RetrogeneDB ID:

retro_lcha_108

Retrocopy
location
Organism:Coelacanth (Latimeria chalumnae)
Coordinates:JH128490.1:116697..118215(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSLACG00000004282
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:aldh2.2
Ensembl ID:ENSLACG00000011798
Aliases:None
Description:aldehyde dehydrogenase 2, tandem duplicate 2 [Source:ZFIN;Acc:ZDB-GENE-030326-5]


Retrocopy-Parental alignment summary:






>retro_lcha_108
TCTCTGCAGAAGTTTGCAGCCCCATATTCAACTGCAGCTTTGCCAAATCCCATAACGAAACCTGATGTCCACTACACCAA
ATTATTCATCAGTAATGAATGGCGTGATGCTGTGAGTGGAAAAACATTTCCAACTTTCAACCCTACAACTGGAGATATAA
TTACTCATGTTGCAGAGGGAGATAAAGCTGATGTTGACTTAGCTGTAAAAGCAGCAAGAGATGCCTTCAAGTTAGGGTCA
CCATGGCGTCGCATGGATGCATCTCATCGTGGGCTGCTGTTACACCGCCTGGCTGATCTTGTTGAACGAGACAGTGTCTA
CTTGGCTTCTTTAGAGACACTGGACAATGGAAAACCTTTTACAGAGTCATATCCTTTGGATTTAGATGAGGTAGTTAAAG
TCTATCGATACTTTGCTGGCTGGGCTGACAAGTGCCATGGAAAGACTATACCCATGGATGGTGATTTCTTTTGTTTTACC
AGGCATGAACCTGTTGGTGTCTGTGGCCAAATTATTCCATGGAATTTTCCCTTGGTCATGCAGGCATGGAAACTGGGACC
TGCCCTGGCTACAGGGAATACTGTAGTCATGAAGATTGCTGAACAGACTCCATTGACAGCCTTACACTTAGCTTCACTGA
TTAAAGAAGCAGGCTTCCCTCCAGGTGTGGTCAATATCATTACTGGTTATGGGTCCACAGCTGGTGCAGCTGTTGCAAGA
CACATGGATGTTGACAAAGTAGCTTTCACAGGGTCTACTGAGGTTGGTCGGTTGATTCAGAAGACAGCTGGTAAATCCAA
CCTTAAGAGGGTTACTTTAGAGCTGGGTGGAAAAAGCCCAAGTATTGTCTTGGCTGATGCAGATATGGAACAAGCAGTAC
AAGAATGTCATGAAGCACTATTTTTCAATATGGGCCAGTGTTGCTGTGCAGGGTCTCGCACTTTTGTTGAGGAATCCATT
TATAATGAGTTCCTTGAAAGGACCATAGAGAAGGCAAAAGAGAGAAAAGTAGGAAACCCCTTTGAGCTAGACACAAAGCA
AGGGCCTCAAATTAGCAAGCAGCAGTTTGACAAAATTCTGGGCTACATTCAGATTGGCAAAAAAGAAGGTGCCAAGCTAA
TGTGTGGAGGAGAACGGTTTGGAGAGAAGGGTTTCTTTATCAAGCCAACTGTGTTTGGAGATGTACAGGATGAAATGAAA
ATTGCAAAAGAAGAAATCTTTGGCCCAGTGCAGCCAGTCTTCAAATTCAAAAAGATTGATGAGGTGATTCAGAGAGCCAA
CACCACCAGATATGGGCTAGCAGCAGCAGTGTTTACACGAGATCTTGATAAAGCAATGTATGTCACTCAAGCACTGCAGG
CTGGCACAGTGTGGGTAAACACATACAACATTGTGGCATACCATGCACCATTTGGAGGCTTCAAAGAATCTGGAAATGGA
AGGGAGCTTGGAGAATATGGTCTTGAAGCATACAGAGAAGTGAAAACTATAACAATCAAGATTCCTCAGAAGAGCTCC

