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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGCATTGCTGTTAACCCATCAAGCAAGCGCATCAATAATAACCCCCCAGATGATGGTGATACTGCTCCTATCATAAAGCTGATCACCGCAGTCTCACTGgttcgtatccctctcgccgtacccacccagtagttttgcggcccttttgcttacacattgttgttccacctgtgatcctctgtctgtgcttcgattgatg...

Basic information

species Physcomitrella patens
transcript PP1S186_65V6.1
intron # 1
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|18348907|gb|BJ180956.1|BJ180956
EST:     ATGATGGTGATACTGCTCCTATCATAAAGCTGATCACCGCAGTCTCACTG                         GTGCGGGTATATCTTATATCAAGGCTTCTTCTACTGCTTTCAAGGCTTCTT
genomic: ATGATGGTGATACTGCTCCTATCATAAAGCTGATCACCGCAGTCTCACTGgttcgtatcc ... taatggatagGTGCGGGTATATCTTATATCAAGGCTTCTTCTACTGCTTTCAAGGCTTCTT
EST: gi|100446819|gb|CJ971118.1|CJ971118
EST:     ATGATGGTGATACTGCTCCTATCATAAAGCTGATCACCGCAGTCTCACTG                         GTGCGGGTATATCTTATATCAAGGCTTCTTCTACTGCTTTCAAGGCTTCTT
genomic: ATGATGGTGATACTGCTCCTATCATAAAGCTGATCACCGCAGTCTCACTGgttcgtatcc ... taatggatagGTGCGGGTATATCTTATATCAAGGCTTCTTCTACTGCTTTCAAGGCTTCTT
EST: gi|100389724|gb|BY952530.1|BY952530
EST:     ATCATAAAGCTGATCACCGCAGTCTCACTG                         GTGCGGGTATATCTTATATCAAGGCTTCTTCTACTGCTTTCAAGGCTTCTT
genomic: ATCATAAAGCTGATCACCGCAGTCTCACTGgttcgtatcc ... taatggatagGTGCGGGTATATCTTATATCAAGGCTTCTTCTACTGCTTTCAAGGCTTCTT
EST: gi|18367834|gb|BJ199917.1|BJ199917
EST:     ATGATGGTGATACTGCTCCTATCATAAAGCTGATCACCGCAGTCTCACTG                         GTGCGGGTATATCTTATATCAAGGCTTCTTCTACTGCTTTCAAGGCTTCTT
genomic: ATGATGGTGATACTGCTCCTATCATAAAGCTGATCACCGCAGTCTCACTGgttcgtatcc ... taatggatagGTGCGGGTATATCTTATATCAAGGCTTCTTCTACTGCTTTCAAGGCTTCTT
EST: gi|18345260|gb|BJ177302.1|BJ177302
EST:     ATGATGGTGATACTGCTCCTATCATAAAGCTGATCACCGCAGTCTCACTG                         GTGCGGGTATATCTTATATCAAGGCTTCTTCTACTGCTTTCAAGGCTTCTT
genomic: ATGATGGTGATACTGCTCCTATCATAAAGCTGATCACCGCAGTCTCACTGgttcgtatcc ... taatggatagGTGCGGGTATATCTTATATCAAGGCTTCTTCTACTGCTTTCAAGGCTTCTT
EST: gi|18366467|gb|BJ198546.1|BJ198546
EST:     ATGATGGTGATACTGCTCCTATCATAAAGCTGATCACCGCAGTCTCACTG                         GTGCGGGTATATCTTATATCAAGGCTTCTTCTACTGCTTTCAAGGCTTCTT
genomic: ATGATGGTGATACTGCTCCTATCATAAAGCTGATCACCGCAGTCTCACTGgttcgtatcc ... taatggatagGTGCGGGTATATCTTATATCAAGGCTTCTTCTACTGCTTTCAAGGCTTCTT
EST: gi|18362406|gb|BJ194476.1|BJ194476
