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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACATCTGAAGAATTGAGCATCAATAGGGTGAAGTTCAAAGCATTCGATCTAGGTGGTCACACGATTGCTCGACGTGTGTGGAGGGACTACTATGCTAAGgtttttttctagtcttatcctttgttgattctagtatcttcccaacatatgtgtaaacgttgttacatagtcatggcattaagcttgagtttttatttga...

Basic information

species Physcomitrella patens
transcript PP1S44_58V6.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S44_58V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: LOC_Os12g37360.1 (Oryza sativa), 5'ss of exon 2
AACATCTGAAGAATTGAGCATCAATAGGGTGAAGTTCAAAGCATTCGATCTAGGTGGTCACACGATTGCTCGACGTGTGTGGAGGGACTACTATGCTAAGgtttttttctagtcttatcctttgttgattctagtatcttcccaacatatgtgtaaacgt-tgttacatagtcatggcattaagcttgagtttttatttga---
 || ||||||||  |||||||    | | | |||||||| || || ||| |||| || ||    |||||||| ||||||||||  ||||||||||||||||| |     |  | ||    ||| |  ||| |  | ||| |  ||    |  || ||| | || |  |    | |    ||     | | | |   |||||   
GACTTCTGAAGAGCTGAGCATTGGGAAGATCAAGTTCAAGGCGTTTGATTTAGGAGGCCATCAAATTGCTCGCCGTGTGTGGAAAGACTACTATGCTAAGgtctcagcttcctttttaattttat--atttttatttctgca-aatgagtaagtcaacttatgatctacttgcttaatgtttcatctca-tgtgggtttgattt

upper sequence: PP1S44_58V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ35155 (Selaginella moellendorffii), 5'ss of exon 2
AACATCTGAAGAATTGAGCATCAATAGGGTGAAGTTCAAAGCATTCGATCTAGGTGGTCACACGATTGCTCGACGTGTGTGGAGGGACTACTATGCTAAGgtttttttctagtcttatcctttgtt-gattctagtatcttccc--------aacatatgtgtaaacgtt------gttacatagtca-tggca-ttaagcttgagtttttatttga-----------------------------------------------------------------------------------
|||||| || ||  | |||||||| | | | || ||||| || |||||||| || ||||||  ||| || ||||| ||||||| |||||||||||| |||||||    ||  ||| |   ||  || || || | |   || ||         |    |  | ||| |||      |||   | | || |||   ||   || ||    || ||  |                                                                                   
AACATCCGAGGAGCTAAGCATCAACAAGATCAAATTCAAGGCCTTCGATCTGGGGGGTCACCAGATCGCGCGACGCGTGTGGAAGGACTACTATGCCAAGgtttgacactcatctgagaattctttcgaatccaatgctttgcctttgaagcgatgctttggcaaaagttctttttgttttcttgccagtggtggtttgactggacgacttgttctagatctagttgctaacgatgttttgtcacaaactcgtcagatgatctgactggattccatggcttgtttactttgatcatccag

upper sequence: PP1S44_58V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ24104 (Selaginella moellendorffii), 5'ss of exon 2
AACATCTGAAGAATTGAGCATCAATAGGGTGAAGTTCAAAGCATTCGATCTAGGTGGTCACACGATTGCTCGACGTGTGTGGAGGGACTACTATGCTAAGgtttttttctagtcttatcctttgttgattctagtatcttcccaacatatgtgtaaacgttg-ttacatagtcatggcattaagcttgagtttttatttga
|||||| || ||  | |||||||| | | | || ||||| || |||||||| || ||||||  ||| || ||||| ||||||| |||||||||||| ||||||     ||  ||| |   ||  || ||     |  |||       ||     |  | ||| ||  || || |     ||     | |     |  | | 
AACATCCGAGGAGCTAAGCATCAACAAGATCAAATTCAAGGCCTTCGATCTGGGGGGTCACCAGATCGCGCGACGCGTGTGGAAGGACTACTATGCCAAGgttggacactcatctgagaattcttttatgtgtttgccttggttttctactcaaactccttgcttgaatcgttact-tgttctttcttatcaaatgctcgt

