RetrogeneDB ID:

retro_nleu_2313

Retrocopy
location
Organism:Gibbon (Nomascus leucogenys)
Coordinates:GL397342.1:7187766..7188878(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ACTA2
Ensembl ID:ENSNLEG00000012233
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_nleu_2313
GAAGGAGAGATCGTGGCGCTGGTCATTGACAATGGTTCCGGCATGTGCAAAGCTCGCTTTCCTAGGAATGACGCCCCCAG
AGCTGTGTTTTCCTCCATCTTTGGGTGTCTCCGGCACTAGAGCATAATGGTGGGCATGGGCCAGGACTCCCACATGGGCG
ATGAGGCCCAGAGCAAGCAAGGCATCCTGACCCTGAAGTACCCCATCGAGCATGACATCATCACCAACTGGGACGACATG
GGGATCTGGCACCTCACCTTCTACAACAAGCTGCGCATGGCCCCAGAGGAGCACCCGGTGCTGTTGACCATGGCTCCCCT
GAACCCCAAGGCCAACAGAGAGAAGATGACTCATCATGTTCGAGATCTTCAATACTCGGGCCATATACATGGCCATCCAG
GCCGTGCTGTCCCTCTACACCTCTCGGCAAACCACTGGCATTGTCATGGACTCTGGGGACTGGGTCACACACACGGTGCC
CATCTACGAGGGCTATGCCCTCCCCCACACCATCCTGTGTCTGGACCTGGCTGGCCGGGACCTGACCCACTACCTCATGA
AGATTCTCACTGAGTGTGGCTACAGCTTCACCACCTTGGCCAAGTGGGAGATCGTGCGCAACGTCAAGGAGAAGCTGTGC
TACGTTGCCCTAGACTTCTAGCAGGAGATGGCCACCGCTGCATCCTCCTCTTCCCTGGAGAAGAGCTACGAGCTGTCCAA
TGGTCAGCTCATCACAATCTGCAATGAGTGGTTCCGGTGTCTGGAGGCACTGTTCCAGCCTTCCTTCCTGAGCATGGAAT
CTTGTGGCATCCATGAGACCACCATCAACTCCTTCATGAAGTACAAGGTGGACATCTGCAAAGACCTGTGCCAACACGGT
GCTGTCAGGCGGCACCACCATGTACCCGGGCATCGCCGACAGGATGCAGAAGGAGATCCCTGCCCTGGCACCCAGCACCA
TGAAGATCAAGATCATTGCACCCCCAGAGCACAAGTACTCGGTGTGGATTGGCGGCTCCATCCTGGCCTCACTGTCCACC
TTCCAGCAGATGTGGATTAGCAAGCAGGAGTACCACGAGTCGGGCCCCTCCATCGTCCACTGCAAATGCTTC

