RetrogeneDB ID:

retro_cfam_880

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:19:49759725..49760515(-)
Located in intron of:ENSCAFG00000005522
Retrocopy
information
Ensembl ID:ENSCAFG00000004091
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCAFG00000006545
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cfam_880
CACAAGGGCATATTTAATGGATTCTCAGTTACACTTAAAGAGGATGGTGTTCGTGGTTTGGCTAAAGGATGGGCTCCGAC
TTTCATTGGCTATTCTATGCAAGGGCTCTGCAAGTTTGGCTTTTATGAAGTTTTCAAAGTCTTGTATAGCAACATGCTTG
GAGAGGAGAATGCCTATCTCTGGCGCACATCACTATATTTGGCTGCCTCTCTCAGTGCTGAATTCTTTGCTGACATTGCC
CTGGCTCCTATGGAAGCTGCTAAGGTTAGAATTCAAACCCAACCAGGTTATGCCAACACCTTGAGGGATGCAGCTCCCAA
AATGTATAAGGAAGAAGGCTTAAAAGCATTCTACAAGGGGGTTGCTCCTCTCTGGATGAGACAGATACCATACACCATGA
TGAAATTTGCCTGCTTTGAACATACTGTTGAAGCATTATATAAGTTTGTGGTTCCCAAGCCCCAAAGTGAATGTTCAAAG
GCAGAGCAACTGGTTGTAACATTTGTAGCAGGTTATATAGCTGGAGTCTTCTGTGCAATTGTTTCTCATCCTGCTGATTC
TGTGGTATCTGTGTTGAATAAAGAGAAAGGTAAGCAGTGCTTCTCAAGTCCTTCAGAGACTCGGATTTAAAGGTGTATGG
AAGGGACTCTTTGCCCGTATCATCATGATTGGCACTCTGACTGCACTACAGTGGTTCATCTATGACTCTGTGAAGGTCTA
CTTCAGGCTCCCTCGCCCACCTCCACCTGAAATGCCAGAGTCTCTGAAGAAGAAGCTTGGGTTAACTCAG

ORF - retro_cfam_880 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 98.11 %
Parental protein coverage: 72.85 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalYKGIFNGFSVTLKEDGVRGLAKGWAPTFIGYSMQGLCKFGFYEVFKVLYSNMLGEENAYLWRTSLYLAAS
.KGIFNGFSVTLKEDGVRGLAKGWAPTFIGYSMQGLCKFGFYEVFKVLYSNMLGEENAYLWRTSLYLAAS
RetrocopyHKGIFNGFSVTLKEDGVRGLAKGWAPTFIGYSMQGLCKFGFYEVFKVLYSNMLGEENAYLWRTSLYLAAS
ParentalASAEFFADIALAPMEAAKVRIQTQPGYANTLRDAAPKMYKEEGLKAFYKGVAPLWMRQIPYTMMKFACFE
.SAEFFADIALAPMEAAKVRIQTQPGYANTLRDAAPKMYKEEGLKAFYKGVAPLWMRQIPYTMMKFACFE
RetrocopyLSAEFFADIALAPMEAAKVRIQTQPGYANTLRDAAPKMYKEEGLKAFYKGVAPLWMRQIPYTMMKFACFE
ParentalRTVEALYKFVVPKPRSECSKAEQLVVTFVAGYIAGVFCAIVSHPADSVVSVLNKEKG-SSASQVLQRLGF
.TVEALYKFVVPKP.SECSKAEQLVVTFVAGYIAGVFCAIVSHPADSVVSVLNKEKG.SSASQVLQRLGF
RetrocopyHTVEALYKFVVPKPQSECSKAEQLVVTFVAGYIAGVFCAIVSHPADSVVSVLNKEKG>SSASQVLQRLGF
ParentalKGVWKGLFARIIMIGTLTALQWFIYDSVKVYFRLPRPPPPEMPESLKKKLGLTQ
KGVWKGLFARIIMIGTLTALQWFIYDSVKVYFRLPRPPPPEMPESLKKKLGLTQ
RetrocopyKGVWKGLFARIIMIGTLTALQWFIYDSVKVYFRLPRPPPPEMPESLKKKLGLTQ

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 .25 RPM 225 .53 RPM
SRP017611_brain 0 .56 RPM 198 .88 RPM
SRP017611_kidney 0 .46 RPM 651 .13 RPM
SRP017611_liver 0 .29 RPM 126 .68 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_880 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_880 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_880 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 27 parental genes, and 32 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000132321 retrocopy
retro_acar_35,
Bos taurus ENSBTAG000000128901 retrocopy
retro_btau_172,
Canis familiaris ENSCAFG00000006545 1 retrocopy
retro_cfam_880 ,
Callithrix jacchus ENSCJAG000000023922 retrocopies
retro_cjac_3315, retro_cjac_812,
Dipodomys ordii ENSDORG000000114311 retrocopy
retro_dord_321,
Equus caballus ENSECAG000000151351 retrocopy
retro_ecab_481,
Echinops telfairi ENSETEG000000126781 retrocopy
retro_etel_1748,
Homo sapiens ENSG000000754151 retrocopy
retro_hsap_392,
Gorilla gorilla ENSGGOG000000158861 retrocopy
retro_ggor_394,
Latimeria chalumnae ENSLACG000000070241 retrocopy
retro_lcha_4,
Macropus eugenii ENSMEUG000000165932 retrocopies
retro_meug_405, retro_meug_658,
Microcebus murinus ENSMICG000000035201 retrocopy
retro_mmur_298,
Myotis lucifugus ENSMLUG000000083301 retrocopy
retro_mluc_1184,
Macaca mulatta ENSMMUG000000230361 retrocopy
retro_mmul_496,
Monodelphis domestica ENSMODG000000077172 retrocopies
retro_mdom_2026, retro_mdom_293,
Mus musculus ENSMUSG000000619041 retrocopy
retro_mmus_1959,
Nomascus leucogenys ENSNLEG000000059731 retrocopy
retro_nleu_2402,
Oryctolagus cuniculus ENSOCUG000000118471 retrocopy
retro_ocun_390,
Otolemur garnettii ENSOGAG000000122222 retrocopies
retro_ogar_1816, retro_ogar_2052,
Pongo abelii ENSPPYG000000048581 retrocopy
retro_pabe_1768,
Pan troglodytes ENSPTRG000000053331 retrocopy
retro_ptro_302,
Pteropus vampyrus ENSPVAG000000058901 retrocopy
retro_pvam_212,
Sorex araneus ENSSARG000000011491 retrocopy
retro_sara_262,
Ictidomys tridecemlineatus ENSSTOG000000276332 retrocopies
retro_itri_485, retro_itri_90,
Tupaia belangeri ENSTBEG000000145481 retrocopy
retro_tbel_1792,
Tursiops truncatus ENSTTRG000000047391 retrocopy
retro_ttru_692,
Vicugna pacos ENSVPAG000000047041 retrocopy
retro_vpac_455,




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