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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgtcttccaaatctcctagggttccgtttacgtattgctgtattcaatgttgtatacctggaccttccagaatcacatccagaggcaactttttgctcttgacctaattttttcttgtatttgcagATGCAACAATGTCATGTATCTGAGAGGTGTTCCTGAGGACGAAGATGCTGCTGAAGACGATGATTGATAATTCTTGATGAGGCACTGTTTTAGGGCCTGT

Basic information

species Physcomitrella patens
transcript PP1S46_244V6.1
intron # 4
splice site 3'
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|162270790|gb|FC446819.1|FC446819
EST:     GAGTTTGTGGATGGGGCATTCACGGGCAACTTGGGAGAAGTCCTCATCAG                         ATGCAACAATGTCATGTATCTGAGAGGTGTTCCTGAGGACGAAGATGCTGC
genomic: GAGTTTGTGGATGGGGCATTCACGGGCAACTTGGGAGAAGTCCTCATCAGgttcgtcttc ... gtatttgcagATGCAACAATGTCATGTATCTGAGAGGTGTTCCTGAGGACGAAGATGCTGC
EST: gi|37850996|gb|BJ609004.1|BJ609004
EST:     GAGTTTGTGGATGGGGCATTCACGGGCAACTTGGGAGAAGTCCTCATCAG                         ATGCAACAATGTCATGTATCTGAGAGGTGTTCCTGAGGACGAAGATGCTGC
genomic: GAGTTTGTGGATGGGGCATTCACGGGCAACTTGGGAGAAGTCCTCATCAGgttcgtcttc ... gtatttgcagATGCAACAATGTCATGTATCTGAGAGGTGTTCCTGAGGACGAAGATGCTGC
EST: gi|15261393|gb|BI436703.1|BI436703
EST:     GAGTTTGTGGATGGGGCATTCACGGGCAACTTGGGAGAAGTCCTCATCAG                         ATGCAACAATGTCATGTATCTGAGAGGTGTTCCTGAGGACGAAGATGCTGC
genomic: GAGTTTGTGGATGGGGCATTCACGGGCAACTTGGGAGAAGTCCTCATCAGgttcgtcttc ... gtatttgcagATGCAACAATGTCATGTATCTGAGAGGTGTTCCTGAGGACGAAGATGCTGC
EST: gi|7067255|gb|AW497110.1|AW497110
EST:     GAGTTTGTGGATGGGGCATTCACGGGCAACTTGGGAGAAGTCCTCATCAG                         ATGCAACAATGTCATGTATCTGAGAGGTGTTCCTGAGGACGAAGATGCTGC
genomic: GAGTTTGTGGATGGGGCATTCACGGGCAACTTGGGAGAAGTCCTCATCAGgttcgtcttc ... gtatttgcagATGCAACAATGTCATGTATCTGAGAGGTGTTCCTGAGGACGAAGATGCTGC
EST: gi|19790253|gb|BQ041775.1|BQ041775
EST:     GAGTTTGTGGATGGGGCATTCACGGGCAACTTGGGAGAAGTCCTCATCAG                         ATGCAACAATGTCATGTATCTGAGAGGTGTTCCTGAGGACGAAGATGCTGC
genomic: GAGTTTGTGGATGGGGCATTCACGGGCAACTTGGGAGAAGTCCTCATCAGgttcgtcttc ... gtatttgcagATGCAACAATGTCATGTATCTGAGAGGTGTTCCTGAGGACGAAGATGCTGC
EST: gi|18370173|gb|BJ201775.1|BJ201775
EST:     GAGTTTGTGGATGGGGCATTCACGGGCAACTTGGGAGAAGTCCTCATCAG                         ATGCAACAATGTCATGTATCTGAGAGGTGTTCCTGAGGACGAAGATGCTGC
genomic: GAGTTTGTGGATGGGGCATTCACGGGCAACTTGGGAGAAGTCCTCATCAGgttcgtcttc ... gtatttgcagATGCAACAATGTCATGTATCTGAGAGGTGTTCCTGAGGACGAAGATGCTGC
EST: gi|18360431|gb|BJ192493.1|BJ192493
EST:     GAGTTTGTGGATGGGGCATTCACGGGCAACTTGGGAGAAGTCCTCATCAG                         ATGCAACAATGTCATGTATCTGAGAGGTGTTCCTGAGGACGAAGATGCTGC
genomic: GAGTTTGTGGATGGGGCATTCACGGGCAACTTGGGAGAAGTCCTCATCAGgttcgtcttc ... gtatttgcagATGCAACAATGTCATGTATCTGAGAGGTGTTCCTGAGGACGAAGATGCTGC
EST: gi|162270791|gb|FC446820.1|FC446820
EST:     GAGTTTGTGGATGGGGCATTCACGGGCAACTTGGGAGAAGTCCTCATCAG                         ATGCAACAATGTCATGTATCTGAGAGGTGTTCCTGAGGACGAAGATGCTGC
genomic: GAGTTTGTGGATGGGGCATTCACGGGCAACTTGGGAGAAGTCCTCATCAGgttcgtcttc ... gtatttgcagATGCAACAATGTCATGTATCTGAGAGGTGTTCCTGAGGACGAAGATGCTGC
EST: gi|67507561|gb|BJ940443.1|BJ940443
EST:     GAGTTTGTGGATGGGGCATTCACGGGCAACTTGGGAGAAGTCCTCATCAG                         ATGCAACAATGTCATGTATCTGAGAGGTGTTCCTGAGGACGAAGATGCTGC
genomic: GAGTTTGTGGATGGGGCATTCACGGGCAACTTGGGAGAAGTCCTCATCAGgttcgtcttc ... gtatttgcagATGCAACAATGTCATGTATCTGAGAGGTGTTCCTGAGGACGAAGATGCTGC
EST: gi|18360389|gb|BJ192451.1|BJ192451
EST:     GAGTTTGTGGATGGGGCATTCACGGGCAACTTGGGAGAAGTCCTCATCAG                         ATGCAACAATGTCATGTATCTGAGAGGTGTTCCTGAGGACGAAGATGCTGC
genomic: GAGTTTGTGGATGGGGCATTCACGGGCAACTTGGGAGAAGTCCTCATCAGgttcgtcttc ... gtatttgcagATGCAACAATGTCATGTATCTGAGAGGTGTTCCTGAGGACGAAGATGCTGC
EST: gi|18363001|gb|BJ195073.1|BJ195073
EST:     GAGTTTGTGGATGGGGCATTCACGGGCAACTTGGGAGAAGTCCTCATCAG                         ATGCAACAATGTCATGTATCTGAGAGGTGTTCCTGAGGACGAAGATGCTGC
genomic: GAGTTTGTGGATGGGGCATTCACGGGCAACTTGGGAGAAGTCCTCATCAGgttcgtcttc ... gtatttgcagATGCAACAATGTCATGTATCTGAGAGGTGTTCCTGAGGACGAAGATGCTGC
EST: gi|67569504|gb|BJ942328.1|BJ942328
EST:     GAGTTTGTGGATGGGGCATTCACGGGCAACTTGGGAGAAGTCCTCATCAG                         ATGCAACAATGTCATGTATCTGAGAGGTGTTCCTGAGGACGAAGATGCTGC
genomic: GAGTTTGTGGATGGGGCATTCACGGGCAACTTGGGAGAAGTCCTCATCAGgttcgtcttc ... gtatttgcagATGCAACAATGTCATGTATCTGAGAGGTGTTCCTGAGGACGAAGATGCTGC
EST: gi|67692772|gb|BJ953005.1|BJ953005
EST:     GAGTTTGTGGATGGGGCATTCACGGGCAACTTGGGAGAAGTCCTCATCAG                         ATGCAACAATGTCATGTATCTGAGAGGTGTTCCTGAGGACGAAGATGCTGC
genomic: GAGTTTGTGGATGGGGCATTCACGGGCAACTTGGGAGAAGTCCTCATCAGgttcgtcttc ... gtatttgcagATGCAACAATGTCATGTATCTGAGAGGTGTTCCTGAGGACGAAGATGCTGC
EST: gi|67691336|gb|BJ951569.1|BJ951569
EST:     GAGTTTGTGGATGGGGCATTCACGGGCAACTTGGGAGAAGTCCTCATCAG                         ATGCAACAATGTCATGTATCTGAGAGGTGTTCCTGAGGACGAAGATGCTGC
genomic: GAGTTTGTGGATGGGGCATTCACGGGCAACTTGGGAGAAGTCCTCATCAGgttcgtcttc ... gtatttgcagATGCAACAATGTCATGTATCTGAGAGGTGTTCCTGAGGACGAAGATGCTGC
EST: gi|15728429|gb|BI740783.1|BI740783
EST:     GAGTTTGTGGATGGGGCATTCACGGGCAACTTGGGAGAAGTCCTCATCAG                         ATGCAACAATGTCATGTATCTGAGAGGTGTTCCTGAGGACGAAGATGCTGC
genomic: GAGTTTGTGGATGGGGCATTCACGGGCAACTTGGGAGAAGTCCTCATCAGgttcgtcttc ... gtatttgcagATGCAACAATGTCATGTATCTGAGAGGTGTTCCTGAGGACGAAGATGCTGC
EST: gi|37838403|gb|BJ596411.1|BJ596411
EST:     GAGTTTGTGGATGGGGCATTCACGGGCAACTTGGGAGAAGTCCTCATCAG                         ATGCAACAATGTCATGTATCTGAGAGGTGTTCCTGAGGACGAAGATGCTGC
genomic: GAGTTTGTGGATGGGGCATTCACGGGCAACTTGGGAGAAGTCCTCATCAGgttcgtcttc ... gtatttgcagATGCAACAATGTCATGTATCTGAGAGGTGTTCCTGAGGACGAAGATGCTGC

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: 34 (upstream exon), 25 (downstream exon)
Score: 11

CTCGCAAGCACGGAAGAGTTTGTGGATGGGGCATTCACGGGCAACTTGGGAGAAGTCCTCATCAGgttcgtcttc ... gtatttgcagATGCAACAATGTCATGTATCTGAGAGGTGTTCCTGAGGACGAAGATGCTGCTGAAGACGATGATTGATAATTCTTGATGAGGCACTGTTTTAGGGCCTGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcacatccagaggcaactttttgctcttgacctaattttttcttgtatttgcagATGCAACAATGTCATGTATCTGAGAGGTGTTCCTGAGGACGAAGATGCTGCTGAAGACGATGATTGATAATTCTTGATGAGGCACTGTTTTAGGGCCTGT
                              acctaat  putative branch site (score: 11)
 ttttttcttgtattt  CT-rich tract
 taattttttcttgtat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgtcttccaaatctcctagggttccgtttacgtattgctgtattcaatgttgtatacctggaccttccagaatcacatccagaggcaactttttgctcttgacctaattttttcttgtatttgcagATGCAACAATGTCATGTATCTGAGAGGTGTTCCTGAGGACGAAGATGCTGCTGAAGACGATGATTGATAATTCTTGATGAGGCACTGTTTTAGGGCCTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA