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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGGCACGACCTCGCTATGGTGCATGAGCAGCATCACTGGAAGCGCGCGCAGAAAAAGGGGAAGGACTATGAATTCAAGgtcagttccttgcactttctggcgaacttcggtagggttttagggtgtcgtgagttgagcagatggcttactcgttggttaccctaaaagattgggtagtaattgagactttccagaagagaattggttgattgaaacgatttgcaaaccgtgtgcgtggttattgtgttcag

Basic information

species Physcomitrella patens
transcript PP1S49_23V6.1
intron # 2
splice site 5'
intron type U2

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|162232922|gb|FC407536.1|FC407536
EST:     AGCATCACTGGAAGCGCGCGCAGAAGAAGGGGAAGGACTATGAATTCAAG                         TGGAATAAGATATTGAACAAGACGCAGCGCGAATCGTACTACCACAACTGG
genomic: AGCATCACTGGAAGCGCGCGCAGAAAAAGGGGAAGGACTATGAATTCAAGgtcagttcct ... ttgtgttcagTGGAATAAGATATTGAACAAGACGCAGCGCGAATCGTACTACCACAACTGG
EST: gi|67700246|gb|BJ960479.1|BJ960479
EST:     AGCATCACTGGAAGCGCGCGCAGAAAAAGGGGAAGGACTATGAATTCAAG                         TGGAATAAGATATTGAACAAGACGCAGCGCGAATCGTACTACCACAACTGG
genomic: AGCATCACTGGAAGCGCGCGCAGAAAAAGGGGAAGGACTATGAATTCAAGgtcagttcct ... ttgtgttcagTGGAATAAGATATTGAACAAGACGCAGCGCGAATCGTACTACCACAACTGG
EST: gi|67697030|gb|BJ957263.1|BJ957263
EST:     AGCATCACTGGAAGCGCGCGCAGAAAAAGGGGAAGGACTATGAATTCAAG                         TGGAATAAGATATTGAACAAGACGCAGCGCGAATCGTACTACCACAACTGG
genomic: AGCATCACTGGAAGCGCGCGCAGAAAAAGGGGAAGGACTATGAATTCAAGgtcagttcct ... ttgtgttcagTGGAATAAGATATTGAACAAGACGCAGCGCGAATCGTACTACCACAACTGG
EST: gi|67573644|gb|BJ946468.1|BJ946468
EST:     AGCATCACTGGAAGCGCGCGCAGAAAAAGGGGAAGGACTATGAATTCAAG                         TGGAATAAGATATTGAACAAGACGCAGCGCGAATCGTACTACCACAACTGG
genomic: AGCATCACTGGAAGCGCGCGCAGAAAAAGGGGAAGGACTATGAATTCAAGgtcagttcct ... ttgtgttcagTGGAATAAGATATTGAACAAGACGCAGCGCGAATCGTACTACCACAACTGG
EST: gi|22491979|gb|BU051902.1|BU051902
EST:     AGCATCACTGGAAGCGCGCGCAGAAAAAGGGGAAGGACTATGAATTCAAG                         TGGAATAAGATATTGAACAAGACGCAGCGCGAATCGTACTACCACAACTGG
genomic: AGCATCACTGGAAGCGCGCGCAGAAAAAGGGGAAGGACTATGAATTCAAGgtcagttcct ... ttgtgttcagTGGAATAAGATATTGAACAAGACGCAGCGCGAATCGTACTACCACAACTGG
EST: gi|162210638|gb|FC386326.1|FC386326
EST:     AGCATCACTGGAAGCGCGCGCAGAAGAAGGGGAAGGACTATGAATTCAAG                         TGGAATAAGATATTGAACAAGACGCAGCGCGAATCGTACTACCACAACTGG
genomic: AGCATCACTGGAAGCGCGCGCAGAAAAAGGGGAAGGACTATGAATTCAAGgtcagttcct ... ttgtgttcagTGGAATAAGATATTGAACAAGACGCAGCGCGAATCGTACTACCACAACTGG
EST: gi|162231189|gb|FC406989.1|FC406989
EST:     AGCATCACTGGAAGCGCGCGCAGAAGAAGGGGAAGGACTATGAATTCAAG                         TGGAATAAGATATTGAACAAGACGCAGCGCGAATCGTACTACCACAACTGG
genomic: AGCATCACTGGAAGCGCGCGCAGAAAAAGGGGAAGGACTATGAATTCAAGgtcagttcct ... ttgtgttcagTGGAATAAGATATTGAACAAGACGCAGCGCGAATCGTACTACCACAACTGG
EST: gi|22131474|gb|BQ826634.1|BQ826634
EST:     AGCATCACTGGAAGCGCGCGCAGAAAAAGGGGAAGGACTATGAATTCAAG                         TGGAATAAGATATTGAACAAAACACAGCGCGAATCGTACTACCACAACTGG
genomic: AGCATCACTGGAAGCGCGCGCAGAAAAAGGGGAAGGACTATGAATTCAAGgtcagttcct ... ttgtgttcagTGGAATAAGATATTGAACAAGACGCAGCGCGAATCGTACTACCACAACTGG

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: 32 (upstream exon), 33 (downstream exon)
Score: 20

CTGGCACGACCTCGCTATGGTGCATGAGCAGCATCACTGGAAGCGCGCGCAGAAAAAGGGGAAGGACTATGAATTCAAGgtcagttcct ... ttgtgttcagTGGAATAAGATATTGAACAAGACGCAGCGCGAATCGTACTACCACAACTGGGCAGATTACTTCCCTTAAACATGGATTAGTGTTAAATGTTAGGATAGTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGGCACGACCTCGCTATGGTGCATGAGCAGCATCACTGGAAGCGCGCGCAGAAAAAGGGGAAGGACTATGAATTCAAGgtcagttccttgcactttctggcgaacttcggtagggttttagggtgtcgtgagttgagcagatggcttactcgttggttaccctaaaagattgggtagtaattgagactttccagaagagaattggttgattgaaacgatttgcaaaccgtgtgcgtggttattgtgttcag

- - - - - - - - - - - - - - - - - -  TGGAAG