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

...agggcgtgtgctttgacggggtggtgggtgtttcggaaggcagtgtggtgggcgggagagtgttggacttggtgctgagttgtggcagcgttgtgttcagGTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG

Basic information

species Physcomitrella patens
transcript PP1S348_15V6.1
intron # 5
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|37827533|gb|BJ585545.1|BJ585545
EST:     ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAG                         GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
genomic: ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAGgtgggtagac ... ttgtgttcagGTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
EST: gi|162269401|gb|FC445269.1|FC445269
EST:     ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAG                         GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
genomic: ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAGgtgggtagac ... ttgtgttcagGTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
EST: gi|162241149|gb|FC417768.1|FC417768
EST:     ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAG                         GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
genomic: ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAGgtgggtagac ... ttgtgttcagGTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
EST: gi|67725735|gb|BJ975994.1|BJ975994
EST:     ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAG                         GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
genomic: ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAGgtgggtagac ... ttgtgttcagGTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
EST: gi|67727562|gb|BJ977821.1|BJ977821
EST:     ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAG                         GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
genomic: ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAGgtgggtagac ... ttgtgttcagGTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
EST: gi|162207491|gb|FC383736.1|FC383736
EST:     ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAG                         GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
genomic: ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAGgtgggtagac ... ttgtgttcagGTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
EST: gi|162241150|gb|FC417769.1|FC417769
EST:     ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAG                         GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
genomic: ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAGgtgggtagac ... ttgtgttcagGTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
EST: gi|67726117|gb|BJ976376.1|BJ976376
EST:     ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAG                         GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
genomic: ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAGgtgggtagac ... ttgtgttcagGTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
EST: gi|67726885|gb|BJ977144.1|BJ977144
EST:     ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAG                         GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
genomic: ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAGgtgggtagac ... ttgtgttcagGTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
EST: gi|162270401|gb|FC447101.1|FC447101
EST:     ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCANGAGGAGGGAG                         GTGACGACCAACCTA-GGGAGA
genomic: ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAGgtgggtagac ... ttgtgttcagGTGACGACCAACCTAAGGGAGA
EST: gi|37840320|gb|BJ598328.1|BJ598328
EST:     ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAG                         GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
genomic: ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAGgtgggtagac ... ttgtgttcagGTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
EST: gi|67725283|gb|BJ975542.1|BJ975542
EST:     ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAG                         GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
genomic: ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAGgtgggtagac ... ttgtgttcagGTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
EST: gi|208345060|gb|DC925641.1|DC925641
EST:     ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAG                         GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
genomic: ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAGgtgggtagac ... ttgtgttcagGTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
EST: gi|208362548|gb|DC943747.1|DC943747
EST:     ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAG                         GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
genomic: ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAGgtgggtagac ... ttgtgttcagGTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
EST: gi|67716763|gb|BJ967023.1|BJ967023
EST:     ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAG                         GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
genomic: ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAGgtgggtagac ... ttgtgttcagGTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
EST: gi|208358628|gb|DC949963.1|DC949963
EST:     ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAG                         GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
genomic: ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAGgtgggtagac ... ttgtgttcagGTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
EST: gi|7207565|gb|AW561613.1|AW561613
EST:     ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAG                         GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
genomic: ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAGgtgggtagac ... ttgtgttcagGTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
EST: gi|18341253|gb|BJ173287.1|BJ173287
EST:     ANTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAG                         GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
genomic: ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAGgtgggtagac ... ttgtgttcagGTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
EST: gi|37849430|gb|BJ607438.1|BJ607438
EST:     ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAG                         GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
genomic: ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAGgtgggtagac ... ttgtgttcagGTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
EST: gi|162249893|gb|FC425694.1|FC425694
EST:     ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAG                         GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
genomic: ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAGgtgggtagac ... ttgtgttcagGTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
EST: gi|67726399|gb|BJ976658.1|BJ976658
EST:     ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAG                         GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
genomic: ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAGgtgggtagac ... ttgtgttcagGTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
EST: gi|162227061|gb|FC402262.1|FC402262
EST:     ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAG                         GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
genomic: ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAGgtgggtagac ... ttgtgttcagGTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
EST: gi|37852754|gb|BJ610762.1|BJ610762
EST:     ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAG                         GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
genomic: ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAGgtgggtagac ... ttgtgttcagGTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
EST: gi|162269402|gb|FC445270.1|FC445270
EST:     ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAG                         GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAGTGAC
genomic: ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAGgtgggtagac ... ttgtgttcagGTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAGTGAC
EST: gi|162227060|gb|FC402261.1|FC402261
EST:     ATTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAG                         GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
genomic: ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAGgtgggtagac ... ttgtgttcagGTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
EST: gi|67723293|gb|BJ973552.1|BJ973552
EST:     GCAGGAGGAGGGAN                         GTGACGACCANCCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
genomic: GCAGGAGGAGGGAGgtgggtagac ... ttgtgttcagGTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
EST: gi|37830224|gb|BJ588236.1|BJ588236
EST:     ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAG                         GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
genomic: ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAGgtgggtagac ... ttgtgttcagGTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
EST: gi|162270400|gb|FC447100.1|FC447100
EST:     ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAG                         GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
genomic: ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAGgtgggtagac ... ttgtgttcagGTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
EST: gi|67691435|gb|BJ951668.1|BJ951668
EST:     ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAG                         GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
genomic: ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAGgtgggtagac ... ttgtgttcagGTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
EST: gi|208365445|gb|DC950912.1|DC950912
EST:     ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAG                         GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
genomic: ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAGgtgggtagac ... ttgtgttcagGTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
EST: gi|18339751|gb|BJ171778.1|BJ171778
EST:     ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAG                         GTNACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
genomic: ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAGgtgggtagac ... ttgtgttcagGTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
EST: gi|18338400|gb|BJ170424.1|BJ170424
EST:     ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAG                         GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
genomic: ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAGgtgggtagac ... ttgtgttcagGTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
EST: gi|162206220|gb|FC382290.1|FC382290
EST:     ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAG                         GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
genomic: ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAGgtgggtagac ... ttgtgttcagGTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
EST: gi|37846290|gb|BJ604298.1|BJ604298
EST:     ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAG                         GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
genomic: ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAGgtgggtagac ... ttgtgttcagGTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
EST: gi|162207492|gb|FC383737.1|FC383737
EST:     ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAG                         GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAGTGA
genomic: ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAGgtgggtagac ... ttgtgttcagGTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAGTGA
EST: gi|208354137|gb|DC957385.1|DC957385
EST:     ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAG                         GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG
genomic: ACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAGgtgggtagac ... ttgtgttcagGTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG

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: 35 (upstream exon), 35 (downstream exon)
Score: 47

GATACGTTGAGCGAGGAGTCGTACAAGGACAGCACGTTGATCATGCAGCTACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAGgtgggtagac ... ttgtgttcagGTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agggcgtgtgctttgacggggtggtgggtgtttcggaaggcagtgtggtgggcgggagagtgttggacttggtgctgagttgtggcagcgttgtgttcagGTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG