RetrogeneDB ID:

retro_cfam_1696

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:4:42463594..42464261(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL5
Ensembl ID:ENSCAFG00000020150
Aliases:None
Description:ribosomal protein L5 [Source:HGNC Symbol;Acc:10360]


Retrocopy-Parental alignment summary:






>retro_cfam_1696
ATGATAGTTTGTGCAGCTTATGCTTATGAACTCCCAAAGTATGGTATGAAGGTTGGCATGACAAATCATAATGCAGCATA
TTATACCAGCCTGATGCTGGCCCACAGACTTTTCAACAGGTTTGGCATAGACAAGTTCTATGAAGGCCAATCGGAGTGAC
CAGAGATGAATACAATATGGAAAGCTCTGATGATCAACCTGGTGCCTTCACCGGCTATTTGGATGCAAGGTGTCTTAGAA
CTACTACTGGAAATAAAGTTCTTGGGGCCCTCAAGGGAGCTGTGGATGGAGGCTTGTCTACCCATTACAGTACCAAATGA
TTCCTTAGTTGTGATTGAGAAAGCAAGGAATTAAATGCATAAGTACATTGGAAGTACATTATGGATCAGAATGTTACAGA
TTATATGCATTACCTAATAGAAGTAGACGCTTATAAGAAACAATTATCTCAATACATGAACAACAGAGTAACTCCAGACA
TGATGGAGAACATGTTTAAGAAAGCTCACACTGTTATATGAGAGAATCCAGGCTATGAGAAGAAGCCTAAGAAAGAAGTA
AAAAGTAAAGGTGGAACTGTCCCAGAATGTCTCTTGCTCAGAAGAAAGACTGGATAGATCAGAAGAAAATAAGCTTCCTT
AGAGCTCAAGAGTGGGCTGGTGAGAGC

ORF - retro_cfam_1696 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.69 %
Parental protein coverage: 75.76 %
Number of stop codons detected: 4
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYEGQVE-VTGDEYNVESIDGQPGA
MIVCAAYA.ELPKYG.KVG.TN..AAY.T.L.LA.RL.NRFG.DK.YEGQ.E.VT.DEYN.ES.D.QPGA
RetrocopyMIVCAAYAYELPKYGMKVGMTNHNAAYYTSLMLAHRLFNRFGIDKFYEGQSE<VTRDEYNMESSDDQPGA
ParentalFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRFPGYDSESKEFNAEVHRKHIMGQNVADYMRYL
FT.YLDA...RTTTGNKV.GALKGAVDGGLS...STK.F...D.ESKE.NA.VH.K.IM.QNV.DYM.YL
RetrocopyFTGYLDARCLRTTTGNKVLGALKGAVDGGLSTHYSTK*FLSCD*ESKELNA*VHWKYIMDQNVTDYMHYL
ParentalMEEDEDAYKKQFSQYIKNNVTPDMMEEMYKKAHAAIRENPVYEKKPKKEVKKK-RWNRPKMSLAQKKDRV
.E...DAYKKQ.SQY..N.VTPDMME.M.KKAH..I.ENP.YEKKPKKEVK.K.RWN.P.MSLAQKKD..
RetrocopyIE--VDAYKKQLSQYMNNRVTPDMMENMFKKAHTVI*ENPGYEKKPKKEVKSK<RWNCPRMSLAQKKDWI
ParentalAQKKASFLRAQERAAES
.QKK.SFLRAQE.A.ES
RetrocopyDQKKISFLRAQEWAGES

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(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 296 .85 RPM
SRP017611_brain 0 .00 RPM 121 .23 RPM
SRP017611_kidney 0 .00 RPM 549 .17 RPM
SRP017611_liver 0 .00 RPM 265 .18 RPM
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_1696 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_1696 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_1696 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 13 parental genes, and 67 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG00000020150 4 retrocopies
Felis catus ENSFCAG000000246805 retrocopies
Loxodonta africana ENSLAFG000000119166 retrocopies
Macropus eugenii ENSMEUG000000063613 retrocopies
Myotis lucifugus ENSMLUG000000089561 retrocopy
Monodelphis domestica ENSMODG000000116351 retrocopy
Nomascus leucogenys ENSNLEG000000105002 retrocopies
Ornithorhynchus anatinus ENSOANG000000046691 retrocopy
Procavia capensis ENSPCAG000000118652 retrocopies
Petromyzon marinus ENSPMAG000000020401 retrocopy
Pongo abelii ENSPPYG0000000115232 retrocopies
Sarcophilus harrisii ENSSHAG000000064171 retrocopy
Tarsius syrichta ENSTSYG000000140388 retrocopies



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