RetrogeneDB ID:

retro_cfam_1403

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:30:13466572..13466916(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:POLR2D
Ensembl ID:ENSCAFG00000004311
Aliases:None
Description:polymerase (RNA) II (DNA directed) polypeptide D [Source:HGNC Symbol;Acc:9191]


Retrocopy-Parental alignment summary:






>retro_cfam_1403
ACAGCTGAGACACTACTCAGTTCAGAAGTTCATATGCTTCTGAACAATTGAAAGCAACAGAATGAGAGTGCAGAGGATGA
ATAGGAACTGTCTGAGGTCTTCCTGAAAACTTTAAATTACACACAGCCCATTTCAGTTGTTTCAAAAATAGACTATTGCC
AGTGTCCATAGCTAGTTGCTCCAGAAAAAGCTTCATGAGTTTACATTGGCCTGTTTGGCCAGCCTTTGCCCAAAGAGCTG
CTGAGAAGTCAAAGGCCCTGATCCTAAGCCTGGAGGGGTGGTTTGAAGATGAGGAGCTACAGCAGATTCTTGATGATACC
TAGACCAAGTGTAGTTTTCAATAT

ORF - retro_cfam_1403 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.21 %
Parental protein coverage: 80.99 %
Number of stop codons detected: 5
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalTAETLLNSEVHMLLEHRKQQNESAEDEQELSEVFMKTLNYT-ARFSRFKNRETIASVRSLLLQKKLHKFE
TAETLL.SEVHMLL...KQQNESAEDE.ELSEVF.KTLNYT...F..F....TIASV.S.LLQKKLH.F.
RetrocopyTAETLLSSEVHMLLNN*KQQNESAEDE*ELSEVFLKTLNYT>SPFQLFQ-K*TIASVHS*LLQKKLHEFT
ParentalLACLANLCPET-AEESKALIPSLEGRFEDEELQQILDDIQTKRSFQY
LACLA.LCP...AE.SKALI.SLEG.FEDEELQQILDD..TK.SFQY
RetrocopyLACLASLCPKS>AEKSKALILSLEGWFEDEELQQILDDT*TKCSFQY

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
SRP012049_cerebellum 0 .00 RPM 18 .77 RPM
SRP017611_brain 0 .00 RPM 9 .05 RPM
SRP017611_kidney 0 .00 RPM 15 .25 RPM
SRP017611_liver 0 .00 RPM 3 .26 RPM

ChIP-Seq - click to see more details

Canis familiaris was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cfam_1403 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_1403 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_1403 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 17 parental genes, and 26 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000117461 retrocopy
retro_amel_1020,
Canis familiaris ENSCAFG00000004311 2 retrocopies
retro_cfam_1403 , retro_cfam_2188,
Choloepus hoffmanni ENSCHOG000000138503 retrocopies
retro_chof_1003, retro_chof_1568, retro_chof_1920,
Dasypus novemcinctus ENSDNOG000000085271 retrocopy
retro_dnov_734,
Felis catus ENSFCAG000000278161 retrocopy
retro_fcat_1148,
Gorilla gorilla ENSGGOG000000047231 retrocopy
retro_ggor_1658,
Macaca mulatta ENSMMUG000000019891 retrocopy
retro_mmul_1011,
Monodelphis domestica ENSMODG000000186534 retrocopies
retro_mdom_1320, retro_mdom_457, retro_mdom_689, retro_mdom_851,
Mustela putorius furoENSMPUG000000166851 retrocopy
retro_mputfur_611,
Mus musculus ENSMUSG000000242581 retrocopy
retro_mmus_1331,
Oryctolagus cuniculus ENSOCUG000000214491 retrocopy
retro_ocun_35,
Ochotona princeps ENSOPRG000000053272 retrocopies
retro_opri_233, retro_opri_725,
Pongo abelii ENSPPYG000000127591 retrocopy
retro_pabe_1933,
Pan troglodytes ENSPTRG000000124361 retrocopy
retro_ptro_1571,
Sorex araneus ENSSARG000000090371 retrocopy
retro_sara_420,
Sarcophilus harrisii ENSSHAG000000148171 retrocopy
retro_shar_728,
Ictidomys tridecemlineatus ENSSTOG000000233293 retrocopies
retro_itri_1323, retro_itri_145, retro_itri_600,


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