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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGTCTGAGCATCCCAGGGTACAGGACACGCTATGACAATGTTGACCTAGTTACCATCCGAGAAAATACTGAAGGCGAGTACAGTGGTTTGGAGCATCAGgtgagttctggatactgcaagtgttggattgtattcggaattctacattcttagggtttttgttttaagcgaaacgagcttcgagtgctactagggtaat...

Basic information

species Physcomitrella patens
transcript PP1S199_33V6.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S199_33V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ18109 (Selaginella moellendorffii), 5'ss of exon 3
ATGTCTGAGCATCCCAGGGTACAGGACACGCTATGACAATGTTGACCTAGTTACCATCCGAGAAAATACTGAAGGCGAGTACAGTGGTTTGGAGCATCAGgtgagttctggatactgcaagtgttggattgtattcggaattctacattcttagggtttttgttttaagcgaaacgagcttcgagtgctactagggtaat
 ||||| |||||||| || |||| ||| || |||||||| || || || ||||||||||| || || || || |||||||||||||| ||||| ||||| || ||      |   |||  || || || |   ||||    |||    | ||  ||||  | ||  |                                 
GTGTCTCAGCATCCCCGGCTACAAGACGCGATATGACAACGTCGATCTCGTTACCATCCGGGAGAACACCGAGGGCGAGTACAGTGGATTGGAACATCAAgtaagc---aaagcttgctggttttcgagt---ttcga---tcttggctgtt--ggttccttttgcag--------------------------------

upper sequence: PP1S199_33V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ09610 (Selaginella moellendorffii), 5'ss of exon 2
ATGTCTGAGCATCCCAGGGTACAGGACACGCTATGACAATGTTGACCTAGTTACCATCCGAGAAAATACTGAAGGCGAGTACAGTGGTTTGGAGCATCAGgtgagttctggatactgcaagtgttggattgtattcggaattctacattcttagggtttttgttttaagcgaaacgagcttcgagtgctactagggtaat
 ||||| |||||||| || |||| ||| || |||||||| || || || ||||||||||| || || || || |||||||||||||| ||||| ||||| || ||      |   |||  || || || |    |||    |||    | ||  ||||| | |   |                                 
GTGTCTCAGCATCCCCGGCTACAAGACGCGATATGACAACGTCGATCTCGTTACCATCCGGGAGAACACCGAGGGCGAGTACAGTGGATTGGAACATCAAgtaagc---aaagcttgctggttttcgagt---ctcga---tcttggctgtt--ggtttctttcacag--------------------------------
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|208387706|gb|DC937271.1|DC937271
EST:     TTACCATCCGAGAAA-TACTGAAGGCGAGTACAGTGGTTTGGANCATCAG                         GTGGTGAAGGGA
genomic: TTACCATCCGAGAAAATACTGAAGGCGAGTACAGTGGTTTGGAGCATCAGgtgagttctg ... gcgttatcagGTGGTGAGGGGA
EST: gi|162174845|gb|FC351637.1|FC351637
EST:     TTACCATCCGAGAAAATACTGAAGGCGAGTACAGTGGTTTGGAGCATCAG                         GTGGTGAGGGGAGTGGTGGAGAGCATAAAAATTATCACCAGGAATGCCAGT
genomic: TTACCATCCGAGAAAATACTGAAGGCGAGTACAGTGGTTTGGAGCATCAGgtgagttctg ... gcgttatcagGTGGTGAGGGGAGTGGTGGAGAGCATAAAAATTATCACCAGGAATGCCAGT
EST: gi|100356789|gb|BY965281.1|BY965281
EST:     TTACCATCCGAGAAAATACTGAAGGCGAGTACAGTGGTTTGGAGCATCAG                         GTGGTGAGGGGAGTGGTGGAGAGCATAAAAATTATCACCAGGAATGCCAGT
genomic: TTACCATCCGAGAAAATACTGAAGGCGAGTACAGTGGTTTGGAGCATCAGgtgagttctg ... gcgttatcagGTGGTGAGGGGAGTGGTGGAGAGCATAAAAATTATCACCAGGAATGCCAGT
EST: gi|208347370|gb|DC909733.1|DC909733
EST:     TTACCATCCGAGAAAATACTGAAGGCGAGTACAGTGGTTTGGAGCATCAG                         GTGGTGAGGGGAGTGGTGGAAAGCATAAAAATTATCACCAGGAATGCCAGT
genomic: TTACCATCCGAGAAAATACTGAAGGCGAGTACAGTGGTTTGGAGCATCAGgtgagttctg ... gcgttatcagGTGGTGAGGGGAGTGGTGGAGAGCATAAAAATTATCACCAGGAATGCCAGT
EST: gi|100394804|gb|BY989933.1|BY989933
EST:     TTACCATCCGAGAAAATACTGAAGGCGAGTACAGTGGTTTGGAGCATCAN                         GTGGTGAGGGGAGTGGTGGAGAGCATAAAAATTATCACCAGGAATGCCAGT
genomic: TTACCATCCGAGAAAATACTGAAGGCGAGTACAGTGGTTTGGAGCATCAGgtgagttctg ... gcgttatcagGTGGTGAGGGGAGTGGTGGAGAGCATAAAAATTATCACCAGGAATGCCAGT
EST: gi|162182687|gb|FC359434.1|FC359434
EST:     TTACCATCCGAGAAAATACTGAAGGCGAGTACAGTGGTTTGGAGCATCAN                         GTGGTGAGGGGAGTGGTGGAGAGCATAAAAATTATCACCAGGAATGCCAGT
genomic: TTACCATCCGAGAAAATACTGAAGGCGAGTACAGTGGTTTGGAGCATCAGgtgagttctg ... gcgttatcagGTGGTGAGGGGAGTGGTGGAGAGCATAAAAATTATCACCAGGAATGCCAGT
EST: gi|208390159|gb|DC941966.1|DC941966
EST:     TTACCATCCGAGAAAATACTGAAGGCGAGTACAGTGGTTTGGANCATCAG                         GTGGTGANGGGAATTGGTGGA
genomic: TTACCATCCGAGAAAATACTGAAGGCGAGTACAGTGGTTTGGAGCATCAGgtgagttctg ... gcgttatcagGTGGTGAGGGGAGT-GGTGGA
EST: gi|208375010|gb|DC956406.1|DC956406
EST:     GAGAAAATACTGAAGGCGAGTACAGTGGTTTGGAGCATCAG                         GTGGTGAGGGGAGTNGTGGAGAGCATAAAAATTATCACCAGGAATGCCAGT
genomic: GAGAAAATACTGAAGGCGAGTACAGTGGTTTGGAGCATCAGgtgagttctg ... gcgttatcagGTGGTGAGGGGAGTGGTGGAGAGCATAAAAATTATCACCAGGAATGCCAGT
EST: gi|208361101|gb|DC957552.1|DC957552
EST:     GGCGAGTACAGTGGTTTGGAGCATTCAG                         GTGGTGAGGGGAGTGGTNGAGAGCATAAAAAATTATCACCAGGAATGCCA
genomic: GGCGAGTACAGTGGTTTGGAGCA-TCAGgtgagttctg ... gcgttatcagGTGGTGAGGGGAGTGGTGGAGAGCAT-AAAAATTATCACCAGGAATGCCA
EST: gi|162171538|gb|FC347840.1|FC347840
EST:     TTACCATCCGAGAAAATACTGAAGGCGAGTACAGTGGTTTGGAGCATCAN                         GTGGTGAGGGGAGTGGTGGAGAGCATAAAAATTATCACCAGGAATGCCA
genomic: TTACCATCCGAGAAAATACTGAAGGCGAGTACAGTGGTTTGGAGCATCAGgtgagttctg ... gcgttatcagGTGGTGAGGGGAGTGGTGGAGAGCATAAAAATTATCACCAGGAATGCCA
EST: gi|100388374|gb|BY951976.1|BY951976
EST:     TTACCATCCGAGAAAATACTGAAGGCGAGTACAGTGGTTTGGAGCATCAG                         GTGGTGAGGGGAGTGGTGGAGAGCATAAAA-TTATCACCAGGAATGCCAGT
genomic: TTACCATCCGAGAAAATACTGAAGGCGAGTACAGTGGTTTGGAGCATCAGgtgagttctg ... gcgttatcagGTGGTGAGGGGAGTGGTGGAGAGCATAAAAATTATCACCAGGAATGCCAGT
EST: gi|67573305|gb|BJ946129.1|BJ946129
EST:     TTACCATCCGAGAAAATACTGAAGGCGAGTACAGTGGTTTGGAGCATCAG                         GTGGTGAGGGGAGTGGTGGAGAGCATAAAAATTATCACCAGGAATGCCAGT
genomic: TTACCATCCGAGAAAATACTGAAGGCGAGTACAGTGGTTTGGAGCATCAGgtgagttctg ... gcgttatcagGTGGTGAGGGGAGTGGTGGAGAGCATAAAAATTATCACCAGGAATGCCAGT
EST: gi|67717729|gb|BJ967988.1|BJ967988
EST:     TTACCATCCGAGAAAATACTGAAGGCGAGTACAGTGGTTTGGAGCATCAN                         GTGGTGAGGGGAGTGGTGGAGAGCATAAAAATTATCACCAGGAATGCCAGT
genomic: TTACCATCCGAGAAAATACTGAAGGCGAGTACAGTGGTTTGGAGCATCAGgtgagttctg ... gcgttatcagGTGGTGAGGGGAGTGGTGGAGAGCATAAAAATTATCACCAGGAATGCCAGT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 29 (upstream exon), 34 (downstream exon)
Score: 5

ATGTCTGAGCATCCCAGGGTACAGGACACGCTATGACAATGTTGACCTAGTTACCATCCGAGAAAATACTGAAGGCGAGTACAGTGGTTTGGAGCATCAGgtgagttctg ... gcgttatcagGTGGTGAGGGGAGTGGTGGAGAGCATAAAAATTATCACCAGGAATGCCAGTTTGCGTGTGGCTAAATACGCATTCCATTATGCTCGGCTACATGGCAGGA




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGTCTGAGCATCCCAGGGTACAGGACACGCTATGACAATGTTGACCTAGTTACCATCCGAGAAAATACTGAAGGCGAGTACAGTGGTTTGGAGCATCAGgtgagttctggatactgcaagtgttggattgtattcggaattctacattcttagggtttttgttttaagcgaaacgagcttcgagtgctactagggtaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA