retro_fcat_845,
Homo sapiens ENSG000001028987 retrocopies
retro_hsap_1322, retro_hsap_1480, retro_hsap_1858, retro_hsap_207, retro_hsap_4181, retro_hsap_4854, retro_hsap_544,
Gorilla gorilla ENSGGOG000000239255 retrocopies
retro_ggor_1032, retro_ggor_2152, retro_ggor_279, retro_ggor_2806, retro_ggor_3028,
Loxodonta africana ENSLAFG000000310371 retrocopy
retro_lafr_623,
Macropus eugenii ENSMEUG0000000987411 retrocopies
retro_meug_1023, retro_meug_136, retro_meug_1539, retro_meug_1585, retro_meug_1778, retro_meug_2140, retro_meug_253, retro_meug_282, retro_meug_352, retro_meug_676, retro_meug_748,
Myotis lucifugus ENSMLUG000000251753 retrocopies
retro_mluc_1265, retro_mluc_2194, retro_mluc_911,
Macaca mulatta ENSMMUG000000120386 retrocopies
retro_mmul_1160, retro_mmul_1270, retro_mmul_2127, retro_mmul_2169, retro_mmul_2593, retro_mmul_27,
Monodelphis domestica ENSMODG000000055176 retrocopies
retro_mdom_1031, retro_mdom_1291, retro_mdom_1488, retro_mdom_1489, retro_mdom_1903, retro_mdom_37,
Mustela putorius furoENSMPUG000000067374 retrocopies
retro_mputfur_229, retro_mputfur_614, retro_mputfur_714, retro_mputfur_962,
Mus musculus ENSMUSG000000084501 retrocopy
retro_mmus_232,
Nomascus leucogenys ENSNLEG000000048897 retrocopies
retro_nleu_1295, retro_nleu_1791, retro_nleu_1855, retro_nleu_2374, retro_nleu_2384, retro_nleu_2953, retro_nleu_731,
Oryctolagus cuniculus ENSOCUG000000063221 retrocopy
retro_ocun_115,
Otolemur garnettii ENSOGAG000000155682 retrocopies
retro_ogar_2713, retro_ogar_2811,
Ochotona princeps ENSOPRG000000137274 retrocopies
retro_opri_1089, retro_opri_1102, retro_opri_1170, retro_opri_229,
Procavia capensis ENSPCAG000000153441 retrocopy
retro_pcap_56,
Pongo abelii ENSPPYG000000074727 retrocopies
retro_pabe_1101, retro_pabe_1229, retro_pabe_1515, retro_pabe_3421, retro_pabe_3772, retro_pabe_433, retro_pabe_502,
Pan troglodytes ENSPTRG000000082487 retrocopies
retro_ptro_1001, retro_ptro_1239, retro_ptro_2835, retro_ptro_3230, retro_ptro_338, retro_ptro_409, retro_ptro_903,
Pteropus vampyrus ENSPVAG000000166051 retrocopy
retro_pvam_843,
Rattus norvegicus ENSRNOG000000189454 retrocopies
retro_rnor_1149, retro_rnor_1616, retro_rnor_2427, retro_rnor_545,
Sorex araneus ENSSARG000000074721 retrocopy
retro_sara_333,
Sarcophilus harrisii ENSSHAG000000061001 retrocopy
retro_shar_274,
Sus scrofa ENSSSCG000000302953 retrocopies
retro_sscr_1223, retro_sscr_710, retro_sscr_740,
Ictidomys tridecemlineatus ENSSTOG000000028781 retrocopy
retro_itri_800,
Tupaia belangeri ENSTBEG000000110161 retrocopy
retro_tbel_7,
Tarsius syrichta ENSTSYG000000107023 retrocopies
retro_tsyr_1689, retro_tsyr_380, retro_tsyr_745,
Tursiops truncatus ENSTTRG000000092512 retrocopies
retro_ttru_1534, retro_ttru_433,
Drosophila melanogaster FBgn00311451 retrocopy
retro_dmel_27,




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