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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACAATACTTTGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAGgtatgacatttctgctgaatcactcaatctgatcaaatatgcaacattcctatccgttttcgagatgctataccagttgtagttttctgtgatatcacataatactcggtatgcgtcacttactcgactcaagtgcttgatcaaaccag

Basic information

species Physcomitrella patens
transcript PP1S97_166V6.1
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|100381423|gb|BY950104.1|BY950104
EST:     CTGGATGTTTTCTGGGAGCGCCACGANTCCA-CCACGCTNCA-CCGTCAG                         GGGTA-CGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCC
genomic: CTGGATGTTTTCTGGAAGCGCCACGA-TCCAACCACGCT-CAACCGTCAGgtatgacatt ... atcaaaccagGG-TAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCC
EST: gi|162236116|gb|FC411118.1|FC411118
EST:     TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAG                         GGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
genomic: TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAGgtatgacatt ... atcaaaccagGGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
EST: gi|162247221|gb|FC423045.1|FC423045
EST:     TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAG                         GGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCT
genomic: TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAGgtatgacatt ... atcaaaccagGGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCT
EST: gi|208349651|gb|DC917829.1|DC917829
EST:     TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAG                         GGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
genomic: TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAGgtatgacatt ... atcaaaccagGGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
EST: gi|67693837|gb|BJ954070.1|BJ954070
EST:     TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAG                         GGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
genomic: TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAGgtatgacatt ... atcaaaccagGGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
EST: gi|208394315|gb|DC904135.1|DC904135
EST:     TGCTGGATGTTTTCTGGAANCGCCACGATCCAACCACGCTCAACCGTCAG                         GGTAACGACAGGGGAACCCANTACAGATCTGGCATCTACTTTTACTCTCC
genomic: TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAGgtatgacatt ... atcaaaccagGGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCC
EST: gi|208359302|gb|DC954197.1|DC954197
EST:     TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAG                         GGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
genomic: TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAGgtatgacatt ... atcaaaccagGGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
EST: gi|22492712|gb|BU052635.1|BU052635
EST:     TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAG                         GGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
genomic: TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAGgtatgacatt ... atcaaaccagGGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
EST: gi|162236117|gb|FC411119.1|FC411119
EST:     TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAG                         GGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
genomic: TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAGgtatgacatt ... atcaaaccagGGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
EST: gi|162223584|gb|FC399409.1|FC399409
EST:     TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAG                         GGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
genomic: TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAGgtatgacatt ... atcaaaccagGGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
EST: gi|208397380|gb|DC908256.1|DC908256
EST:     TGCTGGATGTTTTCTGGAANCGCCACGATCCAACCACGCTCAACCGTCAG                         GGTAACGACAGGGGAACC-ANTACANATCTGGCATCTACTTT-ACTCTCC
genomic: TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAGgtatgacatt ... atcaaaccagGGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCC
EST: gi|208351470|gb|DC921775.1|DC921775
EST:     TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAG                         GGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
genomic: TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAGgtatgacatt ... atcaaaccagGGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
EST: gi|162204709|gb|FC381118.1|FC381118
EST:     TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAG                         GGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
genomic: TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAGgtatgacatt ... atcaaaccagGGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
EST: gi|162265427|gb|FC440753.1|FC440753
EST:     TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAG                         GGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
genomic: TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAGgtatgacatt ... atcaaaccagGGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
EST: gi|208398630|gb|DC920525.1|DC920525
EST:     TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAG                         GGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
genomic: TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAGgtatgacatt ... atcaaaccagGGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
EST: gi|67698661|gb|BJ958894.1|BJ958894
EST:     TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAG                         GGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
genomic: TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAGgtatgacatt ... atcaaaccagGGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
EST: gi|162200498|gb|FC376159.1|FC376159
EST:     CCACGATCCAACCACGCTCAACCGTCAG                         GGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
genomic: CCACGATCCAACCACGCTCAACCGTCAGgtatgacatt ... atcaaaccagGGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
EST: gi|19782856|gb|BQ039927.1|BQ039927
EST:     TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAG                         GGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