ORF - retro_nleu_2313 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.0 %
Parental protein coverage: 99.2 %
Number of stop codons detected: 3
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalEEDSTALVCDNGSGLCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPI
E....ALV.DNGSG.CKA.F...DAPRAVF.SI.G..RH...MVGMGQ.DS..GDEAQSK.GILTLKYPI
RetrocopyEGEIVALVIDNGSGMCKARFPRNDAPRAVFSSIFGCLRH*SIMVGMGQ-DSHMGDEAQSKQGILTLKYPI
ParentalEHGIITNWDDMEKIWHHSFYNELRVAPEEHPTLLTEAPLN-PKANREKMTQIMFETFNVPAMYVAIQAVL
EH.IITNWDDM..IWH..FYN.LR.APEEHP.LLT.APLN.P....E....IMFE.FN..A.Y.AIQAVL
RetrocopyEHDIITNWDDMG-IWHLTFYNKLRMAPEEHPVLLTMAPLN>PRPT-ERR*LIMFEIFNTRAIYMAIQAVL
ParentalSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVR
SLY.S..TTGIV.DSGD.VTH.VPIYEGYALPH.I..LDLAGRDLT.YLMKILTE.GYSF.T.A..EIVR
RetrocopySLYTSRQTTGIVMDSGDWVTHTVPIYEGYALPHTILCLDLAGRDLTHYLMKILTECGYSFTTLAKWEIVR
ParentalDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYN
..KEKLCYVALDF..EMATAASSSSLEKSYEL..GQ.ITI.NE.FRC.E.LFQPSF..MES.GIHETT.N
RetrocopyNVKEKLCYVALDF*QEMATAASSSSLEKSYELSNGQLITICNEWFRCLEALFQPSFLSMESCGIHETTIN
ParentalSIMKCDIDIRKDLYANNVL-SGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASL
S.MK...DI.KDL........G.T.MYPGIADRMQKEI.ALAPSTMKIKIIAPPE.KYSVWIGGSILASL
RetrocopySFMKYKVDICKDLCQHGAV>GGTT-MYPGIADRMQKEIPALAPSTMKIKIIAPPEHKYSVWIGGSILASL
ParentalSTFQQMWISKQEYDEAGPSIVHRKCF
STFQQMWISKQEY.E.GPSIVH.KCF
RetrocopySTFQQMWISKQEYHESGPSIVHCKCF

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Nomascus leucogenys was not studied using ChIP-Seq data.

EST - click to see more details

Nomascus leucogenys was not studied using EST data.

TSS - click to see more details

Nomascus leucogenys was not studied using FANTOM5 data.

Lab - click to see more details

retro_nleu_2313 was not experimentally validated.

Retrocopy orthology:
Nomascus leucogenys 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 16 parental genes, and 46 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000007593 retrocopies
retro_chof_1909, retro_chof_2042, retro_chof_21,
Dasypus novemcinctus ENSDNOG000000067191 retrocopy
retro_dnov_32,
Echinops telfairi ENSETEG000000085261 retrocopy
retro_etel_41,
Macropus eugenii ENSMEUG000000108431 retrocopy
retro_meug_1374,
Myotis lucifugus ENSMLUG000000155093 retrocopies
retro_mluc_190, retro_mluc_427, retro_mluc_90,
Nomascus leucogenys ENSNLEG00000012233 1 retrocopy
retro_nleu_2313 ,
Nomascus leucogenys ENSNLEG0000001338515 retrocopies
retro_nleu_1008, retro_nleu_1058, retro_nleu_1059, retro_nleu_1150, retro_nleu_1347, retro_nleu_1474, retro_nleu_1729, retro_nleu_2193, retro_nleu_2393, retro_nleu_2574, retro_nleu_2669, retro_nleu_3032, retro_nleu_344, retro_nleu_813, retro_nleu_974,
Nomascus leucogenys ENSNLEG000000143471 retrocopy
retro_nleu_1585,
Nomascus leucogenys ENSNLEG000000151571 retrocopy
retro_nleu_2751,
Nomascus leucogenys ENSNLEG000000155063 retrocopies
retro_nleu_1525, retro_nleu_1536, retro_nleu_1930,
Oryctolagus cuniculus ENSOCUG000000081933 retrocopies
retro_ocun_1306, retro_ocun_1421, retro_ocun_919,
Pongo abelii ENSPPYG000000024591 retrocopy
retro_pabe_3027,
Sorex araneus ENSSARG000000057781 retrocopy
retro_sara_732,
Tupaia belangeri ENSTBEG000000176163 retrocopies
retro_tbel_1555, retro_tbel_3014, retro_tbel_4616,
Tarsius syrichta ENSTSYG000000081555 retrocopies
retro_tsyr_1282, retro_tsyr_2102, retro_tsyr_858, retro_tsyr_9, retro_tsyr_92,
Vicugna pacos ENSVPAG000000106213 retrocopies
retro_vpac_12, retro_vpac_355, retro_vpac_651,


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