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|37837834|gb|BJ595842.1|BJ595842
EST:     TAGGTGGTCACACGATTGCTCGACGTGTGTGGAGGGACTACTATGCTAAG                         GTGGATGCTATCGTTTACCTTGTCGACGCAGTTGACAAGGAGAGGTTTCCT
genomic: TAGGTGGTCACACGATTGCTCGACGTGTGTGGAGGGACTACTATGCTAAGgtttttttct ... ctttgtgcagGTGGATGCTATCGTTTACCTTGTCGACGCAGTTGACAAGGAGAGGTTTCCT
EST: gi|18337821|gb|BJ169845.1|BJ169845
EST:     TAGGTGGTCACACGATTGCTCGACGTGTGTGGAGGGACTACTATGCTAAG                         GTGGATGCTATCGTTTACCTTGTCGACGCAGTTGACAAGGAGAGGTTTCCT
genomic: TAGGTGGTCACACGATTGCTCGACGTGTGTGGAGGGACTACTATGCTAAGgtttttttct ... ctttgtgcagGTGGATGCTATCGTTTACCTTGTCGACGCAGTTGACAAGGAGAGGTTTCCT
EST: gi|18341570|gb|BJ173605.1|BJ173605
EST:     TAGGTGGTCACACGATTGCTCGACGTGTGTGGAGGGACTACTATGCTAAG                         GTGGATGCTATCGTTTACCTTGTCGACGCAGTTGACAAGGAGAGGTTTCCT
genomic: TAGGTGGTCACACGATTGCTCGACGTGTGTGGAGGGACTACTATGCTAAGgtttttttct ... ctttgtgcagGTGGATGCTATCGTTTACCTTGTCGACGCAGTTGACAAGGAGAGGTTTCCT
EST: gi|37851441|gb|BJ609449.1|BJ609449
EST:     TAGGTGGTCACACGATTGCTCGACGTGTGTGGAGGGACTACTATGCTAAG                         GTGGATGCTATCGTTTACCTTGTCGACGCAGTTGACAAGGAGAGGTTTCCT
genomic: TAGGTGGTCACACGATTGCTCGACGTGTGTGGAGGGACTACTATGCTAAGgtttttttct ... ctttgtgcagGTGGATGCTATCGTTTACCTTGTCGACGCAGTTGACAAGGAGAGGTTTCCT
EST: gi|162233564|gb|FC410946.1|FC410946
EST:     TAGGTGGTCACACGATTGCTCGACGTGTGTGGAGGGACTACTATGCTAAG                         GTGGATGCTATCGTTTACCTTGTCGACGCAGTTGACAAGGAGAGGTTTCCT
genomic: TAGGTGGTCACACGATTGCTCGACGTGTGTGGAGGGACTACTATGCTAAGgtttttttct ... ctttgtgcagGTGGATGCTATCGTTTACCTTGTCGACGCAGTTGACAAGGAGAGGTTTCCT
EST: gi|208383033|gb|DC927783.1|DC927783
EST:     TAGGTGGTCACACGATTGCTCGACGTGTGTGGAGGGACTACTATGCTAAG                         GTGGATGCTATCGTTTACCTTGTCGACGCAGTTGACAAGGAGAGGTTTCCT
genomic: TAGGTGGTCACACGATTGCTCGACGTGTGTGGAGGGACTACTATGCTAAGgtttttttct ... ctttgtgcagGTGGATGCTATCGTTTACCTTGTCGACGCAGTTGACAAGGAGAGGTTTCCT
EST: gi|18363127|gb|BJ195199.1|BJ195199
EST:     TAGGTGGTCACACGATTGCTCGACGTGTGTGGAGGGACTACTATGCTAAG                         GTGGATGCTATCGTTTACCTTGTCGACGC
genomic: TAGGTGGTCACACGATTGCTCGACGTGTGTGGAGGGACTACTATGCTAAGgtttttttct ... ctttgtgcagGTGGATGCTATCGTTTACCTTGTCGACGC
EST: gi|37849290|gb|BJ607298.1|BJ607298
EST:     TAGGTGGTCACACGATTGCTCGACGTGTGTGGAGGGACTACTATGCTAAG                         GTGGATGCTATCGTTTACCTTGTCGACGCAGTTGACAAGGAGAGGTTTCCT
