RetrogeneDB ID:

retro_amel_296

Retrocopy
location
Organism:Panda (Ailuropoda melanoleuca)
Coordinates:GL192377.1:885280..885901(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL14
Ensembl ID:ENSAMEG00000001709
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_amel_296
GTTCTTAGGTGCTTTATGGAGGTTGGCTGGGTGACTTACGTCTCCTTTGGCCCTCCCATAGGGAAGTTGGTTGGGATTGT
AAATGTTACTGCTCAGAACAGCACTTTGGCTATGGACTTTGCTCTCAGGTAAGAAGACGGGCTCTGCCTTTCAAATCCAT
GCAGTTCATCGACTTCATCCTCAAGTTCCCACACAGTGCTGGCCAGAAGTATGCCCCACAAGCCTGGCAGAAGGCAGGTA
TCAGTACAAAATGGGCAGCCGCAAGATGGGCCACGTAGATTGAAGCCAGAGGGAAAAAAAGCCAAGACGACAGATATTCA
TCATTGTAAAGTCATGAAGGTAAAGAAAATGGGGAACAGACAGCACCATGTCAGGAAGCTGTAAAAAGCAGATCTCGTGA
ACGTTTCTCCCAAAAAAACACTGTCTGCTAAGGGTGCCGCTATGGCAGCTGCTGCAAAGTTTCCAGCAAAAAAGATGGCC
ACTGCAGGCAAGAGCGCTCCAGCCCAGAAGGTTCCTGCCCCGAAAGCTGCAGGCCAGAATGCAGCACCTCCTAGGTCTCA
GGAAGGTCAGAAAGCTCCGGCCCAGAAAGCACCTGCTCTGAAGGCATCTGGCAGAAAAGCG

ORF - retro_amel_296 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 69.34 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalVFRRFVEVGRVAYVSFGPHAGKLVAIVDVIDQNRALVD-GPCTQVRRQAMPFKCMQLTDFILKFPHSARQ
V.R.F.EVG.V.YVSFGP..GKLV.IV.V..QN..L...G.C.QVRR.A.PFK.MQ..DFILKFPHSA.Q
RetrocopyVLRCFMEVGWVTYVSFGPPIGKLVGIVNVTAQNSTLAM<GLCSQVRRRALPFKSMQFIDFILKFPHSAGQ
ParentalKYVRQAWQKADINTKWAATRWAKKIEARERK-AKMTDFDRYKVMKAKKMRNRIIKLEVRKLQKAALLKAS
KY..QAWQKA.I.TKWAA.RWA..IEAR..K.AK.TD....KVMK.KKM.NR.....VRKL.KA.L...S
RetrocopyKYAPQAWQKAGISTKWAAARWAT*IEARGKK>AKTTDIHHCKVMKVKKMGNR--QHHVRKL*KADLVNVS
ParentalPKKAPAAKGAAAAAAAAKVPAKKMAAAGKKAPAQKVPAPKAAGQKAAPPKAQKGQKAPAQKAPAPKASGK
PKK...AKGAA.AAAA.K.PAKKMA.AGK.APAQKVPAPKAAGQ.AAPP..Q.GQKAPAQKAPA.KASG.
RetrocopyPKKTLSAKGAAMAAAA-KFPAKKMATAGKSAPAQKVPAPKAAGQNAAPPRSQEGQKAPAQKAPALKASGR
ParentalKA
KA
RetrocopyKA

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_296 retrocopy.

TSS - click to see more details

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab - click to see more details

retro_amel_296 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 27 parental genes, and 88 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG00000001709 4 retrocopies
retro_amel_1876, retro_amel_1933, retro_amel_296 , retro_amel_660,
Canis familiaris ENSCAFG000000051381 retrocopy
retro_cfam_31,
Callithrix jacchus ENSCJAG000000178849 retrocopies
retro_cjac_1249, retro_cjac_1393, retro_cjac_1835, retro_cjac_2138, retro_cjac_2139, retro_cjac_2332, retro_cjac_2797, retro_cjac_3240, retro_cjac_630,
Cavia porcellus ENSCPOG000000007111 retrocopy
retro_cpor_529,
Equus caballus ENSECAG000000268132 retrocopies
retro_ecab_377, retro_ecab_743,
Echinops telfairi ENSETEG000000128946 retrocopies
retro_etel_2117, retro_etel_2155, retro_etel_251, retro_etel_315, retro_etel_356, retro_etel_387,
Felis catus ENSFCAG000000156554 retrocopies
retro_fcat_1000, retro_fcat_1457, retro_fcat_587, retro_fcat_671,
Homo sapiens ENSG000001888466 retrocopies
retro_hsap_1015, retro_hsap_1047, retro_hsap_2796, retro_hsap_3104, retro_hsap_3352, retro_hsap_4777,
Gorilla gorilla ENSGGOG000000259583 retrocopies
retro_ggor_122, retro_ggor_1945, retro_ggor_2272,
Latimeria chalumnae ENSLACG000000156391 retrocopy
retro_lcha_29,
Microcebus murinus ENSMICG000000092174 retrocopies
retro_mmur_1218, retro_mmur_1352, retro_mmur_279, retro_mmur_3,
Myotis lucifugus ENSMLUG000000144294 retrocopies
retro_mluc_1294, retro_mluc_2263, retro_mluc_420, retro_mluc_563,
Monodelphis domestica ENSMODG000000152622 retrocopies
retro_mdom_1499, retro_mdom_1939,
Mustela putorius furoENSMPUG000000179611 retrocopy
retro_mputfur_90,
Mus musculus ENSMUSG000000257943 retrocopies
retro_mmus_2904, retro_mmus_2929, retro_mmus_3011,
Nomascus leucogenys ENSNLEG000000056822 retrocopies
retro_nleu_763, retro_nleu_918,
Oryctolagus cuniculus ENSOCUG000000103093 retrocopies
retro_ocun_410, retro_ocun_464, retro_ocun_656,
Pan troglodytes ENSPTRG000000119634 retrocopies
retro_ptro_1893, retro_ptro_2100, retro_ptro_2135, retro_ptro_713,
Pteropus vampyrus ENSPVAG000000139147 retrocopies
retro_pvam_1108, retro_pvam_1413, retro_pvam_246, retro_pvam_446, retro_pvam_683, retro_pvam_903, retro_pvam_904,
Rattus norvegicus ENSRNOG000000190074 retrocopies
retro_rnor_2268, retro_rnor_2620, retro_rnor_415, retro_rnor_591,
Sorex araneus ENSSARG000000039742 retrocopies
retro_sara_349, retro_sara_504,
Sarcophilus harrisii ENSSHAG000000015915 retrocopies
retro_shar_397, retro_shar_539, retro_shar_696, retro_shar_737, retro_shar_788,
Sus scrofa ENSSSCG000000112722 retrocopies
retro_sscr_521, retro_sscr_63,
Ictidomys tridecemlineatus ENSSTOG000000214601 retrocopy
retro_itri_946,
Tarsius syrichta ENSTSYG000000021615 retrocopies
retro_tsyr_1036, retro_tsyr_1404, retro_tsyr_176, retro_tsyr_361, retro_tsyr_956,
Tursiops truncatus ENSTTRG000000067081 retrocopy
retro_ttru_113,
Xenopus tropicalis ENSXETG000000220181 retrocopy
retro_xtro_3,




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