RetrogeneDB ID:

retro_amel_1128

Retrocopy
location
Organism:Panda (Ailuropoda melanoleuca)
Coordinates:GL192928.1:611693..612475(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSAMEG00000015463
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSAMEG00000005805
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_amel_1128
GGTCCCAAGAAGCATCTGAAGTGTGCAGCAGCTCCAAAACATTGGATGCTGGATAAACTGACCAGTGTGTTTGCCCCTTA
CCCATATGCTGCTCCCCATAAGCTGAGAGTGTGTCTCCATCTCATCATTTTCCTAAGGAACGGACTTAGGTATGCCCTAA
CAGGGGATGAAGTAAAGAAGATCTATGTGCTGTGTTTTATTAAGATTGATGGCAAGGTCCAAACTGATATAACCTACCCT
GCTGGTTTTATGGATGTCGTCAGCACTGACAAGACTGGGGAGAATTTCCATCTGATCTATGACACCAAGAGTCGTTCTGC
TGTTCATTGGATTACACCTGAGGAGGCCAAGTATAAGTTGTGCAAAGTGAGAAAGAACTTTGTGGGGACAAAAGGAATCC
CTCATCTGGTGATCCATGATGCTCCTACCATCCACTGTCATGATCACCTCATCCAGGGGAATGACACCATTCAGATTGAT
TTGGAGACTGGAAAGATTACTTATTTCATCAAGTTTGATACTGGTAATCTGTGTATAAGTGGACATGTTAACCTGGGAAG
AATTCGTATGATCATCAGCAGAGAGAGACACCCTGGTTCTTTTGATGTAATTCACATGAAAGATACCAATGGGAACAGCT
TTGCCACCCGACTCTCCCAACATTTTTGTTACTGGCGAAGGCAACAAACGAATTTCTCATCCCTGTGGAAAGGGTATCCA
TCTCACCATTGCTGAAGAGAGAGACGAGAGTCTGGTGGCCCAACAGACCAGTGAGTAAAATG

ORF - retro_amel_1128 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.65 %
Parental protein coverage: 97.4 %
Number of stop codons detected: 0
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDEVKKICMQRFIKID
GPKKHLK..AAPKHWMLDKLT.VFAP.P...PHKLR.CL.LIIFLRN.L.YALTGDEVKKI....FIKID
RetrocopyGPKKHLKCAAAPKHWMLDKLTSVFAPYPYAAPHKLRVCLHLIIFLRNGLRYALTGDEVKKIYVLCFIKID
ParentalGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAKYKLCKVRKIFVGTKGIPHLVTHD
GKV.TDITYPAGFMDV.S.DKTGENF.LIYDTK.R.AVH.ITPEEAKYKLCKVRK.FVGTKGIPHLV.HD
RetrocopyGKVQTDITYPAGFMDVVSTDKTGENFHLIYDTKSRSAVHWITPEEAKYKLCKVRKNFVGTKGIPHLVIHD
ParentalARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNLCMVTGGANLGRIGVITNRERHPGSFDVVHVKDA
A.TI...D.LI..NDTIQIDLETGKIT.FIKFDTGNLC...G..NLGRI..I..RERHPGSFDV.H.KD.
RetrocopyAPTIHCHDHLIQGNDTIQIDLETGKITYFIKFDTGNLC-ISGHVNLGRIRMIISRERHPGSFDVIHMKDT
ParentalNGNSFATRLS-NIFVIGKGNKPWISLPRGKGIRLTIAEERDKRL-QPNRAAGKM
NGNSFATRLS.NIFV.G.GNK..IS.P.GKGI.LTIAEERD..L..PNR...KM
RetrocopyNGNSFATRLS>NIFVTGEGNKR-ISHPCGKGIHLTIAEERDESL>WPNRPVSKM

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_1128 retrocopy.

