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

...tcgctcgctcgctcgctcgctctccctcacacatacacacacaaaaacacacacaaccaggtctagtcagatattgatgtgaaataatctgctgcgacagGCTGCTGTTATCATGGAGGTTATTACTGGTAAGGGTGTTCTTGGACAACTAGGAATCAACCCCCTGGCTGTGAAGGGACCTTTCCTTGCAGGTTTTTTGT

Basic information

species Physcomitrella patens
transcript PP1S42_224V6.1
intron # 2
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|162201899|gb|FC376897.1|FC376897
EST:     GACGCTTTCAAGAGCTTCAAGTGGGTCGTCTAGCTATGGTCGGCTTTGCG                         GCTGCTGTTATCATGGAGGTTATTACTGGTAAGGGTGTTCTTGGACAACTA
genomic: GACGCTTTCAAGAGCTTCAAGTGGGTCGTCTAGCTATGGTCGGCTTTGCGgtaatctcgc ... gctgcgacagGCTGCTGTTATCATGGAGGTTATTACTGGTAAGGGTGTTCTTGGACAACTA
EST: gi|100428334|gb|BY977752.1|BY977752
EST:     GACGCTTTCAAGAGCTTCAAGTGGGTCGTCTAGCTATGGTCGGCTTTGCG                         GCTGGCTGT-ATCATGGAGGTTATTACTGGTAA
genomic: GACGCTTTCAAGAGCTTCAAGTGGGTCGTCTAGCTATGGTCGGCTTTGCGgtaatctcgc ... gctgcgacagGCTG-CTGTTATCATGGAGGTTATTACTGGTAA
EST: gi|162241275|gb|FC416906.1|FC416906
EST:     GACGCTTTCAAGAGCTTCAAGTGGGTCGTCTAGCTATGGTCGGCTTTGCG                         GCTGCTGTTATCATGGAGGTTATTACTGGTAAGGGTGTTCTTGGACAACTA
genomic: GACGCTTTCAAGAGCTTCAAGTGGGTCGTCTAGCTATGGTCGGCTTTGCGgtaatctcgc ... gctgcgacagGCTGCTGTTATCATGGAGGTTATTACTGGTAAGGGTGTTCTTGGACAACTA
EST: gi|100441914|gb|BY981137.1|BY981137
EST:     GACGCTTTCAAGAGCTTCAAGTGGGTCGTCTAGCTATGGTCGGCTTTGCG                         GCTGCTGTTATCATGGAGGTTAT-ACTGGTAAGGGTGTTCTTGGACAACTA
genomic: GACGCTTTCAAGAGCTTCAAGTGGGTCGTCTAGCTATGGTCGGCTTTGCGgtaatctcgc ... gctgcgacagGCTGCTGTTATCATGGAGGTTATTACTGGTAAGGGTGTTCTTGGACAACTA
EST: gi|100409864|gb|BY956142.1|BY956142
EST:     GACGCTTTCAAGAGCTTCAAGTGGGTCGTCTAGCTATGGTCGGCTTTGCG                         GCTGCTGTTATCATGGAGGTTATTACTGGTAAGGGTGTTCTTGGACAACTA
genomic: GACGCTTTCAAGAGCTTCAAGTGGGTCGTCTAGCTATGGTCGGCTTTGCGgtaatctcgc ... gctgcgacagGCTGCTGTTATCATGGAGGTTATTACTGGTAAGGGTGTTCTTGGACAACTA
EST: gi|100363522|gb|BY966431.1|BY966431
EST:     GACGCTTTCAAGAGCTTCAAGTGGGTCGTCTAGCTATGGTCGGCTTTGCG                         GCTGCTGTTATCATGGAGGTTATTACTGGTAAGGGTGTTCTTGGACAACTA
genomic: GACGCTTTCAAGAGCTTCAAGTGGGTCGTCTAGCTATGGTCGGCTTTGCGgtaatctcgc ... gctgcgacagGCTGCTGTTATCATGGAGGTTATTACTGGTAAGGGTGTTCTTGGACAACTA
EST: gi|100390176|gb|BY952584.1|BY952584
EST:     GACGCTTTCAAGAGCTTCAAGTGGGTCGTCTAGCTATGGTCGGCTTTGCG                         GCTGCTGTTATCATGGAGGTTATTACTGGTAAGGGTGTTCTTGGACAACTA
genomic: GACGCTTTCAAGAGCTTCAAGTGGGTCGTCTAGCTATGGTCGGCTTTGCGgtaatctcgc ... gctgcgacagGCTGCTGTTATCATGGAGGTTATTACTGGTAAGGGTGTTCTTGGACAACTA
EST: gi|208355784|gb|DC910550.1|DC910550
EST:     GACGCTTTCAAGAGCTTCAAGTGGGTCGTCTAGCTATGGTCGGCTTTGCG                         GCTGCTGTTATCATGGAGGTTATTACTGGTAAGGGTGTTCTTGGACAACTA
genomic: GACGCTTTCAAGAGCTTCAAGTGGGTCGTCTAGCTATGGTCGGCTTTGCGgtaatctcgc ... gctgcgacagGCTGCTGTTATCATGGAGGTTATTACTGGTAAGGGTGTTCTTGGACAACTA
EST: gi|100394423|gb|BY972061.1|BY972061
EST:     GACGCTTTCAAGAGCTTCAAGTGGGTCGTCTAGCTATGGTCGGCTTTGCG                         GCTGCTGTTATCATGGAGGTTATTACTGGTAAGGGTGTTCTTGGACAACTA
genomic: GACGCTTTCAAGAGCTTCAAGTGGGTCGTCTAGCTATGGTCGGCTTTGCGgtaatctcgc ... gctgcgacagGCTGCTGTTATCATGGAGGTTATTACTGGTAAGGGTGTTCTTGGACAACTA
EST: gi|100408289|gb|BY974110.1|BY974110
EST:     GACGCTTTCAAGAGCTTCAAGTGGGTCGTCTAGCTATGGTCGGCTTTGCG                         GCTGCTGTTATCATGGAGGTTATTACTGGTAAGGGTGTTCTTGGACAACTA
genomic: GACGCTTTCAAGAGCTTCAAGTGGGTCGTCTAGCTATGGTCGGCTTTGCGgtaatctcgc ... gctgcgacagGCTGCTGTTATCATGGAGGTTATTACTGGTAAGGGTGTTCTTGGACAACTA
EST: gi|15728403|gb|BI740770.1|BI740770
EST:     GACGCTTTCAAGAGCTTCAAGTGGGTCGTCTAGCTATGGTCGGCTTTGCG                         GCTGCTGTTATCATGGAGGTTATTACTGGTAAGGGTGTTCTTGGACAACTA
genomic: GACGCTTTCAAGAGCTTCAAGTGGGTCGTCTAGCTATGGTCGGCTTTGCGgtaatctcgc ... gctgcgacagGCTGCTGTTATCATGGAGGTTATTACTGGTAAGGGTGTTCTTGGACAACTA
EST: gi|162225958|gb|FC400976.1|FC400976
EST:     GACGCTTTCAAGAGCTTCAAGTGGGTCGTCTAGCTATGGTCGGCTTTGCG                         GCTGCTGTTATCATGGAGGTTATTACTGGTAAGGGTGTTCTTGGACAACTA
genomic: GACGCTTTCAAGAGCTTCAAGTGGGTCGTCTAGCTATGGTCGGCTTTGCGgtaatctcgc ... gctgcgacagGCTGCTGTTATCATGGAGGTTATTACTGGTAAGGGTGTTCTTGGACAACTA
EST: gi|208364166|gb|DC943422.1|DC943422
EST:     GACGCTTTCAAGAGCTTCAAGTGGGTCGTCTAGCTATGGTCGGCTTTGCG                         GCTGCTGTTATCATGGAGGTTATTACTGGTAAGGGTGTTCTTGGACAACTA
genomic: GACGCTTTCAAGAGCTTCAAGTGGGTCGTCTAGCTATGGTCGGCTTTGCGgtaatctcgc ... gctgcgacagGCTGCTGTTATCATGGAGGTTATTACTGGTAAGGGTGTTCTTGGACAACTA
EST: gi|208380328|gb|DC907653.1|DC907653
EST:     GACGCTCTCAAGAGCTTCAAGTGGGTCGTCTAGCTATGGTCGGCTTTGCG                         GCTGCTGTTATCATGGAGGTTATTACTGGTAAGGGTGTTCTTGGACAACTA
genomic: GACGCTTTCAAGAGCTTCAAGTGGGTCGTCTAGCTATGGTCGGCTTTGCGgtaatctcgc ... gctgcgacagGCTGCTGTTATCATGGAGGTTATTACTGGTAAGGGTGTTCTTGGACAACTA
EST: gi|100410651|gb|BY992202.1|BY992202
EST:     GACGCTTTCAAGAGCTTCAAGTGGGTCGTCTAGCTATGGTCGGCTTTGCG                         GCTGCTGTTATCATGGAGGTTATTACTGGTAAGGGTGTTCTTGGACAACTA
genomic: GACGCTTTCAAGAGCTTCAAGTGGGTCGTCTAGCTATGGTCGGCTTTGCGgtaatctcgc ... gctgcgacagGCTGCTGTTATCATGGAGGTTATTACTGGTAAGGGTGTTCTTGGACAACTA

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), 33 (downstream exon)
Score: 13

TGACATGAGCGGATACGGTTTGGGTGGCAAGGGCTCCTTCTTCGGATTCGGACGCTTTCAAGAGCTTCAAGTGGGTCGTCTAGCTATGGTCGGCTTTGCGgtaatctcgc ... gctgcgacagGCTGCTGTTATCATGGAGGTTATTACTGGTAAGGGTGTTCTTGGACAACTAGGAATCAACCCCCTGGCTGTGAAGGGACCTTTCCTTGCAGGTTTTTTGT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacacacacaaccaggtctagtcagatattgatgtgaaataatctgctgcgacagGCTGCTGTTATCATGGAGGTTATTACTGGTAAGGGTGTTCTTGGACAACTAGGAATCAACCCCCTGGCTGTGAAGGGACCTTTCCTTGCAGGTTTTTTGT
                          tattgat  putative branch site (score: 13)
                                  tgaaataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcgctcgctcgctcgctcgctctccctcacacatacacacacaaaaacacacacaaccaggtctagtcagatattgatgtgaaataatctgctgcgacagGCTGCTGTTATCATGGAGGTTATTACTGGTAAGGGTGTTCTTGGACAACTAGGAATCAACCCCCTGGCTGTGAAGGGACCTTTCCTTGCAGGTTTTTTGT

- - - - - - - - - - - - - - -cacatac