EST:     CTATCATAAAGCTGATCACCGCAGTCTCACTG                         GTGCGGGTATATCTTATATCAAGGCTTCTTCTACTGCTTTCAAGGCTTCTT
genomic: CTATCATAAAGCTGATCACCGCAGTCTCACTGgttcgtatcc ... taatggatagGTGCGGGTATATCTTATATCAAGGCTTCTTCTACTGCTTTCAAGGCTTCTT
EST: gi|18368657|gb|BJ200742.1|BJ200742
EST:     ATGATGGTGATACTGCTCCTATCATAAAGCTGATCACCGCAGTCTCACTG                         GTGCGGGTATATCTTATATCAAGGCTTCTTCTACTGCTTTCAAGGCTTCTT
genomic: ATGATGGTGATACTGCTCCTATCATAAAGCTGATCACCGCAGTCTCACTGgttcgtatcc ... taatggatagGTGCGGGTATATCTTATATCAAGGCTTCTTCTACTGCTTTCAAGGCTTCTT
EST: gi|18326970|gb|BJ158971.1|BJ158971
EST:     GCTCCTATCATAAAGCTGATCACCGCAGTCTCACTG                         GTGCGGGTATATCTTATATCAAGGCTTCTTCTACTGCTTTCAAGGCTTCTT
genomic: GCTCCTATCATAAAGCTGATCACCGCAGTCTCACTGgttcgtatcc ... taatggatagGTGCGGGTATATCTTATATCAAGGCTTCTTCTACTGCTTTCAAGGCTTCTT
EST: gi|18362113|gb|BJ194181.1|BJ194181
EST:     ATGATGGTGATACTGCTCCTATCATAAAGCTGATCACCGCAGTCTCACTG                         GTGCGGGTATATCTTATATCAAGGCTTCTTCTACTGCTTTCAAGGCTTCTT
genomic: ATGATGGTGATACTGCTCCTATCATAAAGCTGATCACCGCAGTCTCACTGgttcgtatcc ... taatggatagGTGCGGGTATATCTTATATCAAGGCTTCTTCTACTGCTTTCAAGGCTTCTT
EST: gi|208385579|gb|DC937124.1|DC937124
EST:     ATGATGGTGATACTGCTCCTATCATAAAGCTGATCACCGCAGTCTCACTG                         GTGCGGGTATATCTTATATCAAGGCTTCTTCTACTGCTTTCAAGGCTTCTT
genomic: ATGATGGTGATACTGCTCCTATCATAAAGCTGATCACCGCAGTCTCACTGgttcgtatcc ... taatggatagGTGCGGGTATATCTTATATCAAGGCTTCTTCTACTGCTTTCAAGGCTTCTT
EST: gi|18360390|gb|BJ192452.1|BJ192452
EST:     ATGATGGTGATACTGCTCCTATCATAAAGCTGATCACCGCAGTCTCACTG                         GTGCGGGTATATCTTATATCAAGGCTTCTTCTACTGCTTTCAAGGCTTCTT
genomic: ATGATGGTGATACTGCTCCTATCATAAAGCTGATCACCGCAGTCTCACTGgttcgtatcc ... taatggatagGTGCGGGTATATCTTATATCAAGGCTTCTTCTACTGCTTTCAAGGCTTCTT
EST: gi|18374229|gb|BJ205807.1|BJ205807
EST:     ATGATGGTGATACTGCTCCTATCATAAAGCTGATCACCGCAGTCTCACTG                         GTGCGGGTATATCTTATATCAAGGCTTCTTCTACTGCTTTCAAGGCTTCTT
genomic: ATGATGGTGATACTGCTCCTATCATAAAGCTGATCACCGCAGTCTCACTGgttcgtatcc ... taatggatagGTGCGGGTATATCTTATATCAAGGCTTCTTCTACTGCTTTCAAGGCTTCTT
EST: gi|18372230|gb|BJ203832.1|BJ203832
EST:     ATGATGGTGATACTGCTCCTATCATAAAGCTGATCACCGCAGTCTCACTG                         GTGCGGGTATATCTTATATCAAGGCTTCTTCTACTGCTTTCAAGGCTTCTT
genomic: ATGATGGTGATACTGCTCCTATCATAAAGCTGATCACCGCAGTCTCACTGgttcgtatcc ... taatggatagGTGCGGGTATATCTTATATCAAGGCTTCTTCTACTGCTTTCAAGGCTTCTT