genomic: TAGGTGGTCACACGATTGCTCGACGTGTGTGGAGGGACTACTATGCTAAGgtttttttct ... ctttgtgcagGTGGATGCTATCGTTTACCTTGTCGACGCAGTTGACAAGGAGAGGTTTCCT
EST: gi|67569045|gb|BJ941869.1|BJ941869
EST:     TAGGTGGTCACACGATTGCTCGACGTGTGTGGAGGGACTACTATGCTAAG                         GTGGATGCTATCGTTTACCTTGTCGACGCAGTTGACAAGGAGAGGTTTCCT
genomic: TAGGTGGTCACACGATTGCTCGACGTGTGTGGAGGGACTACTATGCTAAGgtttttttct ... ctttgtgcagGTGGATGCTATCGTTTACCTTGTCGACGCAGTTGACAAGGAGAGGTTTCCT
EST: gi|67692279|gb|BJ952512.1|BJ952512
EST:     TAGGTGGTCACACGATTGCTCGACGTGTGTGGAGGGACTACTATGCTAAG                         GTGGATGCTATCGTTTACCTTGTCGACGCAGTTGACAAGGAGAGGTTTCCT
genomic: TAGGTGGTCACACGATTGCTCGACGTGTGTGGAGGGACTACTATGCTAAGgtttttttct ... ctttgtgcagGTGGATGCTATCGTTTACCTTGTCGACGCAGTTGACAAGGAGAGGTTTCCT
EST: gi|208349652|gb|DC917830.1|DC917830
EST:     TAGGTGGTCACACGATTGCTCGACGTGTGTGGAGGGACTACTATGCTAAG                         GTGGATGCTATCGTTTACCTTGTCGACGCAGTTGACAAGGAGAGGTTTCCT
genomic: TAGGTGGTCACACGATTGCTCGACGTGTGTGGAGGGACTACTATGCTAAGgtttttttct ... ctttgtgcagGTGGATGCTATCGTTTACCTTGTCGACGCAGTTGACAAGGAGAGGTTTCCT
EST: gi|37841128|gb|BJ599136.1|BJ599136
EST:     TAGGTGGTCACACGATTGCTCGACGTGTGTGGAGGGACTACTATGCTAAG                         GTGGATGCTATCGTTTACCTTGTCGACGCAGTTGACAAGGAGAGGTTTCCT
genomic: TAGGTGGTCACACGATTGCTCGACGTGTGTGGAGGGACTACTATGCTAAGgtttttttct ... ctttgtgcagGTGGATGCTATCGTTTACCTTGTCGACGCAGTTGACAAGGAGAGGTTTCCT
EST: gi|162262185|gb|FC437928.1|FC437928
EST:     TAGGTGGTCACACGATTGCTCGACGTGTGTGGAGGGACTACTATGCTAAG                         GTGGATGCTATCGTTTACCTTGTCGACGCAGTTGACAAGGAGAGGTTTCCT
genomic: TAGGTGGTCACACGATTGCTCGACGTGTGTGGAGGGACTACTATGCTAAGgtttttttct ... ctttgtgcagGTGGATGCTATCGTTTACCTTGTCGACGCAGTTGACAAGGAGAGGTTTCCT
EST: gi|162260872|gb|FC437929.1|FC437929
EST:     TAGGTGGTCACACGATTGCTCGACGTGTGTGGAGGGACTACTATGCTAAG                         GTGGATGCTATCGTTTACCTTGTCGACGCAGTTGACAAGGAGAGGTTTCCT
genomic: TAGGTGGTCACACGATTGCTCGACGTGTGTGGAGGGACTACTATGCTAAGgtttttttct ... ctttgtgcagGTGGATGCTATCGTTTACCTTGTCGACGCAGTTGACAAGGAGAGGTTTCCT
EST: gi|18375235|gb|BJ206813.1|BJ206813
EST:     TAGGTGGTCACACGATTGCTCGACGTGTGTGGAGGGACTACTATGCTAAG                         GTGGATGCTATCGTTTACCTTGTC
genomic: TAGGTGGTCACACGATTGCTCGACGTGTGTGGAGGGACTACTATGCTAAGgtttttttct ... ctttgtgcagGTGGATGCTATCGTTTACCTTGTC
EST: gi|162233563|gb|FC410945.1|FC410945
EST:     TAGGTGGTCACACGATTGCTCGACGTGTGTGGAGGGACTACTATGCTAAG                         GTGGATGCTATCGTTTACCTTGTCGACGCAGTTGACAAGGAGAGGTTTCCT
