RetrogeneDB ID:

retro_amel_889

Retrocopy
location
Organism:Panda (Ailuropoda melanoleuca)
Coordinates:GL192713.1:974100..974673(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL19
Ensembl ID:ENSAMEG00000004121
Aliases:None
Description:ribosomal protein L19 [Source:HGNC Symbol;Acc:10312]


Retrocopy-Parental alignment summary:






>retro_amel_889
CTCAGGCTTTGGAAGAGGCTTGCCTCCGGTGTCCTCCATTATGGCAGAAAGAAGGTCTGGTTGGATCTCAATGAGACCAA
TGTAATTGCCAGTGCCAACTCCCATCAGCAGATCCAGAAGTTGACCAAAGACGGGCTGATCATCTGGGAGCCTGTGACTC
TCCATTCCTGGACTCCATGGCAGAAAAGCACTTTGGCCCCGCCAGAAGGACAGGCATGTGGGCATGGGGGAATGAAAGAC
TCCTGCCAGCACTCAGATGACCAAGAAGGTTGCCTGGATGAGGAGGATGAGAATTCTGTGATGGCTGCATAGAAGATACT
ATGAATCTAGGAAGGTTGACCACCACGCATATCACAGCCTGTACTTCAAAGTGAAGGTAAGATGTTGAAAAACAAGCAGA
TTCTCATGGACTACATCCATAAGCTGCAGTCAGACGAGGCTCACAAGATGCTTCTGGCTGACCAGGCTGAGGCCTGCGGT
ATAAGTAAGAAAGCACATGAGTGCCTTGAAGAGTGGCTCCAGGCCAGGAAAGAGGAAATTATCATGACTCTGTCCAAGGA
GGAAGAGGTCAAG

ORF - retro_amel_889 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 63.92 %
Parental protein coverage: 97.96 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalLRLQKRLASSVLRCGKKKVWLDPNETNEIANANSRQQIRKLIKDGLIIRKPVTVHSRARCRKNTLA-RRK
LRL.KRLAS.VL..G.KKVWLD.NETN.IA.ANS.QQI.KL.KDGLII..PVT.HS.....K.TLA.R.K
RetrocopyLRLWKRLASGVLHYGRKKVWLDLNETNVIASANSHQQIQKLTKDGLIIWEPVTLHSWTPWQKSTLA>RQK
ParentalGRHMGIGKRKGTANARMPEKVTWMRRMRILRRLLRRYRESKKIDRHMYHSLYLKVK-GNVFKNKRILMEH
.RH.G.G..K..A...M..KV.WMRRMRIL..L.RRY.ES.K.D.H.YHSLY.KVK.G...KNK.ILM..
RetrocopyDRHVGMGE*KTPASTQMTKKVAWMRRMRIL*WLHRRYYESRKVDHHAYHSLYFKVK<GKMLKNKQILMDY
ParentalIHKLKADKARKKLLADQAEARRSKTKEARKRREERLQAKKEEIIKTLSKEEETK
IHKL..D.A.K.LLADQAEA.....K.A....EE.LQA.KEEII.TLSKEEE.K
RetrocopyIHKLQSDEAHKMLLADQAEA-CGISKKAHECLEEWLQARKEEIIMTLSKEEEVK

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_889 retrocopy.

TSS - click to see more details

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab - click to see more details

retro_amel_889 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 14 parental genes, and 163 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG00000004121 5 retrocopies
retro_amel_1195, retro_amel_1663, retro_amel_451, retro_amel_531, retro_amel_889 ,
Callithrix jacchus ENSCJAG000000085204 retrocopies
retro_cjac_131, retro_cjac_220, retro_cjac_32, retro_cjac_64,
Dasypus novemcinctus ENSDNOG000000197427 retrocopies
retro_dnov_1478, retro_dnov_1897, retro_dnov_2, retro_dnov_2170, retro_dnov_2431, retro_dnov_691, retro_dnov_720,
Dipodomys ordii ENSDORG000000043301 retrocopy
retro_dord_105,
Equus caballus ENSECAG000000250806 retrocopies
retro_ecab_104, retro_ecab_319, retro_ecab_351, retro_ecab_456, retro_ecab_497, retro_ecab_905,
Homo sapiens ENSG0000010829821 retrocopies
retro_hsap_1085, retro_hsap_1802, retro_hsap_2072, retro_hsap_2157, retro_hsap_2209, retro_hsap_2406, retro_hsap_2651, retro_hsap_2679, retro_hsap_2850, retro_hsap_3012, retro_hsap_3155, retro_hsap_3274, retro_hsap_3401, retro_hsap_3885, retro_hsap_3933, retro_hsap_399, retro_hsap_3991, retro_hsap_4219, retro_hsap_4680, retro_hsap_4774, retro_hsap_739,
Macaca mulatta ENSMMUG000000042352 retrocopies
retro_mmul_283, retro_mmul_63,
Mus musculus ENSMUSG0000001740425 retrocopies
retro_mmus_1174, retro_mmus_1235, retro_mmus_1248, retro_mmus_1273, retro_mmus_1323, retro_mmus_1397, retro_mmus_1591, retro_mmus_1614, retro_mmus_1699, retro_mmus_1700, retro_mmus_1877, retro_mmus_1885, retro_mmus_1964, retro_mmus_2301, retro_mmus_2688, retro_mmus_2749, retro_mmus_2967, retro_mmus_3110, retro_mmus_3187, retro_mmus_3310, retro_mmus_341, retro_mmus_3413, retro_mmus_507, retro_mmus_571, retro_mmus_600,
Nomascus leucogenys ENSNLEG0000000074819 retrocopies
retro_nleu_1182, retro_nleu_1570, retro_nleu_1602, retro_nleu_1620, retro_nleu_1889, retro_nleu_2171, retro_nleu_2236, retro_nleu_2284, retro_nleu_2335, retro_nleu_2430, retro_nleu_2446, retro_nleu_2538, retro_nleu_2695, retro_nleu_2702, retro_nleu_2735, retro_nleu_3116, retro_nleu_479, retro_nleu_540, retro_nleu_656,
Pongo abelii ENSPPYG0000000849220 retrocopies
retro_pabe_1546, retro_pabe_1687, retro_pabe_1709, retro_pabe_1815, retro_pabe_2177, retro_pabe_2300, retro_pabe_2320, retro_pabe_2496, retro_pabe_2625, retro_pabe_2799, retro_pabe_2800, retro_pabe_3166, retro_pabe_3278, retro_pabe_3299, retro_pabe_3513, retro_pabe_3635, retro_pabe_3829, retro_pabe_4, retro_pabe_973, retro_pabe_980,
Pteropus vampyrus ENSPVAG000000084989 retrocopies
retro_pvam_1191, retro_pvam_1332, retro_pvam_183, retro_pvam_244, retro_pvam_468, retro_pvam_792, retro_pvam_914, retro_pvam_918, retro_pvam_950,
Rattus norvegicus ENSRNOG0000000474137 retrocopies
retro_rnor_1029, retro_rnor_1039, retro_rnor_1295, retro_rnor_1338, retro_rnor_1405, retro_rnor_1440, retro_rnor_1449, retro_rnor_1478, retro_rnor_1512, retro_rnor_1525, retro_rnor_1558, retro_rnor_1577, retro_rnor_1765, retro_rnor_1766, retro_rnor_1795, retro_rnor_1814, retro_rnor_1860, retro_rnor_1885, retro_rnor_1905, retro_rnor_1907, retro_rnor_1970, retro_rnor_1981, retro_rnor_208, retro_rnor_2169, retro_rnor_2522, retro_rnor_2536, retro_rnor_2708, retro_rnor_2773, retro_rnor_2783, retro_rnor_2921, retro_rnor_2943, retro_rnor_326, retro_rnor_426, retro_rnor_434, retro_rnor_464, retro_rnor_465, retro_rnor_829,
Sarcophilus harrisii ENSSHAG000000164824 retrocopies
retro_shar_159, retro_shar_287, retro_shar_317, retro_shar_415,
Sus scrofa ENSSSCG000000175093 retrocopies
retro_sscr_1108, retro_sscr_398, retro_sscr_913,


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