EST: gi|18371374|gb|BJ202976.1|BJ202976
EST:     CTATCATAAAGCTGATCACCGCAGTCTCACTG                         GTGCGGGTATATCTTATATCAAGGCTTCTTCTACTGCTTTCAAGGCTTCTT
genomic: CTATCATAAAGCTGATCACCGCAGTCTCACTGgttcgtatcc ... taatggatagGTGCGGGTATATCTTATATCAAGGCTTCTTCTACTGCTTTCAAGGCTTCTT
EST: gi|18366521|gb|BJ198600.1|BJ198600
EST:     ATGATGGTGATACTGCTCCTATCATAAAGCTGATCACCGCAGTCTCACTG                         GTGCGGGTATATCTTATATCAAGGCTTCTTCTACTGCTTTCAAGGCTTCTT
genomic: ATGATGGTGATACTGCTCCTATCATAAAGCTGATCACCGCAGTCTCACTGgttcgtatcc ... taatggatagGTGCGGGTATATCTTATATCAAGGCTTCTTCTACTGCTTTCAAGGCTTCTT
EST: gi|18353706|gb|BJ185761.1|BJ185761
EST:     TAAAGCTGATCACCGCAGTCTCACTG                         GTGCGGGTATATCTTATATCAAGGCTTCTTCTACTGCTTTCAAGGCTTCTT
genomic: TAAAGCTGATCACCGCAGTCTCACTGgttcgtatcc ... taatggatagGTGCGGGTATATCTTATATCAAGGCTTCTTCTACTGCTTTCAAGGCTTCTT
EST: gi|18347912|gb|BJ179959.1|BJ179959
EST:     ATGATGGTGATACTGCTCCTATCATAAAGCTNATCACCGCAGTCTCACTG                         GTGCGGGTATATCTTATATCAAGGCTTCTTCTACTGCTTTCAAGGCTTCTT
genomic: ATGATGGTGATACTGCTCCTATCATAAAGCTGATCACCGCAGTCTCACTGgttcgtatcc ... taatggatagGTGCGGGTATATCTTATATCAAGGCTTCTTCTACTGCTTTCAAGGCTTCTT
EST: gi|18372929|gb|BJ204531.1|BJ204531
EST:     ATGATGGTGATACTGCTCCTATCATAAAGCTGATCACCGCAGTCTCACTG                         GTGCGGGTATATCTTATATCAAGGCTTCTTCTACTGCTTTCAAGGCTTCTT
genomic: ATGATGGTGATACTGCTCCTATCATAAAGCTGATCACCGCAGTCTCACTGgttcgtatcc ... taatggatagGTGCGGGTATATCTTATATCAAGGCTTCTTCTACTGCTTTCAAGGCTTCTT
EST: gi|18372218|gb|BJ203820.1|BJ203820
EST:     ATCATAAAGCTGATCACCGCAGTCTCACTG                         GTGCGGGTATATCTTATATCAAGGCTTCTTCTACTGCTTTCAAGGCTTCTT
genomic: ATCATAAAGCTGATCACCGCAGTCTCACTGgttcgtatcc ... taatggatagGTGCGGGTATATCTTATATCAAGGCTTCTTCTACTGCTTTCAAGGCTTCTT

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: 24 (upstream exon), 18 (downstream exon)
Score: 3

ATGCATTGCTGTTAACCCATCAAGCAAGCGCATCAATAATAACCCCCCAGATGATGGTGATACTGCTCCTATCATAAAGCTGATCACCGCAGTCTCACTGgttcgtatcc ... taatggatagGTGCGGGTATATCTTATATCAAGGCTTCTTCTACTGCTTTCAAGGCTTCTTCTGAATGGCAGCCGCGGAGGTATCGGAGCTACCCCCTCTCGAAGAATTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGCATTGCTGTTAACCCATCAAGCAAGCGCATCAATAATAACCCCCCAGATGATGGTGATACTGCTCCTATCATAAAGCTGATCACCGCAGTCTCACTGgttcgtatccctctcgccgtacccacccagtagttttgcggcccttttgcttacacattgttgttccacctgtgatcctctgtctgtgcttcgattgatg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT