RetrogeneDB ID:

retro_cfam_1011

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:21:20889340..20889921(+)
Located in intron of:ENSCAFG00000004851
Retrocopy
information
Ensembl ID:ENSCAFG00000004857
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL19
Ensembl ID:ENSCAFG00000016493
Aliases:None
Description:60S ribosomal protein L19 [Source:UniProtKB/Swiss-Prot;Acc:D0VWQ5]


Retrocopy-Parental alignment summary:






>retro_cfam_1011
CTCAGGCTTCAGAAGAGGCTTGCCTCCAGTGTCCTCCGTTGTGGCAAAAAGAAGGTCTGGTTGGACCCCAATGAGACCAA
TGAAATCGCCAATGCAAACTCCCGTCAGCAGATACGAAAACTGATCAAAGATGGGCTGATAATCCGGAAGCCTGTGACTA
TCCATTCCCGAGCTCGGTGCCGGAAAAACGCTCTGGCCCGCCGGAAGGGCAGGCATATGGGCATTGGTAAGAGAAAAGGT
ACTGCCAATGCTCGAATGCCTGAGAAGGTAACGTGGATGAGGAGGATGAGAATTCTACGCAGGCTGCTCAGAAGATACCG
TGAATCTAAGAAGATTGACCGCCACATGTATCATAGCCTGTACCTGAAAGTGAAGGGTAACGTGTTCAAGAACAAGCGGA
TTCTCATGGAACACTTCCACAAGCTGAAGGCAGACAAGGCTCGCAAGAAGCTTCTGGCTGACCAGGCTGAGGCCTGCAGA
TCTAAGACCAAGGAGGCCCGCAAGCGCCGTGAAGAGCGCGGCTCCAGGCCAAGAAGGAGGAAATCATCAAGACTCTGTCC
AAGGAGGAAGAGACCAAGAAA

ORF - retro_cfam_1011 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 95.9 %
Parental protein coverage: 99.48 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalLRLQKRLASSVLRCGKKKVWLDPNETNEIANANSRQQIRKLIKDGLIIRKPVTVHSRARCRKNTLARRKG
LRLQKRLASSVLRCGKKKVWLDPNETNEIANANSRQQIRKLIKDGLIIRKPVT.HSRARCRKN.LARRKG
RetrocopyLRLQKRLASSVLRCGKKKVWLDPNETNEIANANSRQQIRKLIKDGLIIRKPVTIHSRARCRKNALARRKG
ParentalRHMGIGKRKGTANARMPEKVTWMRRMRILRRLLRRYRESKKIDRHMYHSLYLKVKGNVFKNKRILMEHIH
RHMGIGKRKGTANARMPEKVTWMRRMRILRRLLRRYRESKKIDRHMYHSLYLKVKGNVFKNKRILMEH.H
RetrocopyRHMGIGKRKGTANARMPEKVTWMRRMRILRRLLRRYRESKKIDRHMYHSLYLKVKGNVFKNKRILMEHFH
ParentalKLKADKARKKLLADQAEARRSKTKEARK-RREE-RLQAKKEEIIKTLSKEEETKK
KLKADKARKKLLADQAEA.RSKTKEARK.R.E..RLQAKKEEIIKTLSKEEETKK
RetrocopyKLKADKARKKLLADQAEACRSKTKEARKRREER<RLQAKKEEIIKTLSKEEETKK

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 2 .23 RPM 477 .69 RPM
SRP017611_brain 3 .18 RPM 112 .50 RPM
SRP017611_kidney 27 .93 RPM 996 .24 RPM
SRP017611_liver 0 .44 RPM 226 .75 RPM
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_1011 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_1011 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_1011 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 12 parental genes, and 135 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG00000016493 14 retrocopies
Choloepus hoffmanni ENSCHOG000000060237 retrocopies
Callithrix jacchus ENSCJAG000000085204 retrocopies
Dasypus novemcinctus ENSDNOG000000197427 retrocopies
Equus caballus ENSECAG000000250806 retrocopies
Macropus eugenii ENSMEUG0000001390010 retrocopies
Macaca mulatta ENSMMUG000000042352 retrocopies
Mustela putorius furoENSMPUG000000150415 retrocopies
Nomascus leucogenys ENSNLEG0000000074819 retrocopies
Pongo abelii ENSPPYG0000000849220 retrocopies
Rattus norvegicus ENSRNOG0000000474137 retrocopies
Tursiops truncatus ENSTTRG000000066874 retrocopies



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