RetrogeneDB ID:

retro_cpor_152

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_0:33020671..33021141(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:IFT20
Ensembl ID:ENSCPOG00000003153
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cpor_152
CTGGCGCACTTCCCCCTGACCACTGCTGCCACCCCTTCAAGGCAGAACTTCTCCAGGGACCTGCAAGCGGAACAGTCACG
GCCAGAGACATCCTGGGTGAAGTGCGCCTGCACTTTGATGAGCTGAATAAGCTTCAAGTGCGGGACCCAGGCTACCTGTA
GACCACAGAGCTCTAGACAGAAGGCAAAGACTCTGTGGACAAAACCGGCCAGGTTCGGAAACCAGCTGGTAGCCCAACTG
GACTTGTGGACCAACTTGCAAAAAAAGTAGAGAACGAGAAGACAAAGGTCACTGGTGCGCAGAACTTGCTCAAATCTATA
GCAAAGCAGCAAGAATCCCAACAGCAGCAACTCCAGGCACTAACAGCAGAAAAGAAAATGTAGCTAGAAAGGTATCGAGT
TGAATATGAAGCTTTGGGAAAAGCAGAAACAGAACAAAAGTAATTTACTGGCCAATTTGTTTTGCAGAAA

ORF - retro_cpor_152 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 62.89 %
Parental protein coverage: 100. %
Number of stop codons detected: 4
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMTHLLLTATVTPSEQNFPRE-PRRETAMAKDILGEAGLHFDELNKLRVLDPEVTQQTIELKEECKDFVDK
..H..LT...TPS.QNF.R..P...T..A.DILGE..LHFDELNKL.V.DP.....T.EL..E.KD.VDK
RetrocopyLAHFPLTTAATPSRQNFSRD<PASGTVTARDILGEVRLHFDELNKLQVRDPGYL*TT-EL*TEGKDSVDK
ParentalIGQFQKIVGGLIELVDQLAKEAENEKMKAIGARNLLKSIAKQREAQQQQLQALIAEKKMQLERYRVEYEA
.GQ..K..G....LVDQLAK..ENEK.K..GA.NLLKSIAKQ.E.QQQQLQAL.AEKKM.LERYRVEYEA
RetrocopyTGQVRKPAGSPTGLVDQLAKKVENEKTKVTGAQNLLKSIAKQQESQQQQLQALTAEKKM*LERYRVEYEA
ParentalLCKVEAEQNEFIDQFIFQK
L.K.E.EQ..F..QF..QK
RetrocopyLGKAETEQK*FTGQFVLQK

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
SRP017611_brain 0 .00 RPM 14 .09 RPM
SRP017611_kidney 0 .00 RPM 20 .73 RPM
SRP017611_liver 0 .00 RPM 11 .71 RPM
SRP040447_lung 0 .00 RPM 12 .71 RPM
SRP040447_skeletal_muscle 0 .00 RPM 3 .92 RPM

ChIP-Seq - click to see more details

Cavia porcellus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cpor_152 retrocopy.

TSS - click to see more details

Cavia porcellus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cpor_152 was not experimentally validated.

Retrocopy orthology:
Cavia porcellus 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 22 parental genes, and 37 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000051112 retrocopies
retro_amel_1011, retro_amel_1337,
Bos taurus ENSBTAG000000081101 retrocopy
retro_btau_257,
Callithrix jacchus ENSCJAG000000125342 retrocopies
retro_cjac_2404, retro_cjac_687,
Cavia porcellus ENSCPOG00000003153 1 retrocopy
retro_cpor_152 ,
Echinops telfairi ENSETEG000000188432 retrocopies
retro_etel_1045, retro_etel_1181,
Homo sapiens ENSG000001090831 retrocopy
retro_hsap_1314,
Gorilla gorilla ENSGGOG000000045682 retrocopies
retro_ggor_1026, retro_ggor_1217,
Microcebus murinus ENSMICG000000050741 retrocopy
retro_mmur_987,
Myotis lucifugus ENSMLUG000000087092 retrocopies
retro_mluc_180, retro_mluc_1924,
Macaca mulatta ENSMMUG000000191432 retrocopies
retro_mmul_2165, retro_mmul_2234,
Monodelphis domestica ENSMODG000000192331 retrocopy
retro_mdom_681,
Mustela putorius furoENSMPUG000000143531 retrocopy
retro_mputfur_247,
Mus musculus ENSMUSG000000011051 retrocopy
retro_mmus_3245,
Nomascus leucogenys ENSNLEG000000018832 retrocopies
retro_nleu_1067, retro_nleu_1941,
Oryctolagus cuniculus ENSOCUG000000077731 retrocopy
retro_ocun_438,
Otolemur garnettii ENSOGAG000000033332 retrocopies
retro_ogar_1169, retro_ogar_72,
Ochotona princeps ENSOPRG000000058266 retrocopies
retro_opri_110, retro_opri_1185, retro_opri_205, retro_opri_293, retro_opri_375, retro_opri_872,
Pongo abelii ENSPPYG000000080872 retrocopies
retro_pabe_1097, retro_pabe_1322,
Pan troglodytes ENSPTRG000000089111 retrocopy
retro_ptro_1079,
Sus scrofa ENSSSCG000000237191 retrocopy
retro_sscr_315,
Ictidomys tridecemlineatus ENSSTOG000000075541 retrocopy
retro_itri_713,
Tupaia belangeri ENSTBEG000000055572 retrocopies
retro_tbel_180, retro_tbel_1954,


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