genomic: TAGGTGGTCACACGATTGCTCGACGTGTGTGGAGGGACTACTATGCTAAGgtttttttct ... ctttgtgcagGTGGATGCTATCGTTTACCTTGTCGACGCAGTTGACAAGGAGAGGTTTCCT
EST: gi|37840342|gb|BJ598350.1|BJ598350
EST:     TAGGTGGTCACACGATTGCTCGACGTGTGTGGAGGGACTACTATGCTAAG                         GTGGATGCTATCGTTTACCTTGTCGACGCAGTTGACAAGGAGAGGTTTCCT
genomic: TAGGTGGTCACACGATTGCTCGACGTGTGTGGAGGGACTACTATGCTAAGgtttttttct ... ctttgtgcagGTGGATGCTATCGTTTACCTTGTCGACGCAGTTGACAAGGAGAGGTTTCCT
EST: gi|13250958|gb|BG361861.1|BG361861
EST:     TAGGTGGTCACACGATTGCTCGACGTGTGTGGAGGGACTACTATGCTAAG                         GTGGATGCTATCGTTTACCTTGTCGACGCAGTTGACAAGGAGAGGTTTCCT
genomic: TAGGTGGTCACACGATTGCTCGACGTGTGTGGAGGGACTACTATGCTAAGgtttttttct ... ctttgtgcagGTGGATGCTATCGTTTACCTTGTCGACGCAGTTGACAAGGAGAGGTTTCCT
EST: gi|162214418|gb|FC391177.1|FC391177
EST:     TAGGTGGTCACACGATTGCTCGACGTGTGTGGAGGGACTACTATGCTAAG                         GTGGATGCTATCGTTTACCTTGTCGACGCAGTTGACAAGGAGAGGTTTCCT
genomic: TAGGTGGTCACACGATTGCTCGACGTGTGTGGAGGGACTACTATGCTAAGgtttttttct ... ctttgtgcagGTGGATGCTATCGTTTACCTTGTCGACGCAGTTGACAAGGAGAGGTTTCCT
EST: gi|208363206|gb|DC954378.1|DC954378
EST:     TAGGTGGTCACACGATTGCTCGACGTGTGTGGAGGGACTACTATGCTAAG                         GTGGATGCTATCGTTTACCTTGTCGACGCAGTTGACAAGGAGAGGTTTCCT
genomic: TAGGTGGTCACACGATTGCTCGACGTGTGTGGAGGGACTACTATGCTAAGgtttttttct ... ctttgtgcagGTGGATGCTATCGTTTACCTTGTCGACGCAGTTGACAAGGAGAGGTTTCCT
EST: gi|18339760|gb|BJ171787.1|BJ171787
EST:     TAGGTGGTCACACGATTGCTCGACGTGTGTGGAGGGACTACTATGCTAAG                         GTGGATGCTATCGTTTACCTTGTCGACGCAGTTGACAAGGAGAGGTTTCCT
genomic: TAGGTGGTCACACGATTGCTCGACGTGTGTGGAGGGACTACTATGCTAAGgtttttttct ... ctttgtgcagGTGGATGCTATCGTTTACCTTGTCGACGCAGTTGACAAGGAGAGGTTTCCT

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: 35 (upstream exon), 35 (downstream exon)
Score: 31

AACATCTGAAGAATTGAGCATCAATAGGGTGAAGTTCAAAGCATTCGATCTAGGTGGTCACACGATTGCTCGACGTGTGTGGAGGGACTACTATGCTAAGgtttttttct ... ctttgtgcagGTGGATGCTATCGTTTACCTTGTCGACGCAGTTGACAAGGAGAGGTTTCCTGAATCAAAGAAAGAACTCGACTCCTTGCTCTCGGATGACTCGCTCTCCC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACATCTGAAGAATTGAGCATCAATAGGGTGAAGTTCAAAGCATTCGATCTAGGTGGTCACACGATTGCTCGACGTGTGTGGAGGGACTACTATGCTAAGgtttttttctagtcttatcctttgttgattctagtatcttcccaacatatgtgtaaacgttgttacatagtcatggcattaagcttgagtttttatttga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG