Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTTACGGCTGATTATTTGGGAGAGGAATCTGAGGTTTTAGATGCGGAGAATGAGGTTGAGGAGGAAGCGGACAACCCTTTAGTTCCCAGTGCATTTGAGgttaggatttgcaaaaatctacgctcatttgtttcccactacgttgtcacgatgtttgtgtattcagcttgaatgttttcttgatgggaaactgacagggatagcctcattgttatccag

Basic information

species Physcomitrella patens
transcript PP1S45_62V6.1
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|100426412|gb|BY958885.1|BY958885
EST:     ATGAGGTTGAGGAGGAAGCGGACAACCCTTTAGTTCCCAGTGCATTTGAG                         GTTCAGAATTTGCTCATGCAGGTCTGTGATGAGACCTCTAACATCGCCGAG
genomic: ATGAGGTTGAGGAGGAAGCGGACAACCCTTTAGTTCCCAGTGCATTTGAGgttaggattt ... tgttatccagGTTCAGAATTTGCTCATGCAGGTCTGTGATGAGACCTCTAACATCGCCGAG
EST: gi|67569095|gb|BJ941919.1|BJ941919
EST:     ATGAGGTTGAGGAGGAAGCGGACAACCCTTTAGTTCCCAGTGCATTTGAG                         GTTCAGAATTTGCTCATGCAGGTCTGTGATGAGACCTCTAACATCGCCGAG
genomic: ATGAGGTTGAGGAGGAAGCGGACAACCCTTTAGTTCCCAGTGCATTTGAGgttaggattt ... tgttatccagGTTCAGAATTTGCTCATGCAGGTCTGTGATGAGACCTCTAACATCGCCGAG
EST: gi|100426360|gb|BY958859.1|BY958859
EST:     ATGAGGTTGAGGAGGAAGCGGACAACCCTTTAGTTCCCAGTGCATTTGAG                         GTTCAGAATTTGCTCATGCAGGTCTGTGATGAGACCTCTAACATCGCCGAG
genomic: ATGAGGTTGAGGAGGAAGCGGACAACCCTTTAGTTCCCAGTGCATTTGAGgttaggattt ... tgttatccagGTTCAGAATTTGCTCATGCAGGTCTGTGATGAGACCTCTAACATCGCCGAG
EST: gi|208366599|gb|DC954879.1|DC954879
EST:     ATGAGG-TGAGGAGG-AGCGGACAACCC-TTAGNTCCCAGTGCA-TTGAG                         GTTCAGAA-TTGCTCATGCAGGTCTGTGATGAGACCTCTAACATCGCCGAG
genomic: ATGAGGTTGAGGAGGAAGCGGACAACCCTTTAGTTCCCAGTGCATTTGAGgttaggattt ... tgttatccagGTTCAGAATTTGCTCATGCAGGTCTGTGATGAGACCTCTAACATCGCCGAG
EST: gi|208393169|gb|DC907992.1|DC907992
EST:     ATGAGGTTGAGGAGGAAGCGGACAACCCTTTAGTTCCCAGTGCATTTGAG                         GTTCAGAATTTGCTCATGCAGGTCTGTGATGAGACCTCTAACATCGCCGAG
genomic: ATGAGGTTGAGGAGGAAGCGGACAACCCTTTAGTTCCCAGTGCATTTGAGgttaggattt ... tgttatccagGTTCAGAATTTGCTCATGCAGGTCTGTGATGAGACCTCTAACATCGCCGAG
EST: gi|100355974|gb|BY946131.1|BY946131
EST:     ATGAGGTTGAGGAGGAAGCGGACAACCCTTTAGTTCCCAGTGCATTTGAG                         GTCCAGAATTTGCTCATGCAGGTCTGTGATGAGACCTCTAACATCGCCGAG
genomic: ATGAGGTTGAGGAGGAAGCGGACAACCCTTTAGTTCCCAGTGCATTTGAGgttaggattt ... tgttatccagGTTCAGAATTTGCTCATGCAGGTCTGTGATGAGACCTCTAACATCGCCGAG
EST: gi|67571987|gb|BJ944811.1|BJ944811
EST:     ATGAGGTTGAGGAGGAAGCGGACAACCCTTTAGTTCCCAGTGCATTTGAG                         GTTCAGAATTTGCTCATGCAGGTCTGTGATGAGACCTCTAACATCGCCGAG
genomic: ATGAGGTTGAGGAGGAAGCGGACAACCCTTTAGTTCCCAGTGCATTTGAGgttaggattt ... tgttatccagGTTCAGAATTTGCTCATGCAGGTCTGTGATGAGACCTCTAACATCGCCGAG
EST: gi|67695352|gb|BJ955585.1|BJ955585
EST:     AGTGCATTTGAG                         GTTCAGAATTTGCTCATGCAGGTCTGTGATGAGACCTCTAACATCGCCGAG
genomic: AGTGCATTTGAGgttaggattt ... tgttatccagGTTCAGAATTTGCTCATGCAGGTCTGTGATGAGACCTCTAACATCGCCGAG
EST: gi|67569203|gb|BJ942027.1|BJ942027
EST:     ATGAGGTTGAGGAGGAAGCGGACAACCCTTTAGTTCCCAGTGCATTTGAG                         GTTCAGAATTTGCTCATGCAGGTCTGTGATGAGACCTCTAACATCGCCGAG
genomic: ATGAGGTTGAGGAGGAAGCGGACAACCCTTTAGTTCCCAGTGCATTTGAGgttaggattt ... tgttatccagGTTCAGAATTTGCTCATGCAGGTCTGTGATGAGACCTCTAACATCGCCGAG
EST: gi|208392034|gb|DC941882.1|DC941882
EST:     ATGAGGTTGAGGAGGAAGCGGACAACCCTTTAGTTCCCAGTGCATTTGAG                         GTTCAGAATTTGCTCATGCAGGTCTGTGATGAGACCTCTAACATCGCCGAG
genomic: ATGAGGTTGAGGAGGAAGCGGACAACCCTTTAGTTCCCAGTGCATTTGAGgttaggattt ... tgttatccagGTTCAGAATTTGCTCATGCAGGTCTGTGATGAGACCTCTAACATCGCCGAG
EST: gi|208371076|gb|DC931550.1|DC931550
EST:     ATGAGGTTGAGGAGGAAGCGGACAACCCTTTAGTTCCCAGTGCATTTGAG                         GTTCAGAATTTGCTCATGCAGGTCTGTGATGAGACCTCTAACATCGCCGAG
genomic: ATGAGGTTGAGGAGGAAGCGGACAACCCTTTAGTTCCCAGTGCATTTGAGgttaggattt ... tgttatccagGTTCAGAATTTGCTCATGCAGGTCTGTGATGAGACCTCTAACATCGCCGAG
EST: gi|100363968|gb|BY966260.1|BY966260
EST:     ATGAGGTTGAGGAGGAAGCGGACAACCCTTTAGTTCCCAGTGCATTTGAG                         GTGCAGAATTTGCTCATGCAGGTCTGTGATGAGACCTCTAACATCGCCGAG
genomic: ATGAGGTTGAGGAGGAAGCGGACAACCCTTTAGTTCCCAGTGCATTTGAGgttaggattt ... tgttatccagGTTCAGAATTTGCTCATGCAGGTCTGTGATGAGACCTCTAACATCGCCGAG
EST: gi|162203524|gb|FC380440.1|FC380440
EST:     ATGAGGTTGAGGAGGAAGCGGACAACCCTTTAGTTCCCAGTGCATTTGAG                         GTTCAGAATTTGCTCATGCAGGTCTGTGATGAGACCTCTAACATCGCCGAG
genomic: ATGAGGTTGAGGAGGAAGCGGACAACCCTTTAGTTCCCAGTGCATTTGAGgttaggattt ... tgttatccagGTTCAGAATTTGCTCATGCAGGTCTGTGATGAGACCTCTAACATCGCCGAG
EST: gi|100450615|gb|CJ974352.1|CJ974352
EST:     ATGAGGTTGAGGAGGAAGCGGACAACCCTTTAGTTCCCAGTGCATTTGAG                         GTTCAGAATTTGCTCATGCAGGTCTGTGATGAGACCTCTAACATCGCCGAG
genomic: ATGAGGTTGAGGAGGAAGCGGACAACCCTTTAGTTCCCAGTGCATTTGAGgttaggattt ... tgttatccagGTTCAGAATTTGCTCATGCAGGTCTGTGATGAGACCTCTAACATCGCCGAG
EST: gi|18326048|gb|BJ158047.1|BJ158047
EST:     ATGAGGTTGAGGAGGAAGCGGACAACCCTTTAGTTCCCAGTGCATTTGAG                         GTTCAGAATTTGCTCATGCAGGTCTGTGATGAGACCTCTAACATCGCCGAG
genomic: ATGAGGTTGAGGAGGAAGCGGACAACCCTTTAGTTCCCAGTGCATTTGAGgttaggattt ... tgttatccagGTTCAGAATTTGCTCATGCAGGTCTGTGATGAGACCTCTAACATCGCCGAG

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-Seq library.


Block sizes: 33 (upstream exon), 35 (downstream exon)
Score: 13

GGTTACGGCTGATTATTTGGGAGAGGAATCTGAGGTTTTAGATGCGGAGAATGAGGTTGAGGAGGAAGCGGACAACCCTTTAGTTCCCAGTGCATTTGAGgttaggattt ... tgttatccagGTTCAGAATTTGCTCATGCAGGTCTGTGATGAGACCTCTAACATCGCCGAGGTTCAGCTGAAG





























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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTTACGGCTGATTATTTGGGAGAGGAATCTGAGGTTTTAGATGCGGAGAATGAGGTTGAGGAGGAAGCGGACAACCCTTTAGTTCCCAGTGCATTTGAGgttaggatttgcaaaaatctacgctcatttgtttcccactacgttgtcacgatgtttgtgtattcagcttgaatgttttcttgatgggaaactgacagggatagcctcattgttatccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA