RetrogeneDB ID:

retro_cfam_2167

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:X:59085531..59086342(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCAFG00000017231
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:TPM1
Ensembl ID:ENSCAFG00000016966
Aliases:None
Description:tropomyosin 1 (alpha) [Source:HGNC Symbol;Acc:12010]


Retrocopy-Parental alignment summary:






>retro_cfam_2167
GACAAGAAGAATGCCTTGGATCGAGCCGAGCAGGCGGAGGCCGATAAGAGGGCTGCGGAGGACAGGAGCAAGAGCTGGAA
GATGAGCTGGTGTCGCTGCAAAAGAAACTCAAGGGCACCGAAGATGAACTGGACAAATACTCCGAGGCTGTAAAGATGCC
CAGGAGAAGTTGGAGCTGGCGGAGAAAAAGGCCACTGACGCTGAAGCCGATGTACCTTCTCTGAACAGACGCATCCAGCT
GGTTGAGGAAGAGTTGGATCGTGCCCAGGAGCGACTGACAACAGCTTTGCAGAAGCTGGAGGAGGCTGAGAAGGCAGTGG
ACGAGAGCAAGAGAGGCATGAAAGTCATTGAAAGCCGAGCCCAAAAGGATGAGGAGAAAATGGAAATTCAGGAGATTCAA
CTGAAAGAGGCCAAGCACATTGCTGAAGATGCCAACCGCAAGTATGAAGAGGTGGCCCATAAGCTGGTCATCATTGAGAG
CGACCTGGAACGCGTGGAAGAACGGGCTGAGCTCTCAGAAAGCCAAGTTCGACAGCTGGAAGAACAATTAAGAATAATGG
ATCAGACCTTGAAAGCATTAATGGCTGCAGAGGATAAGTACTCGCAGAAGGAAGACAAATATGAGGAAGAGATCAAGGTT
CTCTCTGACAAGCTGAAGGAGGCCGAGACTCGGGCTGAGTTTGCGGAGAGGTCAATAACTAAATCGGAGAAAAGCATTGA
TGACTTAGAAAAGAAAGTGGCTCATGCCAAAGAAGAAAACCTTAGTATGCATCAGATGCTGGATCAGACTTTACTGGAGT
TAAACAACATG

ORF - retro_cfam_2167 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.05 %
Parental protein coverage: 83.13 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalERDRVLEELHSAEDSLLAADETAA-KLEDELVSLQKKLKGTEDELDKYSEALK-DAQEKLELAEKKATDA
.....L.....AE....AA.......LEDELVSLQKKLKGTEDELDKYSEA.K.DAQEKLELAEKKATDA
RetrocopyDKKNALDRAEQAEADKRAAEDRSK<ELEDELVSLQKKLKGTEDELDKYSEAVK<DAQEKLELAEKKATDA
ParentalEADVASLNRRIQLVEEELDRAQERLATALQKLEEAEKAADESERGMKVIESRAQKDEEKMEIQEIQLKEA
EADV.SLNRRIQLVEEELDRAQERL.TALQKLEEAEKA.DES.RGMKVIESRAQKDEEKMEIQEIQLKEA
RetrocopyEADVPSLNRRIQLVEEELDRAQERLTTALQKLEEAEKAVDESKRGMKVIESRAQKDEEKMEIQEIQLKEA
ParentalKHIAEDADRKYEEVARKLVIIESDLERAEERAELSESKCAELEEELKTVTNNLKSLEAQAEKYSQKEDKY
KHIAEDA.RKYEEVA.KLVIIESDLER.EERAELSES....LEE.L......LK.L.A...KYSQKEDKY
RetrocopyKHIAEDANRKYEEVAHKLVIIESDLERVEERAELSESQVRQLEEQLRIMDQTLKALMAAEDKYSQKEDKY
ParentalEEEIKVLSDKLKEAETRAEFAERSVTKLEKSIDDLEEKVAHAKEENLSMHQMLDQTLLELNNM
EEEIKVLSDKLKEAETRAEFAERS.TK.EKSIDDLE.KVAHAKEENLSMHQMLDQTLLELNNM
RetrocopyEEEIKVLSDKLKEAETRAEFAERSITKSEKSIDDLEKKVAHAKEENLSMHQMLDQTLLELNNM

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 .63 RPM 120 .58 RPM
SRP017611_brain 0 .79 RPM 103 .37 RPM
SRP017611_kidney 14 .59 RPM 141 .85 RPM
SRP017611_liver 6 .60 RPM 73 .67 RPM
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_2167 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_2167 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_2167 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 11 parental genes, and 26 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000157961 retrocopy
Canis familiaris ENSCAFG00000016966 1 retrocopy
retro_cfam_2167 ,
Canis familiaris ENSCAFG000000173114 retrocopies
Choloepus hoffmanni ENSCHOG0000001278811 retrocopies
Callithrix jacchus ENSCJAG000000043552 retrocopies
Macropus eugenii ENSMEUG000000145812 retrocopies
Pongo abelii ENSPPYG000000065341 retrocopy
Rattus norvegicus ENSRNOG000000181841 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000099551 retrocopy
Tursiops truncatus ENSTTRG000000037621 retrocopy
Vicugna pacos ENSVPAG000000032771 retrocopy



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