genomic: TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAGgtatgacatt ... atcaaaccagGGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
EST: gi|162204708|gb|FC381117.1|FC381117
EST:     TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAG                         GGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
genomic: TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAGgtatgacatt ... atcaaaccagGGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
EST: gi|22133285|gb|BQ827650.1|BQ827650
EST:     TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAG                         GGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
genomic: TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAGgtatgacatt ... atcaaaccagGGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
EST: gi|208374469|gb|DC941198.1|DC941198
EST:     TGCTGGATGTTTTCTGGAANCGCCACNATCCAACCACGCTCAACCGTCAG                         GGTANCNACAGGGNAACCCANTACAAATCTGGCATCTACTTT
genomic: TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAGgtatgacatt ... atcaaaccagGGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTT
EST: gi|162227818|gb|FC403968.1|FC403968
EST:     TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAG                         GGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
genomic: TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAGgtatgacatt ... atcaaaccagGGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
EST: gi|162181923|gb|FC357730.1|FC357730
EST:     TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAG                         GGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
genomic: TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAGgtatgacatt ... atcaaaccagGGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
EST: gi|100362334|gb|BY947307.1|BY947307
EST:     GCTGGATGTTTTTCTGGA-GCGCCACGATCCNACCACGCTCAACCGTCAG                         GGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
genomic: GCTGGATGTTTT-CTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAGgtatgacatt ... atcaaaccagGGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
EST: gi|100411853|gb|BY992373.1|BY992373
EST:     TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAG                         GGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
genomic: TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAGgtatgacatt ... atcaaaccagGGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
EST: gi|208349313|gb|DC918035.1|DC918035
EST:     TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAG                         GGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
genomic: TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAGgtatgacatt ... atcaaaccagGGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
EST: gi|162233113|gb|FC408936.1|FC408936
EST:     TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAG                         GGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
genomic: TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAGgtatgacatt ... atcaaaccagGGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
EST: gi|162265428|gb|FC440754.1|FC440754
EST:     TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAG                         GGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
genomic: TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAGgtatgacatt ... atcaaaccagGGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
EST: gi|67575202|gb|BJ948026.1|BJ948026
EST:     TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAG                         GGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
genomic: TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAGgtatgacatt ... atcaaaccagGGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
EST: gi|22132784|gb|BQ827354.1|BQ827354
EST:     TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAG                         GGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
genomic: TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAGgtatgacatt ... atcaaaccagGGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
EST: gi|162247220|gb|FC423044.1|FC423044
EST:     TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAG                         GGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
genomic: TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAGgtatgacatt ... atcaaaccagGGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
EST: gi|162223598|gb|FC399410.1|FC399410
EST:     TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAG                         GGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
genomic: TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAGgtatgacatt ... atcaaaccagGGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
EST: gi|208353708|gb|DC922140.1|DC922140
EST:     TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAG                         GGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
genomic: TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAGgtatgacatt ... atcaaaccagGGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
EST: gi|162208097|gb|FC384253.1|FC384253
EST:     TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAG                         GGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG
genomic: TGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAGgtatgacatt ... atcaaaccagGGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCG

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: 28 (upstream exon), 35 (downstream exon)
Score: 27

TGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACAATACTTTGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAGgtatgacatt ... atcaaaccagGGTAACGACAGGGGAACCCAGTACAGATCTGGCATCTACTTTTACTCTCCGGAGCAAGAGAAAGCCGCATTGGAATCGAAGGAGCAGGTGCAGAAGACAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACAATACTTTGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAACCGTCAGgtatgacatttctgctgaatcactcaatctgatcaaatatgcaacattcctatccgttttcgagatgctataccagttgtagttttctgtgatatcacataatactcggtatgcgtcacttactcgactcaagtgcttgatcaaaccag

- - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG