RetrogeneDB ID:

retro_ptro_2830

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:9:43568953..43569691(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:TPM4
Ensembl ID:ENSPTRG00000010637
Aliases:None
Description:tropomyosin 4 [Source:HGNC Symbol;Acc:12013]


Retrocopy-Parental alignment summary:






>retro_ptro_2830
GTGGCCGGCCTCAACTCCCTGGAGGCGGTGAAACGCAAGATCCAGGCCCTGCAGCAGCAGACGGACGAGGCGGAAGACCG
CGCGCAGGGCCTGCAGCGGGAGCTGGACGGCGAGCGCGAGCGGCGCGAGAAAGCTGAAGGTGATGTGGCCGCCCTCAACC
GACGCATCCAGCTCGTTGAGGAGGAGTTGGACAGGGCTCAGGAACGACTGGCCACGGCCCTGCAGAAGCTGGAGGAGGCA
GAAAAAGCTGCAGATGAGAGTGAGAGAGGAATGAAGGTGATAGAAAACCGGGCCATGAAGGATGAGGAGAAGATTCAGGA
GATGCAGCTCAAAGAGGCCAAGCACATTGCGGAAGAGGCTGACCGCAAATACGAGGAGGTAGCTCGTAAGCTGGTCATCC
TGGAGTGTGAGCTGGAGAGGGCAGAGGAGCGTGCGGAGGTGTCTGAACTAAAATGTGGTGACCTGGAAGAAGAACTCAAG
AATGTTACTAACAATCTGAAATCTCTGGAGGCTGCATCTGAAAAGTATTCTGAAAAGGAGGACAAATATGAAGAAGAAAT
TAAACTTCTGTCTGACAAACTGAAAGAGGCTGAGACCCGTGTTGAATTTGCAGAGAGAACGGTTGCAAAACTGGAAAAGA
CAATTGATGACCTGGAAGAGAAACTTGCCCAGGCCAAAGAAGAGAATGTGGGCTTACATCAGACACTGGATCAGACACTA
AACGAACTTAACTGTATA

ORF - retro_ptro_2830 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 97.58 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAGLNSLEAVKRKIQALQQQADEAEDRAQGLQRELDGERERREKAEGDVAALNRRIQLVEEELDRAQERL
.AGLNSLEAVKRKIQALQQQ.DEAEDRAQGLQRELDGERERREKAEGDVAALNRRIQLVEEELDRAQERL
RetrocopyVAGLNSLEAVKRKIQALQQQTDEAEDRAQGLQRELDGERERREKAEGDVAALNRRIQLVEEELDRAQERL
ParentalATALQKLEEAEKAADESERGMKVIENRAMKDEEKMEIQEMQLKEAKHIAEEADRKYEEVARKLVILEGEL
ATALQKLEEAEKAADESERGMKVIENRAMKDEEK..IQEMQLKEAKHIAEEADRKYEEVARKLVILE.EL
RetrocopyATALQKLEEAEKAADESERGMKVIENRAMKDEEK--IQEMQLKEAKHIAEEADRKYEEVARKLVILECEL
ParentalERAEERAEVSELKCGDLEEELKNVTNNLKSLEAASEKYSEKEDKYEEEIKLLSDKLKEAETRAEFAERTV
ERAEERAEVSELKCGDLEEELKNVTNNLKSLEAASEKYSEKEDKYEEEIKLLSDKLKEAETR.EFAERTV
RetrocopyERAEERAEVSELKCGDLEEELKNVTNNLKSLEAASEKYSEKEDKYEEEIKLLSDKLKEAETRVEFAERTV
ParentalAKLEKTIDDLEEKLAQAKEENVGLHQTLDQTLNELNCI
AKLEKTIDDLEEKLAQAKEENVGLHQTLDQTLNELNCI
RetrocopyAKLEKTIDDLEEKLAQAKEENVGLHQTLDQTLNELNCI

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
SRP007412_brain_prefrontal_cortex 0 .63 RPM 31 .82 RPM
SRP007412_cerebellum 0 .36 RPM 94 .89 RPM
SRP007412_heart 0 .23 RPM 42 .12 RPM
SRP007412_kidney 0 .10 RPM 39 .70 RPM
SRP007412_liver 0 .10 RPM 22 .91 RPM
SRP007412_testis 14 .33 RPM 32 .25 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_2830 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_2830 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_2830 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 13 parental genes, and 43 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000045532 retrocopies
Canis familiaris ENSCAFG000000157961 retrocopy
Callithrix jacchus ENSCJAG000000141351 retrocopy
Gorilla gorilla ENSGGOG000000145104 retrocopies
Monodelphis domestica ENSMODG000000148821 retrocopy
Mus musculus ENSMUSG000000317991 retrocopy
Nomascus leucogenys ENSNLEG000000054132 retrocopies
Pan troglodytes ENSPTRG00000010637 10 retrocopies
Pteropus vampyrus ENSPVAG000000097552 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000242521 retrocopy
Tupaia belangeri ENSTBEG000000129277 retrocopies
Tarsius syrichta ENSTSYG000000106429 retrocopies
Tursiops truncatus ENSTTRG000000145422 retrocopies



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