RetrogeneDB ID:

retro_nleu_2900

Retrocopy
location
Organism:Gibbon (Nomascus leucogenys)
Coordinates:GL397478.1:357356..358381(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CRLF3
Ensembl ID:ENSNLEG00000005850
Aliases:None
Description:cytokine receptor-like factor 3 [Source:HGNC Symbol;Acc:17177]


Retrocopy-Parental alignment summary:






>retro_nleu_2900
ACAAAGGATGTTCTCAAATAGCATTTTAATGATTTAAAGGGAACCCTTGAGGAGCTCCTGGATGAGTGATCGGTGACCTT
TTAGCAAGAGGTGGACATCATTGAGCAGGAGACCATTAAACCATTAGATGACTGCCAGAGGCTCATAGAACACGGAGTCA
ACACTGCAGAGGACTTAGTCTGAGTAGGTGAGATTGCCATGGTTGGTAGTGTAGAAGAGAATGAGAAACTGTATCGCTTT
ACCAAAAAGGTCTCACACATTCAGTTGGACAGCTTACCAGAAGTACCTTTACTGGTTGATGTGCTTTGTTTATCTGCTCA
GTTAGATGACTCAATTCTTAGAGTAAAAGACTACATTTCTAAGCATGGAACAGTAGCATCTCTCTCACCAGTACAGATAT
AATAAGAACTGATACAGAAACCTGAAGTCATCACAGTACGATGGTGTAAGGTGGATGATGATTTTACAGCCCAAGATTAC
AGGCTCTAATTTTGTAAACGTACTTCAAATCATTATGAGGATGTACATGTAGGTTCTGAAACTCAATTCATAGTATTGCA
CATAGACTCCAATGTTGATTATCAGTTCAAAGTCTGCACCTGAGGAGATGGTCAACAGGAGTGGAGCCCTGAAGTGTCCC
CCAGATAGGTCATTTCACATTGGTGCCTCATGAGTGGACAGCTGGTTTGGTGGGGTACAGTCTGAAAATCAAAGTAATAT
TGCATTCTGGAATGATTCTCAGTCCTCAGGTGTTCTCTACTCTAGAACTCCAACTTATTTCTGTGGGCAGACATTAACAT
TCAGAGTTGCAACTGTGGGACAGAAGAGACAGTATGGGGTGTTTGCAGAAAAACAGAATGGAAACGACTCTGTGCAGCAG
GATCAAGCTATATGTATGAGTACAAATGGTGAAGTTTTTGTTAATGGAAAAGAAATGACTAATGAGTTAACCTGTTACTT
CTGGGTCCACTGTCACATTTGACATTGAAGCTGTCACTCTAGGAACTACCAATAATAATGAAGGC

ORF - retro_nleu_2900 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.49 %
Parental protein coverage: 92.29 %
Number of stop codons detected: 8
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalTRDVLKQHFNDLKGTLGKLLDERLVTLLQEVDTIEQETIKPLDDCQKLIEHGVNTAEDLVREGEIAMLGG
T.DVLK.HFNDLKGTL..LLDE..VT..QEVD.IEQETIKPLDDCQ.LIEHGVNTAEDLV..GEIAM.G.
RetrocopyTKDVLK*HFNDLKGTLEELLDE*SVTF*QEVDIIEQETIKPLDDCQRLIEHGVNTAEDLV*VGEIAMVGS
ParentalVGEENEKLWSFTKKASHIQLDSLPEVPLLVDVPCLSAQLDDSILNIVKDHIFKHGTVASRPPVQI-EELI
V.EENEKL..FTKK.SHIQLDSLPEVPLLVDV.CLSAQLDDSIL..VKD.I.KHGTVAS..PVQI..ELI
RetrocopyV-EENEKLYRFTKKVSHIQLDSLPEVPLLVDVLCLSAQLDDSILR-VKDYISKHGTVASLSPVQI**ELI
ParentalEKPGGIIVRWCKVDDDFTAQDYRLQFRKCTSNHFEDVYVGSETEFIVLHIDPNVDYQFRVCARGDGRQEW
.KP..I.VRWCKVDDDFTAQDYRL.F.K.TSNH.EDV.VGSET.FIVLHID.NVDYQF.VC..GDG.QEW
RetrocopyQKPEVITVRWCKVDDDFTAQDYRL*FCKRTSNHYEDVHVGSETQFIVLHIDSNVDYQFKVCT*GDGQQEW
ParentalSPW-SVPQIGHSTLVPHEWTAGFEGYSL-SSRRNIALRNDSESSGVLYSRAPTYFCGQTLTFRVETVGQP
SP..SVPQIGH.TLVPHEWTAG..GYSL.....NIA..NDS.SSGVLYSR.PTYFCGQTLTFRV.TVGQ.
RetrocopySPE<SVPQIGHFTLVPHEWTAGLVGYSL<ENQSNIAFWNDSQSSGVLYSRTPTYFCGQTLTFRVATVGQ-
ParentalDRRDSIGVCAEKQDGYDSLQRDQAVCISTNGAVFVNGKEMTNQL-PAVTSGSTVTFDIEAVTLGTTSNNE
......GV.AEKQ.G.DS.Q.DQA.C.STNG.VFVNGKEMTN.L.P....GSTVTFDIEAVTLGTT.NNE
Retrocopy--KRQYGVFAEKQNGNDSVQQDQAICMSTNGEVFVNGKEMTNEL>PVTS-GSTVTFDIEAVTLGTTNNNE
ParentalG
G
RetrocopyG

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






Nomascus leucogenys was not studied using RNA-Seq expression data.
Nomascus leucogenys was not studied using ChIP-Seq data.
Nomascus leucogenys was not studied using EST data.
Nomascus leucogenys was not studied using FANTOM5 data.
retro_nleu_2900 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 8 parental genes, and 19 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000141631 retrocopy
Homo sapiens ENSG000001763903 retrocopies
Gorilla gorilla ENSGGOG000000050023 retrocopies
Macaca mulatta ENSMMUG000000090692 retrocopies
Mus musculus ENSMUSG000000175611 retrocopy
Nomascus leucogenys ENSNLEG00000005850 4 retrocopies
Pongo abelii ENSPPYG000000081423 retrocopies
Pan troglodytes ENSPTRG000000089632 retrocopies



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