Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCATTAGTAAGGTAGCAGAAGAGGCTGAGAACTACCCTTACGAGATTCAAACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAGgtgagcccttctttccttttgctctttgctaactaagacatactccagctcaaatattggattctgtttcagatgaactctcgactgagggtctctcagctttcttttctagtcccactgtcaggattgcctttccttgccactgtagttagatgtcataaacctaatgatctgtaattgggtaacag

Basic information

species Physcomitrella patens
transcript PP1S4_75V6.1
intron # 3
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|67701024|gb|BJ961257.1|BJ961257
EST:     AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAG                         GAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
genomic: AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAGgtgagccctt ... tgggtaacagGAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
EST: gi|67572953|gb|BJ945777.1|BJ945777
EST:     AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAG                         GAGGCTTGAGCGAGAATGACTTCATCTTCGCGT
genomic: AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAGgtgagccctt ... tgggtaacagGAGGCTTGAGCGAGAATGACTTCATCTTCGCGT
EST: gi|162223589|gb|FC399713.1|FC399713
EST:     AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAG                         GAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
genomic: AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAGgtgagccctt ... tgggtaacagGAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
EST: gi|162228292|gb|FC404371.1|FC404371
EST:     AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAG                         GAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
genomic: AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAGgtgagccctt ... tgggtaacagGAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
EST: gi|162172794|gb|FC348383.1|FC348383
EST:     AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAG                         GAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCANAGATAGATCAAGTTG
genomic: AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAGgtgagccctt ... tgggtaacagGAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
EST: gi|37845568|gb|BJ603576.1|BJ603576
EST:     AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAG                         GAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
genomic: AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAGgtgagccctt ... tgggtaacagGAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
EST: gi|15327270|gb|BI487856.1|BI487856
EST:     AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAG                         GAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
genomic: AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAGgtgagccctt ... tgggtaacagGAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
EST: gi|37839637|gb|BJ597645.1|BJ597645
EST:     AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAG                         GAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
genomic: AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAGgtgagccctt ... tgggtaacagGAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
EST: gi|162172793|gb|FC348382.1|FC348382
EST:     AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAG                         GAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
genomic: AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAGgtgagccctt ... tgggtaacagGAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
EST: gi|162249183|gb|FC421227.1|FC421227
EST:     AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAG                         GAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
genomic: AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAGgtgagccctt ... tgggtaacagGAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
EST: gi|67696335|gb|BJ956568.1|BJ956568
EST:     AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAG                         GAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
genomic: AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAGgtgagccctt ... tgggtaacagGAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
EST: gi|162210448|gb|FC386536.1|FC386536
EST:     AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAG                         GAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
genomic: AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAGgtgagccctt ... tgggtaacagGAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
EST: gi|162209382|gb|FC385497.1|FC385497
EST:     AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAG                         GAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
genomic: AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAGgtgagccctt ... tgggtaacagGAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
EST: gi|162209383|gb|FC385498.1|FC385498
EST:     AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAG                         GAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
genomic: AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAGgtgagccctt ... tgggtaacagGAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
EST: gi|162235543|gb|FC411340.1|FC411340
EST:     AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAG                         GAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
genomic: AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAGgtgagccctt ... tgggtaacagGAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
EST: gi|37830831|gb|BJ588843.1|BJ588843
EST:     AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAG                         GAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
genomic: AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAGgtgagccctt ... tgggtaacagGAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
EST: gi|162235544|gb|FC411341.1|FC411341
EST:     AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAG                         GAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCANAGATAGATCAAGTTG
genomic: AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAGgtgagccctt ... tgggtaacagGAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
EST: gi|162271170|gb|FC447159.1|FC447159
EST:     AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAG                         GAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
genomic: AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAGgtgagccctt ... tgggtaacagGAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
EST: gi|162223590|gb|FC399714.1|FC399714
EST:     AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAG                         GAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
genomic: AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAGgtgagccctt ... tgggtaacagGAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
EST: gi|162228293|gb|FC404372.1|FC404372
EST:     AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAG                         GAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
genomic: AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAGgtgagccctt ... tgggtaacagGAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
EST: gi|37852014|gb|BJ610022.1|BJ610022
EST:     AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAG                         GAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
genomic: AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAGgtgagccctt ... tgggtaacagGAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
EST: gi|162259933|gb|FC435236.1|FC435236
EST:     AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAG                         GAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
genomic: AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAGgtgagccctt ... tgggtaacagGAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
EST: gi|162210449|gb|FC386537.1|FC386537
EST:     AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAG                         GAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
genomic: AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAGgtgagccctt ... tgggtaacagGAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
EST: gi|162228470|gb|FC404120.1|FC404120
EST:     AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAG                         GAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
genomic: AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAGgtgagccctt ... tgggtaacagGAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
EST: gi|162258992|gb|FC435935.1|FC435935
EST:     AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGTTTCGATAG                         GAGGCTTGAGCGAGAATGACTTCATTTTCGCGTCAAAGATAGATCAAGTTG
genomic: AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAGgtgagccctt ... tgggtaacagGAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
EST: gi|67578157|gb|BJ950324.1|BJ950324
EST:     AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAG                         GAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
genomic: AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAGgtgagccctt ... tgggtaacagGAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
EST: gi|162259934|gb|FC435237.1|FC435237
EST:     AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAG                         GAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
genomic: AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAGgtgagccctt ... tgggtaacagGAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
EST: gi|67698062|gb|BJ958295.1|BJ958295
EST:     AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAG                         GAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
genomic: AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAGgtgagccctt ... tgggtaacagGAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
EST: gi|162271171|gb|FC447160.1|FC447160
EST:     AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAG                         GAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
genomic: AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAGgtgagccctt ... tgggtaacagGAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
EST: gi|162245153|gb|FC421601.1|FC421601
EST:     AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAG                         GAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
genomic: AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAGgtgagccctt ... tgggtaacagGAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
EST: gi|162213088|gb|FC389512.1|FC389512
EST:     AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAG                         GAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
genomic: AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAGgtgagccctt ... tgggtaacagGAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
EST: gi|162258993|gb|FC435936.1|FC435936
EST:     AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAG                         GAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
genomic: AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAGgtgagccctt ... tgggtaacagGAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
EST: gi|67574646|gb|BJ947470.1|BJ947470
EST:     AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAG                         GAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG
genomic: AACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAGgtgagccctt ... tgggtaacagGAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTG

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: 49

CGCATTAGTAAGGTAGCAGAAGAGGCTGAGAACTACCCTTACGAGATTCAAACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAGgtgagccctt ... tgggtaacagGAGGCTTGAGCGAGAATGACTTCATCTTCGCGTCAAAGATAGATCAAGTTGAAACTAAAGATCTGACCAGAAGGCTTCGGACATGGTTCTAGAAGTGTAC




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGCATTAGTAAGGTAGCAGAAGAGGCTGAGAACTACCCTTACGAGATTCAAACGCTGGATAGCAACAAAGTTAGGGTCGAGATCTGGACTGCTTCGATAGgtgagcccttctttccttttgctctttgctaactaagacatactccagctcaaatattggattctgtttcagatgaactctcgactgagggtctctcagctttcttttctagtcccactgtcaggattgcctttccttgccactgtagttagatgtcataaacctaatgatctgtaattgggtaacag

- - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC