RetrogeneDB ID:

retro_pabe_1097

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:14:30638059..30638445(+)
Located in intron of:ENSPPYG00000005722
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:IFT20
Ensembl ID:ENSPPYG00000008087
Aliases:None
Description:intraflagellar transport 20 homolog (Chlamydomonas) [Source:HGNC Symbol;Acc:30989]


Retrocopy-Parental alignment summary:






>retro_pabe_1097
ATGACACACCTCCTCCTGACTGTCACTGTCACTCCTTCAGAGCAGAGCTTCTCTAGGGAACCTGGATGGGAAACAACTAT
GGTAAAGGACATCCTGGGTGAAGAGGGATTGCACTTTGATGAGTTGAACAAGCTGTGGGTGTTGGACTCAGAGGTTACCC
AGCAGACCATAGAGCTCAAAGAAGAGTGTAAGAACTTTGTGGACAAAACTGGCCAGTTTCAGAAAACAGTTGGTGGTTTA
ATTGAGCTTGTTGATCAACTTGCAAAATAAGCAGAAAATGAGAAGATGAAGGCTATGGTGCTCAGAACTTGCTCAAATCA
ATAGCAAAGCAGAGAGAAGCTCAACAACTTAGAACTCAGTAACTTCAAGCACTAACAGAAGAAAAA

ORF - retro_pabe_1097 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.85 %
Parental protein coverage: 79.75 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMTHLLLTATVTPSEQNSSREPGWETAMAKDILGEAGLHFDELNKLRVLDPEVTQQTIELKEECKDFVDKI
MTHLLLT.TVTPSEQ..SREPGWET.M.KDILGE.GLHFDELNKL.VLD.EVTQQTIELKEECK.FVDK.
RetrocopyMTHLLLTVTVTPSEQSFSREPGWETTMVKDILGEEGLHFDELNKLWVLDSEVTQQTIELKEECKNFVDKT
ParentalGQFQKIVGGLIELVDQLAKEAENEKMKAI-GARNLLKSIAKQREAQQ---QQLQALIAEK
GQFQK.VGGLIELVDQLAK.AENEKMKA..GA.NLLKSIAKQREAQQ...Q.LQAL..EK
RetrocopyGQFQKTVGGLIELVDQLAK*AENEKMKAM<GAQNLLKSIAKQREAQQLRTQ*LQALTEEK

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
SRP007412_brain_prefrontal_cortex 0 .11 RPM 13 .60 RPM
SRP007412_cerebellum 0 .00 RPM 22 .98 RPM
SRP007412_heart 0 .09 RPM 3 .46 RPM
SRP007412_kidney 0 .03 RPM 10 .31 RPM
SRP007412_liver 0 .09 RPM 13 .19 RPM

ChIP-Seq - click to see more details

Pongo abelii was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_pabe_1097 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_1097 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_1097 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_1314
Gorilla gorilla retro_ggor_1026
Macaca mulatta retro_mmul_2165
Callithrix jacchus retro_cjac_687
Parental genes homology:
Parental genes homology involve 21 parental genes, and 36 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 ENSCPOG000000031531 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 ENSPPYG00000008087 2 retrocopies
retro_pabe_1097 , retro_pabe_1322,
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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