RetrogeneDB ID:

retro_mmus_3245

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:9:12233993..12234373(+)
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:ENSMUSG00000001105
Aliases:Ift20, 0610009H04Rik, AU015496
Description:intraflagellar transport 20 [Source:MGI Symbol;Acc:MGI:1915585]


Retrocopy-Parental alignment summary:






>retro_mmus_3245
ATCTTGGCCAAGGCAGGGCTGCACTTTGATGAGCTGACAAGCTTCAGGTATTGGACCCAGAGGTTACCCAGAAGACCATA
GAGCTCAAGGAAGAGTGCCAGGATTTTGCGGACAACATTGGCCAGTTTCAGAAAACTGTTTTTGATCTAACTGAGCATAT
TAATCAGTTTGACAAAGAAGCAGAGAATGAGAAGGTGAAGGCCATTGGTGCTCAGAACTTGCTGAAATCTATAGTGAAGC
AGAGAGAAGGCCAACTGCAGCAACTGCGAGCACTGTTAGCAGAAAAGATGCAGCTAGAAAGGTATCAGGTGGAATATGAA
GCTTTGTGTAAAGTAGAAGCAGAACAAAGTGAATTTATTGACCAATTTATTTTTCAGAAA

ORF - retro_mmus_3245 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.74 %
Parental protein coverage: 96.97 %
Number of stop codons detected: 0
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalILGEAGLHFDEL-NKLRVLDPEVTQQTVELKEECKDFVDKIGQFQKIVGGLIELVDQLAKEAENEKMKAI
IL..AGLHFDEL..KL.VLDPEVTQ.T.ELKEEC.DF.D.IGQFQK.V..L.E...Q..KEAENEK.KAI
RetrocopyILAKAGLHFDEL<DKLQVLDPEVTQKTIELKEECQDFADNIGQFQKTVFDLTEHINQFDKEAENEKVKAI
ParentalGARNLLKSIAKQREAQQQQLQALIAEKKTQLERYRVEYEALCKVEAEQNEFIDQFIFQK
GA.NLLKSI.KQRE.Q.QQL.AL.AE.K.QLERY.VEYEALCKVEAEQ.EFIDQFIFQK
RetrocopyGAQNLLKSIVKQREGQLQQLRALLAE-KMQLERYQVEYEALCKVEAEQSEFIDQFIFQK

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 0 .00 RPM 32 .40 RPM
SRP007412_cerebellum 0 .00 RPM 31 .18 RPM
SRP007412_heart 0 .00 RPM 23 .41 RPM
SRP007412_kidney 0 .00 RPM 28 .47 RPM
SRP007412_liver 0 .00 RPM 30 .15 RPM
SRP007412_testis 0 .00 RPM 35 .04 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_mmus_3245 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_3245 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_mmus_3245 retrocopy 5' end.

Lab - click to see more details

retro_mmus_3245 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_3245 has 0 orthologous retrocopies within eutheria group .

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 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 ENSMUSG00000001105 1 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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