RetrogeneDB ID:

retro_amel_137

Retrocopy
location
Organism:Panda (Ailuropoda melanoleuca)
Coordinates:GL192338.1:254620..255526(-)
Located in intron of:ENSAMEG00000016277
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSAMEG00000009878
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_amel_137
CAGTCTCTGTTCCGTAGGATGGCATATGTTGAAGTTGTCAAGAACAAGGCTTGCATCAAGAGATACCAAGTGAAATGTAG
AAGACGACAAGAGGGTAAAACTGGTAACTGTGCTCAGAAATGCTTGGTAATTCTGGATAAAATAAGTACGACACACCCAA
ATACAGATGATGGTCCACGTAACCAACAGAGAAATCATTTGTCAGATTGTTCATGTCCATACAGAAAGAGAAATGATAGC
TTGTGCAGTTCATACTCATGAACTCCCAAAGTATGGTGTGAAGGCTGACCTGAAAAATGTTGCTGCAGCATATCATACAG
ACCTGCTGCCGGCCTGCGGGCTTCTCAACAGGTCTGGTAGGGACACGACCTAGGAAGGCCAAGCGGAGGTGACTGGAGAG
GAACGCAATGTGGAAAACACTAACGGTGAACCTGGTGCCTTCACCTGCTGTTTGGATGCAGGGCTGGCCAGAACTACTAC
CGGAAATAAAATCCGGGGGCCCTCGAGGGAGCTGTGGATGGAGGCCTGTCTGTTGCTCACAGTACCAAACAATTCCTTGG
TTATGATTTGGAAAGCAAGGAATTCAATGGAGAAGTACATCAGAAGCATATCATGGATCAGAATATTGCAGATTAAATGT
GTTACCTAATGGAAGAAGATGAAGATGCTTACAAGGAACACTTCTGTTAATACATAAAGAACAAAGTATCTCTGGACATG
GTGAAGGAGATGTATAAGAAAGCTCTCGCTGCTACATGAGAGAAGCCAGTCTGTGAGAAGAAGCCTAAGACAGAAGTTAA
AAAGAAGAGGTGCAACCATCCCAAAATGTCTCTTGCCCAGAAGAAAGATAGCGTAGCTCAGAAGAAGGCAAACTTCCTTA
GAGCTCAGGAGCAGGCTGCTGAGAGC

ORF - retro_amel_137 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.57 %
Parental protein coverage: 99.67 %
Number of stop codons detected: 4
Number of frameshifts detected: 3


Retrocopy - Parental Gene Alignment:

ParentalRSLFRRMGFVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDK-NKYNTPKYR-MRVHVTNRDIIC
.SLFRRM..V.VVKNKA..KRYQVK.RRR.EGKT...A.K.LVI.DK.NKY.TPKYR.M.VHVTNR.IIC
RetrocopyQSLFRRMAYVEVVKNKACIKRYQVKCRRRQEGKTGNCAQKCLVILDK<NKYDTPKYR<MMVHVTNREIIC
ParentalQIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYEGQVEVTGDEYNV
QI.....E..MI.CA...HELPKYGVK..L.N.AAAY.T.LL.A..LLNR.G.D...EGQ.EVTG.E.NV
RetrocopyQIVHVHTEREMIACAVHTHELPKYGVKADLKNVAAAYHTDLLPACGLLNRSGRDTT*EGQAEVTGEERNV
ParentalESIDGQPGAFTCYLDAGLARTTTGNKVFG-ALKGAVDGGLSIPHSTKRFPGYDSESKEFNAEVHRKHIMG
E...G.PGAFTC.LDAGLARTTTGNK..G.AL.GAVDGGLS..HSTK.F.GYD.ESKEFN.EVH.KHIM.
RetrocopyENTNGEPGAFTCCLDAGLARTTTGNKIRG<ALEGAVDGGLSVAHSTKQFLGYDLESKEFNGEVHQKHIMD
ParentalQNVADYMRYLMEEDEDAYKKQFSQYIKNNVTPDMMEEMYKKAHAAIRENPVYEKKPKKEVKKKRWNRPKM
QN.AD.M.YLMEEDEDAYK..F..YIKN.V..DM..EMYKKA.AA..E.PV.EKKPK.EVKKKR.N.PKM
RetrocopyQNIAD*MCYLMEEDEDAYKEHFC*YIKNKVSLDMVKEMYKKALAAT*EKPVCEKKPKTEVKKKRCNHPKM
ParentalSLAQKKDRVAQKKASFLRAQERAAES
SLAQKKD.VAQKKA.FLRAQE.AAES
RetrocopySLAQKKDSVAQKKANFLRAQEQAAES

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_137 retrocopy.

TSS - click to see more details

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab - click to see more details

retro_amel_137 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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