RetrogeneDB ID:

retro_cfam_1611

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:37:19505627..19506235(+)
Located in intron of:ENSCAFG00000023258
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPF2
Ensembl ID:ENSCAFG00000003918
Aliases:RPF2, BXDC1
Description:ribosome production factor 2 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:20870]


Retrocopy-Parental alignment summary:






>retro_cfam_1611
ATTACAAGACCATTTGAGGATCAGACATCATTGGAATTCTTTTCAAAGAAGTCAGATTGTTCTTTATTTATGTTTGGTTC
CCACAGTAAAGAAGTGGTCATATAATCTAGTAATAGTTCGCATATATGACTACCATGTGCTGGATATGATTGAATTAGGT
ATTGGGAAGTTTGCCTCTCTAAAAGATATTAAGAATAGTAAATGTCCCAAGGGAAAAACACCCACATTAATATTTGCTGG
TGATGATTTTGATGAAAGAGAAGACTAGAGAAGGCTGAAAATTCTTCCTATTGATTTCTTCGAAGCCCCACTGTAACAAA
TATCCATCTGGCTGGTTTAGAATATGTTCTGCACTTCTCTGCACTGAATGGGAAGATTTATTTCCAAAGCTATAAGTTGG
TGTTGAAGAAATCTGGTTGCAGAACACCAAGGATCAAATTGGAAGAGATGGGGCCTTCGTTGGATCTGGTTCTGAGGAGG
ACACATCTGGCAGTAGATGATCTTTAGAAATTATCTATGAAAATGCCAAAACCCTCAAGCCAAAGAAGAAGAAAAATGTC
TCCCATGATACTTTTGGCACAACTTACAGAAGGATTCATATGCAGAAG

ORF - retro_cfam_1611 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.5 %
Parental protein coverage: 66.34 %
Number of stop codons detected: 2
Number of frameshifts detected: 3


Retrocopy - Parental Gene Alignment:

ParentalITRPFEDQTSLEFFSKKSDCSLFMFGSHNK-KRPNNLVIGRMYDYHVLDMIELGIEKFVSLKDVKNSKCP
ITRPFEDQTSLEFFSKKSDCSLFMFGSH.K.K...NLVI.R.YDYHVLDMIELGI.KF.SLKD.KNSKCP
RetrocopyITRPFEDQTSLEFFSKKSDCSLFMFGSHSK>KWSYNLVIVRIYDYHVLDMIELGIGKFASLKDIKNSKCP
ParentalEGTKPMLIFAGDDFDVTEDYRRLKNLLIDFF-RGPTVSNIRLAGLEYVLHFTALNGKIYFRSYKLLLKKS
.G..P.LIFAGDDFD..ED.RRLK.L.IDFF.R.PTV.NI.LAGLEYVLHF.ALNGKIYF.SYKL.LKKS
RetrocopyKGKTPTLIFAGDDFDERED*RRLKILPIDFF<RSPTVTNIHLAGLEYVLHFSALNGKIYFQSYKLVLKKS
ParentalGCRTPRIELEEMGLSLDLVLRRTRLASDDLYKLSMKMP-KALKPKKKKNVSHDTFGTTYGRIHMQK
GCRTPRI.LEEMG.SLDLVLRRT.LA.DDL.KLSMKMP.K.LKPKKKKNVSHDTFGTTY.RIHMQK
RetrocopyGCRTPRIKLEEMGPSLDLVLRRTHLAVDDL*KLSMKMP<KTLKPKKKKNVSHDTFGTTYRRIHMQK

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 12 .43 RPM
SRP017611_brain 0 .00 RPM 15 .24 RPM
SRP017611_kidney 0 .00 RPM 35 .73 RPM
SRP017611_liver 0 .00 RPM 9 .28 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_1611 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_1611 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_1611 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 17 parental genes, and 37 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG00000003918 2 retrocopies
retro_cfam_1611 , retro_cfam_903,
Callithrix jacchus ENSCJAG000000052126 retrocopies
retro_cjac_1675, retro_cjac_1768, retro_cjac_2244, retro_cjac_2473, retro_cjac_606, retro_cjac_933,
Cavia porcellus ENSCPOG000000067972 retrocopies
retro_cpor_332, retro_cpor_582,
Equus caballus ENSECAG000000171211 retrocopy
retro_ecab_782,
Erinaceus europaeus ENSEEUG000000061692 retrocopies
retro_eeur_454, retro_eeur_584,
Felis catus ENSFCAG000000015271 retrocopy
retro_fcat_1584,
Homo sapiens ENSG000001974981 retrocopy
retro_hsap_2425,
Gorilla gorilla ENSGGOG000000014691 retrocopy
retro_ggor_83,
Myotis lucifugus ENSMLUG000000056762 retrocopies
retro_mluc_485, retro_mluc_921,
Macaca mulatta ENSMMUG000000215321 retrocopy
retro_mmul_1903,
Mus musculus ENSMUSG000000385101 retrocopy
retro_mmus_2234,
Nomascus leucogenys ENSNLEG000000128543 retrocopies
retro_nleu_2024, retro_nleu_2434, retro_nleu_2445,
Oryctolagus cuniculus ENSOCUG000000160281 retrocopy
retro_ocun_831,
Pongo abelii ENSPPYG000000169252 retrocopies
retro_pabe_1788, retro_pabe_2464,
Pan troglodytes ENSPTRG000000185031 retrocopy
retro_ptro_1398,
Rattus norvegicus ENSRNOG000000005871 retrocopy
retro_rnor_2336,
Tupaia belangeri ENSTBEG000000171519 retrocopies
retro_tbel_1824, retro_tbel_2243, retro_tbel_2376, retro_tbel_2576, retro_tbel_3547, retro_tbel_3635, retro_tbel_3803, retro_tbel_3876, retro_tbel_4509,


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