ORF - retro_lcha_108 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 70.61 %
Parental protein coverage: 96.37 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalSLNRFSA--AAAAIPTPNPQQEVYFNKIFINNEWHDAVSKKTLPSINPATGEVICQVAEGDKADVDKAVK
SL..F.A....AA.P.P.....V...K.FI.NEW.DAVS.KT.P..NP.TG..I..VAEGDKADVD.AVK
RetrocopySLQKFAAPYSTAALPNPITKPDVHYTKLFISNEWRDAVSGKTFPTFNPTTGDIITHVAEGDKADVDLAVK
ParentalAARNAFKLGSPWRRMDASERGVLLNRLADLIERDRTYLATLEALDNGKPYAVAYAVDLNMVVKCLRYYAG
AAR.AFKLGSPWRRMDAS.RG.LL.RLADL.ERD..YLA.LE.LDNGKP....Y..DL..VVK..RY.AG
RetrocopyAARDAFKLGSPWRRMDASHRGLLLHRLADLVERDSVYLASLETLDNGKPFTESYPLDLDEVVKVYRYFAG
ParentalWADKCHGKTIPMDGDFFCYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVIVMKVAEQTPLTALYV
WADKCHGKTIPMDGDFFC.TRHEPVGVCGQIIPWNFPL.MQAWKLGPALATGN..VMK.AEQTPLTAL..
RetrocopyWADKCHGKTIPMDGDFFCFTRHEPVGVCGQIIPWNFPLVMQAWKLGPALATGNTVVMKIAEQTPLTALHL
ParentalANLIKEAGFPPGVVNIIPGFGPTAGAAIASHMDVDKVAFTGSTEVGHLIQKAAGGSNLKRITLELGGKSP
A.LIKEAGFPPGVVNII.G.G.TAGAA.A.HMDVDKVAFTGSTEVG.LIQK.AG.SNLKR.TLELGGKSP
RetrocopyASLIKEAGFPPGVVNIITGYGSTAGAAVARHMDVDKVAFTGSTEVGRLIQKTAGKSNLKRVTLELGGKSP
ParentalNIIMSDADMDYAVEQAHFALFFNQGQCCCAGSRTYVQDSIYDEFLERSVERAKARVVGNPFDLNTEQGPQ
.I...DADM..AV...H.ALFFN.GQCCCAGSRT.V..SIY.EFLER..E.AK.R.VGNPF.L.T.QGPQ
RetrocopySIVLADADMEQAVQECHEALFFNMGQCCCAGSRTFVEESIYNEFLERTIEKAKERKVGNPFELDTKQGPQ
ParentalIDEEQFQKILGYISTGKREGAKLLCGGGVAADRGYFILFFFFFNLHKGQKVQIVSLIFGPVMQVLKFKSI
I...QF.KILGYI..GK.EGAKL.CGG......G.FI....F.......K......IFGPV..V.KFK.I
RetrocopyISKQQFDKILGYIQIGKKEGAKLMCGGERFGEKGFFIKPTVFGDVQDEMKI-AKEEIFGPVQPVFKFKKI
ParentalEEVIERANDTQYGLAAAVFTRDLDKANYVSQGLRAGTVWINCYDVFGAQSPFGGYKTSGNGRELGEYGLE
.EVI.RAN.T.YGLAAAVFTRDLDKA.YV.Q.L.AGTVW.N.Y.......PFGG.K.SGNGRELGEYGLE
RetrocopyDEVIQRANTTRYGLAAAVFTRDLDKAMYVTQALQAGTVWVNTYNIVAYHAPFGGFKESGNGRELGEYGLE
ParentalAYTEVKTVTIKVPQKNS
AY.EVKT.TIK.PQK.S
RetrocopyAYREVKTITIKIPQKSS

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






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
DRP000627_gill 1 .33 RPM 96 .31 RPM
DRP000627_kidney 1 .28 RPM 70 .91 RPM
DRP000627_pectoral_fin 0 .08 RPM 37 .72 RPM
DRP000627_pelvic_fin 0 .17 RPM 112 .70 RPM
DRP000627_pharynx 2 .90 RPM 185 .66 RPM
DRP000627_tail_muscle 1 .34 RPM 145 .83 RPM

ChIP-Seq - click to see more details

Latimeria chalumnae was not studied using ChIP-Seq data.

EST - click to see more details

Latimeria chalumnae was not studied using EST data.

TSS - click to see more details

Latimeria chalumnae was not studied using FANTOM5 data.

Lab - click to see more details

retro_lcha_108 was not experimentally validated.

Retrocopy orthology:
Latimeria chalumnae 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 21 parental genes, and 22 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000136641 retrocopy
retro_amel_51,
Bos taurus ENSBTAG000000087431 retrocopy
retro_btau_48,
Canis familiaris ENSCAFG000000086831 retrocopy
retro_cfam_1493,
Equus caballus ENSECAG000000176732 retrocopies
retro_ecab_1054, retro_ecab_1061,
Felis catus ENSFCAG000000220001 retrocopy
retro_fcat_1590,
Homo sapiens ENSG000001112751 retrocopy
retro_hsap_19,
Gorilla gorilla ENSGGOG000000071081 retrocopy
retro_ggor_33,
Latimeria chalumnae ENSLACG00000011798 1 retrocopy
retro_lcha_108 ,
Microcebus murinus ENSMICG000000034871 retrocopy
retro_mmur_19,
Myotis lucifugus ENSMLUG000000170841 retrocopy
retro_mluc_1918,
Macaca mulatta ENSMMUG000000083361 retrocopy
retro_mmul_247,
Mustela putorius furoENSMPUG000000022821 retrocopy
retro_mputfur_27,
Mus musculus ENSMUSG000000294551 retrocopy
retro_mmus_222,
Nomascus leucogenys ENSNLEG000000000161 retrocopy
retro_nleu_22,
Otolemur garnettii ENSOGAG000000330931 retrocopy
retro_ogar_203,
Pongo abelii ENSPPYG000000049661 retrocopy
retro_pabe_32,
Pteropus vampyrus ENSPVAG000000131891 retrocopy
retro_pvam_163,
Rattus norvegicus ENSRNOG000000013441 retrocopy
retro_rnor_307,
Sus scrofa ENSSSCG000000098891 retrocopy
retro_sscr_9,
Ictidomys tridecemlineatus ENSSTOG000000150091 retrocopy
retro_itri_33,
Xenopus tropicalis ENSXETG000000209301 retrocopy
retro_xtro_12,


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