TSS - click to see more details

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab - click to see more details

retro_amel_1128 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 125 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000146011 retrocopy
retro_acar_82,
Ailuropoda melanoleuca ENSAMEG00000005805 14 retrocopies
retro_amel_1003, retro_amel_1128 , retro_amel_1296, retro_amel_1381, retro_amel_1695, retro_amel_1869, retro_amel_195, retro_amel_259, retro_amel_327, retro_amel_576, retro_amel_767, retro_amel_869, retro_amel_968, retro_amel_971,
Cavia porcellus ENSCPOG000000063373 retrocopies
retro_cpor_1023, retro_cpor_1075, retro_cpor_31,
Equus caballus ENSECAG000000108526 retrocopies
retro_ecab_34, retro_ecab_435, retro_ecab_443, retro_ecab_614, retro_ecab_757, retro_ecab_850,
Homo sapiens ENSG000001298241 retrocopy
retro_hsap_1704,
Gorilla gorilla ENSGGOG0000002307918 retrocopies
retro_ggor_1278, retro_ggor_1319, retro_ggor_1354, retro_ggor_1367, retro_ggor_1478, retro_ggor_1479, retro_ggor_1517, retro_ggor_1520, retro_ggor_1689, retro_ggor_223, retro_ggor_2676, retro_ggor_2719, retro_ggor_572, retro_ggor_711, retro_ggor_844, retro_ggor_894, retro_ggor_895, retro_ggor_939,
Loxodonta africana ENSLAFG000000026544 retrocopies
retro_lafr_1007, retro_lafr_1081, retro_lafr_1238, retro_lafr_208,
Macropus eugenii ENSMEUG0000000796916 retrocopies
retro_meug_131, retro_meug_141, retro_meug_1644, retro_meug_1732, retro_meug_1814, retro_meug_194, retro_meug_2098, retro_meug_2121, retro_meug_228, retro_meug_562, retro_meug_628, retro_meug_673, retro_meug_843, retro_meug_872, retro_meug_972, retro_meug_999,
Meleagris gallopavo ENSMGAG000000096711 retrocopy
retro_mgal_3,
Monodelphis domestica ENSMODG000000110701 retrocopy
retro_mdom_238,
Mustela putorius furoENSMPUG0000000529411 retrocopies
retro_mputfur_1044, retro_mputfur_1176, retro_mputfur_1325, retro_mputfur_1326, retro_mputfur_1393, retro_mputfur_160, retro_mputfur_205, retro_mputfur_48, retro_mputfur_725, retro_mputfur_876, retro_mputfur_988,
Otolemur garnettii ENSOGAG000000118082 retrocopies
retro_ogar_121, retro_ogar_229,
Procavia capensis ENSPCAG000000007613 retrocopies
retro_pcap_334, retro_pcap_35, retro_pcap_360,
Pan troglodytes ENSPTRG000000224701 retrocopy
retro_ptro_1153,
Pteropus vampyrus ENSPVAG0000001288221 retrocopies
retro_pvam_1021, retro_pvam_1082, retro_pvam_1158, retro_pvam_1264, retro_pvam_1298, retro_pvam_1312, retro_pvam_1327, retro_pvam_1364, retro_pvam_1419, retro_pvam_177, retro_pvam_191, retro_pvam_214, retro_pvam_219, retro_pvam_335, retro_pvam_473, retro_pvam_628, retro_pvam_714, retro_pvam_809, retro_pvam_835, retro_pvam_921, retro_pvam_930,
Rattus norvegicus ENSRNOG000000032011 retrocopy
retro_rnor_135,
Ictidomys tridecemlineatus ENSSTOG000000286928 retrocopies
retro_itri_1179, retro_itri_1607, retro_itri_291, retro_itri_306, retro_itri_368, retro_itri_495, retro_itri_738, retro_itri_985,
Tursiops truncatus ENSTTRG0000000616413 retrocopies
retro_ttru_104, retro_ttru_1104, retro_ttru_1129, retro_ttru_1748, retro_ttru_260, retro_ttru_465, retro_ttru_470, retro_ttru_512, retro_ttru_565, retro_ttru_618, retro_ttru_631, retro_ttru_728, retro_ttru_734,


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