RetrogeneDB ID:

retro_cjac_691

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:10:59759045..59759896(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:TPM1
Ensembl ID:ENSCJAG00000004355
Aliases:None
Description:tropomyosin 1 (alpha) [Source:HGNC Symbol;Acc:12010]


Retrocopy-Parental alignment summary:






>retro_cjac_691
ATGGACGCAATCAAGAAGAAGATGCAGATGCTGAAGCTCGACAAGGAGAACGCCTTGGATTGAGCTGAGCAGGCGGAGGC
CGACAAGAAGGCGGCGGAAGACAGGAGCAAGCAGCTGGAATATGAGCTGGTGTCGCTGCAAAAGAAACTCAAGGGCACCG
AAGATGACTGGACAAATACTCTGAGGCTCTCAAAGATGCCCAGGAGAAGCTGGAGCTGGCAGAGAAAAAGGCCACCGATG
CTGAAGCTGACGTAGCTTCTCTGAACAGACACATCCAGCTGGTTGAGGAAGAGTTGGATCATGCCCAGGAGCGTCTGGCA
ATCGCTTTGCAGAAGCTGGAGGAAGCTGAGAAGGCAGCAGGTGAGAGTGAGAGAGGCATGAAAGTCATTGAAAGTCGAGC
CCAAAAGGATGAAGAGAAAATGGAAATTCAGGAGATCCAACTGAAAGAGGCCAAGCACAATGCTGAGGATGCCGACCGCA
AATATGAAGAGGTGGCCCGTATGCTCGTCATCATTGAGAACGACCTGGAACGTGCAGAAGAGCCGGCTGGGCTCTCAGAA
GGCCAGGTCCGACGACTGGAAGAACAATTAAGAATAATGGATCAGACCTTGAAAGCATTAATGGCTGCAGAGGATAAGTA
CTCGCAGAAGGAAGACAAATATGAGGAAGAGATCAAGGTCCTTTCCGACAAGCTGAAGGAGGCTGAGACTCGGGCTGAGT
TTGCGGAGAAGTCAGTAACTAAATTGGCGAAAAGCATTCATGACTTAGAAGAGAAAGTGGCTCATGCCAAAGAAGAAAAC
CTTAGTATGCATCAGATGCTGGATCAGACTTTACTAGAGTTAAACACCATG

ORF - retro_cjac_691 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.68 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMDAIKKKMQMLKLDKENALDRAEQAEADKKAAEDRSKQLEDELVSLQKKLKGTEDE-LDKYSEALKDAQE
MDAIKKKMQMLKLDKENALD.AEQAEADKKAAEDRSKQLE.ELVSLQKKLKGTED..LDKYSEALKDAQE
RetrocopyMDAIKKKMQMLKLDKENALD*AEQAEADKKAAEDRSKQLEYELVSLQKKLKGTEDD<LDKYSEALKDAQE
ParentalKLELAEKKATDAEADVASLNRRIQLVEEELDRAQERLATALQKLEEAEKAADESERGMKVIESRAQKDEE
KLELAEKKATDAEADVASLNR.IQLVEEELD.AQERLA.ALQKLEEAEKAA.ESERGMKVIESRAQKDEE
RetrocopyKLELAEKKATDAEADVASLNRHIQLVEEELDHAQERLAIALQKLEEAEKAAGESERGMKVIESRAQKDEE
ParentalKMEIQEIQLKEAKHIAEDADRKYEEVARKLVIIESDLERAEERAELSEGQVRQLEEQLRIMDQTLKALMA
KMEIQEIQLKEAKH.AEDADRKYEEVAR.LVIIE.DLERAEE.A.LSEGQVR.LEEQLRIMDQTLKALMA
RetrocopyKMEIQEIQLKEAKHNAEDADRKYEEVARMLVIIENDLERAEEPAGLSEGQVRRLEEQLRIMDQTLKALMA
ParentalAEDKYSQKEDKYEEEIKVLSDKLKEAETRAEFAERSVTKLEKSIDDLEEKVAHAKEENLSMHQMLDQTLL
AEDKYSQKEDKYEEEIKVLSDKLKEAETRAEFAE.SVTKL.KSI.DLEEKVAHAKEENLSMHQMLDQTLL
RetrocopyAEDKYSQKEDKYEEEIKVLSDKLKEAETRAEFAEKSVTKLAKSIHDLEEKVAHAKEENLSMHQMLDQTLL
ParentalELNNM
ELN.M
RetrocopyELNTM

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
SRP051959_colon 0 .07 RPM 180 .61 RPM
SRP051959_heart 0 .70 RPM 820 .43 RPM
SRP051959_kidney 0 .02 RPM 59 .77 RPM
SRP051959_liver 0 .00 RPM 28 .33 RPM
SRP051959_lung 0 .05 RPM 84 .75 RPM
SRP051959_lymph_node 0 .05 RPM 29 .06 RPM
SRP051959_skeletal_muscle 2 .45 RPM 1671 .70 RPM
SRP051959_spleen 0 .00 RPM 64 .71 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_691 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_691 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_691 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 11 parental genes, and 32 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000169661 retrocopy
Choloepus hoffmanni ENSCHOG0000001278811 retrocopies
Callithrix jacchus ENSCJAG00000004355 2 retrocopies
retro_cjac_2200, retro_cjac_691 ,
Callithrix jacchus ENSCJAG000000096272 retrocopies
Callithrix jacchus ENSCJAG000000097479 retrocopies
Callithrix jacchus ENSCJAG000000141351 retrocopy
Macropus eugenii ENSMEUG000000145812 retrocopies
Pongo abelii ENSPPYG000000065341 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000099551 retrocopy
Tursiops truncatus ENSTTRG000000037621 retrocopy
Vicugna pacos ENSVPAG000000032771 retrocopy



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