RetrogeneDB ID:

retro_sscr_1172

Retrocopy
location
Organism:Pig (Sus scrofa)
Coordinates:X:108384248..108384615(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSSSCG00000030951
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS25
Ensembl ID:ENSSSCG00000015103
Aliases:None
Description:ribosomal protein S25 [Source:HGNC Symbol;Acc:10413]


Retrocopy-Parental alignment summary:






>retro_sscr_1172
CCGCCCAAGGACGACAAGAAGAAGAAAGATGCCGGAAAGTTGGCCAAGAAAGACAAAGACCCAGTGAACAAATCTGGGGG
CAAGGCCAAAAAGAAGTGGTCCAAAGGCAAAATTCGGGACAAGCTCAATAATTTAGTCTTGTTTGACAAAGCGACATATG
ACAAACTCTGTAAAGAAGTTCCCAACTATAAGCTTATTACTCCAGCTGTTGTCTCTGAGACTGAAGATTCGTGGTTCTCT
GGCCAGGGCAGCCCTTCAGGAGCTCTTGAGCAAAGGACTTATTAAACTGGTTTCAAAGCACAGAGCTCAAGTAGTTTACA
CCTGAAATACCAAGGGTGGAGATGCCCCAGCTGCTGGAGAAGATGCA

ORF - retro_sscr_1172 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.2 %
Parental protein coverage: 99.2 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalPPKDDKKKKDAGKSAKKDKDPVNKSGGKAKKKKWSKGKVRDKLNNLVLFDKATYDKLCKEV-PNYKLITP
PPKDDKKKKDAGK.AKKDKDPVNKSGGKAKKK.WSKGK.RDKLNNLVLFDKATYDKLCKEV.P...L...
RetrocopyPPKDDKKKKDAGKLAKKDKDPVNKSGGKAKKK-WSKGKIRDKLNNLVLFDKATYDKLCKEV>PTISLLLQ
ParentalAVVSERLKIRGSLARAALQELLSKGLIKLVSKHRAQVIYTRNTKGGDAPAAGEDA
...S.RLKIRGSLARAALQELLSKGLIKLVSKHRAQV.YT.NTKGGDAPAAGEDA
Retrocopy-LLSLRLKIRGSLARAALQELLSKGLIKLVSKHRAQVVYT*NTKGGDAPAAGEDA

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
SRP014902_placenta 0 .66 RPM 132 .07 RPM
SRP014902_testis 4 .10 RPM 197 .60 RPM
SRP018288_heart 0 .60 RPM 362 .18 RPM
SRP018288_kidney 3 .84 RPM 263 .80 RPM
SRP018288_liver 4 .64 RPM 277 .28 RPM
SRP018288_lung 0 .20 RPM 251 .21 RPM
SRP018856_adipose 1 .21 RPM 387 .94 RPM
SRP035408_brain 2 .35 RPM 195 .36 RPM
SRP035408_liver 2 .14 RPM 201 .79 RPM
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_1172 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_1172 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_sscr_1172 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 10 parental genes, and 60 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000000515 retrocopies
Canis familiaris ENSCAFG000000123953 retrocopies
Cavia porcellus ENSCPOG000000132982 retrocopies
Felis catus ENSFCAG000000011513 retrocopies
Loxodonta africana ENSLAFG000000171176 retrocopies
Microcebus murinus ENSMICG000000026878 retrocopies
Myotis lucifugus ENSMLUG0000000475215 retrocopies
Monodelphis domestica ENSMODG000000133342 retrocopies
Mustela putorius furoENSMPUG000000049604 retrocopies
Sus scrofa ENSSSCG00000015103 12 retrocopies



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