RetrogeneDB ID:

retro_acar_185

Retrocopy
location
Organism:Anole lizard (Anolis carolinensis)
Coordinates:GL343389.1:554801..555354(-)
Located in intron of:ENSACAG00000005252
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:GNB2L1
Ensembl ID:ENSACAG00000012008
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_acar_185
AACCACCAGAATGTCTCTGGCTCCTGGGACAAAATCATCAAACTCTGGAACACTCTGGGTGTCTGCATGTACACTGTGCA
GCAGGAAAGGCACTCTGAGTGAGTGTCCTGTGTGCACTTCTCCCTCAACAGAAGCAACCCCATCATCGTCTCCTGTGGCT
GGAATAAGTTGGTGAAGGTGTGGAACTTGGCCAACTGTAAGCTGAACATATTGGGCACATTGGGCACATGAACACCATGA
CTGTCTCCCCTGATGGTTCCCTGTGTGCTTCAGGTGACAAAGTCAACCAGGCCATGCGATGGGACCTGAACGAAGGCAAG
CACCTGTACACGCTGGATGGTGGGGACATCATCAATGCCTGTGCTTCAGCCCCAACCACTACTGGCTCTGTGCGGCCACC
GGGCCCAGCATCAAGATCTGGGTCTTGCAAGGCATGATCATTGTGGATGAGCTGAAGCAGGAGGTGATCAGCACCAGCAG
CAAGGCAGAGCCTCCCCAGTGCACCCCATTGGTTTGATCAGCTGACAGACAGACCCTGTTTGCTGGATAAACA

ORF - retro_acar_185 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 79.89 %
Parental protein coverage: 58.99 %
Number of stop codons detected: 3
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalNRQIVSGSRDKTIKLWNTLGVCKYTVQDESHSEWVSCVRFSPNSSNPIIVSCGWDKLVKVWNLANCKLKT
N.Q.VSGS.DK.IKLWNTLGVC.YTVQ.E.HSE.VSCV.FS.N.SNPIIVSCGW.KLVKVWNLANC..K.
RetrocopyNHQNVSGSWDKIIKLWNTLGVCMYTVQQERHSE*VSCVHFSLNRSNPIIVSCGWNKLVKVWNLANC--KL
ParentalN-HIGHTGYLNTVTVSPDGSLCASGGKDGQAMLWDLNEGKHLYTLDGGDIINA-LCFSPNRYWLCAATGP
N.H.......NT.TVSPDGSLCASG.K..QAM.WDLNEGKHLYTLDGGDIINA.LCFSPN.YWLCAATGP
RetrocopyN<HXXXXXXXNTMTVSPDGSLCASGDKVNQAMRWDLNEGKHLYTLDGGDIINA<LCFSPNHYWLCAATGP
ParentalSIKIWDLEGKIIVDELKQEVISTSSKAEPPQCTSLAWSADGQTLFAGYT
SIKIW.L.G.IIVDELKQEVISTSSKAEPPQCT.L..SAD.QTLFAG.T
RetrocopySIKIWVLQGMIIVDELKQEVISTSSKAEPPQCTPLV*SADRQTLFAG*T

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
SRP009831_adrenal 0 .07 RPM 762 .59 RPM
SRP009831_brain 0 .24 RPM 118 .40 RPM
SRP009831_dewlap 0 .00 RPM 328 .17 RPM
SRP009831_embryo 0 .00 RPM 1099 .61 RPM
SRP009831_heart 0 .05 RPM 471 .92 RPM
SRP009831_liver 0 .00 RPM 760 .25 RPM
SRP009831_lung 0 .00 RPM 564 .28 RPM
SRP009831_ovary 0 .00 RPM 224 .58 RPM
SRP009831_skeletal_muscle 0 .00 RPM 330 .24 RPM

ChIP-Seq - click to see more details

Anolis carolinensis was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_acar_185 retrocopy.

TSS - click to see more details

Anolis carolinensis was not studied using FANTOM5 data.

Lab - click to see more details

retro_acar_185 was not experimentally validated.

Retrocopy orthology:
Anolis carolinensis 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 26 parental genes, and 37 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG00000012008 1 retrocopy
retro_acar_185 ,
Ailuropoda melanoleuca ENSAMEG000000000041 retrocopy
retro_amel_1627,
Bos taurus ENSBTAG000000196481 retrocopy
retro_btau_1461,
Canis familiaris ENSCAFG000000248181 retrocopy
retro_cfam_1824,
Callithrix jacchus ENSCJAG000000187521 retrocopy
retro_cjac_2876,
Cavia porcellus ENSCPOG000000087241 retrocopy
retro_cpor_687,
Dipodomys ordii ENSDORG000000107351 retrocopy
retro_dord_117,
Equus caballus ENSECAG000000225673 retrocopies
retro_ecab_172, retro_ecab_218, retro_ecab_986,
Erinaceus europaeus ENSEEUG000000087291 retrocopy
retro_eeur_368,
Echinops telfairi ENSETEG000000160243 retrocopies
retro_etel_1135, retro_etel_114, retro_etel_2086,
Homo sapiens ENSG000002046281 retrocopy
retro_hsap_3226,
Gorilla gorilla ENSGGOG000000253671 retrocopy
retro_ggor_2194,
Macropus eugenii ENSMEUG000000110553 retrocopies
retro_meug_1095, retro_meug_1109, retro_meug_1532,
Myotis lucifugus ENSMLUG000000155071 retrocopy
retro_mluc_811,
Macaca mulatta ENSMMUG000000036041 retrocopy
retro_mmul_1956,
Monodelphis domestica ENSMODG000000040911 retrocopy
retro_mdom_1426,
Mustela putorius furoENSMPUG000000011482 retrocopies
retro_mputfur_1103, retro_mputfur_1111,
Mus musculus ENSMUSG000000203721 retrocopy
retro_mmus_3282,
Nomascus leucogenys ENSNLEG000000026041 retrocopy
retro_nleu_729,
Ornithorhynchus anatinus ENSOANG000000026001 retrocopy
retro_oana_127,
Otolemur garnettii ENSOGAG000000149242 retrocopies
retro_ogar_1257, retro_ogar_1591,
Pongo abelii ENSPPYG000000199391 retrocopy
retro_pabe_149,
Pan troglodytes ENSPTRG000000227341 retrocopy
retro_ptro_2178,
Rattus norvegicus ENSRNOG000000023903 retrocopies
retro_rnor_1831, retro_rnor_2130, retro_rnor_895,
Ictidomys tridecemlineatus ENSSTOG000000070631 retrocopy
retro_itri_1752,
Tupaia belangeri ENSTBEG000000146612 retrocopies
retro_tbel_3897, retro_tbel_3899,


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