Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaatgcgaaattagctgagtctacttacttttctcttatagtcgcatttgagaatgggaactcttttagtcaatcagcatggtatgtatcgtgtaacagtacggtccttgttgatttgtagtgcacatgggcttctcagtgttcaccatagagggttgacgacatgcataactttctgcagGGAGAAATTATAAGGTCATGCCGAGCCATGGGAAAGCCAGTGATCGTGGCTACAAATATGCTTGAGAGTATGATTACTCACCCCACTCCCACACGAGCAG

Basic information

species Physcomitrella patens
transcript PP1S205_25V6.1
intron # 6
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|208371212|gb|DC956004.1|DC956004
EST:     AGTGNCCCTTNTGCAG                         GGAG-AATTATAAGGTCATGCCGAGCCATGGGAAAGCCAGTGATCGTGGCT
genomic: AGTGCCCCTTCTGCAGgtacaatgcg ... ctttctgcagGGAGAAATTATAAGGTCATGCCGAGCCATGGGAAAGCCAGTGATCGTGGCT
EST: gi|100407600|gb|BY991774.1|BY991774
EST:     GAGGAGATCTTGGAGCTGAGCTGCCNATTGAGGAAGTGCCCCTTCTGCAG                         GGAGAAACTATAAGGTCGTGCCGAGCCATGGGAAAGCCAGTGATCGTGGCT
genomic: GAGGAGATCTTGGAGCTGAGCTGCCAATTGAGGAAGTGCCCCTTCTGCAGgtacaatgcg ... ctttctgcagGGAGAAATTATAAGGTCATGCCGAGCCATGGGAAAGCCAGTGATCGTGGCT
EST: gi|162179280|gb|FC356229.1|FC356229
EST:     GAGGAGATCTTGGAGCTGAGCTGCCAATTGAGGAAGTGCCCCTTCTGCAG                         GGAGAAATTATAAGGTCATGCCGAGCCATGGGAAAGCCAGTGATCGTGGCT
genomic: GAGGAGATCTTGGAGCTGAGCTGCCAATTGAGGAAGTGCCCCTTCTGCAGgtacaatgcg ... ctttctgcagGGAGAAATTATAAGGTCATGCCGAGCCATGGGAAAGCCAGTGATCGTGGCT
EST: gi|208359054|gb|DC957802.1|DC957802
EST:     GAGGAGATCTTGGAGCTGAGCTGCCAATTGAGGAAGTGCCCCTTCTGCAG                         GGAGAAATTATAAGGTCATGCCGAGCCATGGGAAAGCCAGTGATCGTGGCT
genomic: GAGGAGATCTTGGAGCTGAGCTGCCAATTGAGGAAGTGCCCCTTCTGCAGgtacaatgcg ... ctttctgcagGGAGAAATTATAAGGTCATGCCGAGCCATGGGAAAGCCAGTGATCGTGGCT
EST: gi|208354342|gb|DC953790.1|DC953790
EST:     CTGAGCTGCCAATTGAGGAAGTGCCCCTTNTGCAG                         GGAGAAATTATAAGGTCATGCCGAGCCATGGGAAAGCCAGTGATCGTGGCT
genomic: CTGAGCTGCCAATTGAGGAAGTGCCCCTTCTGCAGgtacaatgcg ... ctttctgcagGGAGAAATTATAAGGTCATGCCGAGCCATGGGAAAGCCAGTGATCGTGGCT
EST: gi|162227183|gb|FC402826.1|FC402826
EST:     GAGGAGATCTTGGAGCTGAGCTGCCAATTGAGGAAGTGCCCCTTCTGCAG                         GGAGAAATTATAAGGTCATGCCGAGCCATGGGAAAGCCAGTGATCGTGGCT
genomic: GAGGAGATCTTGGAGCTGAGCTGCCAATTGAGGAAGTGCCCCTTCTGCAGgtacaatgcg ... ctttctgcagGGAGAAATTATAAGGTCATGCCGAGCCATGGGAAAGCCAGTGATCGTGGCT
EST: gi|162156500|gb|FC332108.1|FC332108
EST:     GAGGAGATCTTGGAGCTGAGCTGCCAATTGAGGAAGTGCCCCTTCTGCAG                         GGAGAAATTATAAGGTCATGCCGAGCCATGGGAAAGCCAGTGATCGTGGCT
genomic: GAGGAGATCTTGGAGCTGAGCTGCCAATTGAGGAAGTGCCCCTTCTGCAGgtacaatgcg ... ctttctgcagGGAGAAATTATAAGGTCATGCCGAGCCATGGGAAAGCCAGTGATCGTGGCT
EST: gi|162167605|gb|FC344257.1|FC344257
EST:     GAGGAGATCTTGGAGCTGAGCTGCCAATTGAGGAAGTGCCCCTTCTGCAG                         GGAGAAATTATAAGGTCATGCCGAGCCATGGGAAAGCCAGTGATCGTGGCT
genomic: GAGGAGATCTTGGAGCTGAGCTGCCAATTGAGGAAGTGCCCCTTCTGCAGgtacaatgcg ... ctttctgcagGGAGAAATTATAAGGTCATGCCGAGCCATGGGAAAGCCAGTGATCGTGGCT
EST: gi|162203867|gb|FC379964.1|FC379964
EST:     GAGGAGATCTTGGAGCTGAGCTGCCAATTGAGGAAGTGCCCCTTCTGCAG                         GGAGAAATTATAAGGTCATGCCGAGCCATGGGAAAGCCAGTGATCGTGGCT
genomic: GAGGAGATCTTGGAGCTGAGCTGCCAATTGAGGAAGTGCCCCTTCTGCAGgtacaatgcg ... ctttctgcagGGAGAAATTATAAGGTCATGCCGAGCCATGGGAAAGCCAGTGATCGTGGCT
EST: gi|208361679|gb|DC954127.1|DC954127
EST:     AGCTGAGCTGCCAATTGAGGAAGTGCCCCTTCTGCAG                         GGAGAAATTATAAGGTCATGCCGAGCCATGGGAAAGCCAGTGATCGTGGCT
genomic: AGCTGAGCTGCCAATTGAGGAAGTGCCCCTTCTGCAGgtacaatgcg ... ctttctgcagGGAGAAATTATAAGGTCATGCCGAGCCATGGGAAAGCCAGTGATCGTGGCT
EST: gi|162177062|gb|FC353115.1|FC353115
EST:     GAGGAGATCTTGGAGCTGAGCTGCCAATTGAGGAAGTGCCCCTTCTGCAG                         GGAGAAATTATAAGGTCATGCCGAGCCATGGGAAAGCCAGTGATCGTGGCT
genomic: GAGGAGATCTTGGAGCTGAGCTGCCAATTGAGGAAGTGCCCCTTCTGCAGgtacaatgcg ... ctttctgcagGGAGAAATTATAAGGTCATGCCGAGCCATGGGAAAGCCAGTGATCGTGGCT
EST: gi|208381579|gb|DC915445.1|DC915445
EST:     AGCTGAGCTGCCCANTGAGGAAGTGCCCCTTNTGCAG                         GGAG-AANTATAAGGTCATGCCGAGCCAT-GGAAAGCCAGTGATCGTGGCT
genomic: AGCTGAGCTGCCAATTGAGGAAGTGCCCCTTCTGCAGgtacaatgcg ... ctttctgcagGGAGAAATTATAAGGTCATGCCGAGCCATGGGAAAGCCAGTGATCGTGGCT
EST: gi|162177266|gb|FC353423.1|FC353423
EST:     GAGGAGATCTTGGAGCTGAGCTGCCAATTGAGGAAGTGCCCCTTCTGCAG                         GGAGAAATTATAAGGTCATGCCGAGCCATGGGAAAGCCAGTGATCGTGGCT
genomic: GAGGAGATCTTGGAGCTGAGCTGCCAATTGAGGAAGTGCCCCTTCTGCAGgtacaatgcg ... ctttctgcagGGAGAAATTATAAGGTCATGCCGAGCCATGGGAAAGCCAGTGATCGTGGCT
EST: gi|162179457|gb|FC355457.1|FC355457
EST:     GAGGAGATCTTGGAGCTGAGCTGCCAATTGAGGAAGTGCCCCTTCTGCAG                         GGAGAAATTATAAGGTCATGCCGAGCCATGGGAAAGCCAGTGATCGTGGCT
genomic: GAGGAGATCTTGGAGCTGAGCTGCCAATTGAGGAAGTGCCCCTTCTGCAGgtacaatgcg ... ctttctgcagGGAGAAATTATAAGGTCATGCCGAGCCATGGGAAAGCCAGTGATCGTGGCT
EST: gi|162170104|gb|FC347016.1|FC347016
EST:     CTTGGAGCTGAGCTGCCAATTGAGGAAGTGCCCCTTCTGCAG                         GGAGAAATTATAAGGTCATGCCGAGCCATGGGAAAGCCAGTGATCGTGGCT
genomic: CTTGGAGCTGAGCTGCCAATTGAGGAAGTGCCCCTTCTGCAGgtacaatgcg ... ctttctgcagGGAGAAATTATAAGGTCATGCCGAGCCATGGGAAAGCCAGTGATCGTGGCT
EST: gi|162159393|gb|FC334661.1|FC334661
EST:     GAGGAGATCTTGGAGCTGAGCTGCCAATTGAGGAAGTGCCCCTTCTGCAG                         GGAGAAATTATAAGGTCATGCCGAGCCATGGGAAAGCCAGTGATCGTGGCT
genomic: GAGGAGATCTTGGAGCTGAGCTGCCAATTGAGGAAGTGCCCCTTCTGCAGgtacaatgcg ... ctttctgcagGGAGAAATTATAAGGTCATGCCGAGCCATGGGAAAGCCAGTGATCGTGGCT

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: 32 (upstream exon), 32 (downstream exon)
Score: 10

GCTATGGTTGCTCGAGGAGATCTTGGAGCTGAGCTGCCAATTGAGGAAGTGCCCCTTCTGCAGgtacaatgcg ... ctttctgcagGGAGAAATTATAAGGTCATGCCGAGCCATGGGAAAGCCAGTGATCGTGGCTACAAATATGCTTGAGAGTATGATTACTCACCCCACTCCCACACGAGCAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgggcttctcagtgttcaccatagagggttgacgacatgcataactttctgcagGGAGAAATTATAAGGTCATGCCGAGCCATGGGAAAGCCAGTGATCGTGGCTACAAATATGCTTGAGAGTATGATTACTCACCCCACTCCCACACGAGCAG
                                       gcataac  putative branch site (score: 10)
                                             ctttctgc  CT-rich tract
                                         ataacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacaatgcgaaattagctgagtctacttacttttctcttatagtcgcatttgagaatgggaactcttttagtcaatcagcatggtatgtatcgtgtaacagtacggtccttgttgatttgtagtgcacatgggcttctcagtgttcaccatagagggttgacgacatgcataactttctgcagGGAGAAATTATAAGGTCATGCCGAGCCATGGGAAAGCCAGTGATCGTGGCTACAAATATGCTTGAGAGTATGATTACTCACCCCACTCCCACACGAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG