RetrogeneDB ID:

retro_amel_1669

Retrocopy
location
Organism:Panda (Ailuropoda melanoleuca)
Coordinates:GL193916.1:193068..193749(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSAMEG00000005114
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSAMEG00000009878
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_amel_1669
GGAGATATGATAGTTTGTGCAGCTTATGCTTATGAACTCCTAAAGTATGGTATAAAGGTTGGCCTGACAAATTATGATGT
AGCATATTATATTGGCATGTTCCTGGTCCATGGGCTTCTCAACAGGCTTGGCATAGACAAGATCTATGAAGGCCAACTGG
ACGTGACCAGAGATGAATACGATATGGAAAGCATTGATGGTCAACTTGGTGACTTCACCTGCTATTCGGATGCTAGGCTT
ACCAGAACTACTACTGGAAATAAAGTTTTTGGGGCCCTCAAGGGAGCTGTGGATGGAGGCTTGTCTATCCCTCATAGTAC
CAAATTATTCCCTAGTTATGATTCAGAAAGCAAGGAATTCAATGCAGAAGTACTTCAGAAGCACATCATGGGTCAGAATG
TTGCAGATTATATGAGTTACCTAATGGAAGAAGATGACAATGCTTTTAAGAAACAATTCTCTCAATACATAAACAACAAT
GTAACTCCAGACATGATGGAGGACATGTATAAGAAAGTTCACACTGTTACATTACAGAATCTAGTCTATGAGAAGAAGCC
TAAGAAAGAAGTAAAAAAGACAAGGTGGAACTGTCCCAAAATGTCTCTTGCCCAGAAGAAAGACTGGGTAGCTCAGAAGA
AGGCAAGCTTCCTTAGAGCTCAGGAGCGGGCTGCTGAGAGC

ORF - retro_amel_1669 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.62 %
Parental protein coverage: 74.67 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYEGQVEVTGDEYNVESIDGQPG
GDMIVCAAYA.EL.KYG.KVGLTNY..AY..G..L...LLNR.G.DKIYEGQ..VT.DEY..ESIDGQ.G
RetrocopyGDMIVCAAYAYELLKYGIKVGLTNYDVAYYIGMFLVHGLLNRLGIDKIYEGQLDVTRDEYDMESIDGQLG
ParentalAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRFPGYDSESKEFNAEVHRKHIMGQNVADYMRY
.FTCY.DA.L.RTTTGNKVFGALKGAVDGGLSIPHSTK.FP.YDSESKEFNAEV..KHIMGQNVADYM.Y
RetrocopyDFTCYSDARLTRTTTGNKVFGALKGAVDGGLSIPHSTKLFPSYDSESKEFNAEVLQKHIMGQNVADYMSY
ParentalLMEEDEDAYKKQFSQYIKNNVTPDMMEEMYKKAHAAIRENPVYEKKPKKEVKKKRWNRPKMSLAQKKDRV
LMEED..A.KKQFSQYI.NNVTPDMME.MYKK.H.....N.VYEKKPKKEVKK.RWN.PKMSLAQKKD.V
RetrocopyLMEEDDNAFKKQFSQYINNNVTPDMMEDMYKKVHTVTLQNLVYEKKPKKEVKKTRWNCPKMSLAQKKDWV
ParentalAQKKASFLRAQERAAES
AQKKASFLRAQERAAES
RetrocopyAQKKASFLRAQERAAES

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_1669 retrocopy.

TSS - click to see more details

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab - click to see more details

retro_amel_1669 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 66 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG00000009878 5 retrocopies
retro_amel_1200, retro_amel_137, retro_amel_139, retro_amel_1439, retro_amel_1669 ,
Bos taurus ENSBTAG000000020262 retrocopies
retro_btau_120, retro_btau_67,
Cavia porcellus ENSCPOG000000006988 retrocopies
retro_cpor_1047, retro_cpor_1097, retro_cpor_1141, retro_cpor_1259, retro_cpor_1354, retro_cpor_1387, retro_cpor_428, retro_cpor_737,
Dipodomys ordii ENSDORG000000056742 retrocopies
retro_dord_226, retro_dord_670,
Equus caballus ENSECAG000000210651 retrocopy
retro_ecab_654,
Macropus eugenii ENSMEUG000000063613 retrocopies
retro_meug_1168, retro_meug_1537, retro_meug_2146,
Monodelphis domestica ENSMODG000000116351 retrocopy
retro_mdom_748,
Mustela putorius furoENSMPUG000000041506 retrocopies
retro_mputfur_213, retro_mputfur_449, retro_mputfur_451, retro_mputfur_597, retro_mputfur_721, retro_mputfur_833,
Mus musculus ENSMUSG0000005855811 retrocopies
retro_mmus_1000, retro_mmus_1185, retro_mmus_1338, retro_mmus_1789, retro_mmus_1991, retro_mmus_2577, retro_mmus_2846, retro_mmus_297, retro_mmus_3076, retro_mmus_504, retro_mmus_911,
Ornithorhynchus anatinus ENSOANG000000046691 retrocopy
retro_oana_97,
Oryctolagus cuniculus ENSOCUG000000100892 retrocopies
retro_ocun_265, retro_ocun_54,
Petromyzon marinus ENSPMAG000000020401 retrocopy
retro_pmar_23,
Pteropus vampyrus ENSPVAG000000151174 retrocopies
retro_pvam_1427, retro_pvam_355, retro_pvam_505, retro_pvam_527,
Rattus norvegicus ENSRNOG000000235296 retrocopies
retro_rnor_113, retro_rnor_2246, retro_rnor_2418, retro_rnor_2498, retro_rnor_2802, retro_rnor_2922,
Sarcophilus harrisii ENSSHAG000000064171 retrocopy
retro_shar_202,
Sus scrofa ENSSSCG000000068992 retrocopies
retro_sscr_149, retro_sscr_219,
Tupaia belangeri ENSTBEG000000105605 retrocopies
retro_tbel_101, retro_tbel_1054, retro_tbel_1518, retro_tbel_3006, retro_tbel_3530,
Tursiops truncatus ENSTTRG000000130975 retrocopies
retro_ttru_1446, retro_ttru_1548, retro_ttru_1796, retro_ttru_645, retro_ttru_979,


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