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

GTCCCTTTTCAACGCACACAGTCTGGTGGCTTTCGCCTCCCGAGTCGGCTCCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGGgtataatcatctctctttgttgccgcattccctcacacgcccttgctggacacgctcctgtaatggcagtggctggtgtctcttttccgtggttgatggggattagggttcagggttctggactttgacggcgtttttgttttgaggttttgttggattgaggtctgagattctttgtgtgtgcag

Basic information

species Physcomitrella patens
transcript PP1S97_272V6.1
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|162217792|gb|FC394092.1|FC394092
EST:     CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGG                         TAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
genomic: CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGGgtataatcat ... gtgtgtgcagTAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
EST: gi|67574110|gb|BJ946934.1|BJ946934
EST:     CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGG                         TAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
genomic: CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGGgtataatcat ... gtgtgtgcagTAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
EST: gi|162201852|gb|FC377786.1|FC377786
EST:     CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGG                         TAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
genomic: CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGGgtataatcat ... gtgtgtgcagTAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
EST: gi|162235773|gb|FC411076.1|FC411076
EST:     CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGG                         TAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
genomic: CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGGgtataatcat ... gtgtgtgcagTAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
EST: gi|67696887|gb|BJ957120.1|BJ957120
EST:     CAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGG                         TAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
genomic: CAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGGgtataatcat ... gtgtgtgcagTAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
EST: gi|162235772|gb|FC411075.1|FC411075
EST:     CATGGGGCGCATGCACAGCTCTGG                         TAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
genomic: CATGGGGCGCATGCACAGCTCTGGgtataatcat ... gtgtgtgcagTAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
EST: gi|67699351|gb|BJ959584.1|BJ959584
EST:     TGCAACCATCAATTTTTTATCATGGGGCGCATGCACAGCTCTGG                         TAAGGGTATGTCCTTTTCGGNTCTGCCGTACAAGAGGAGCCCGCCATCTTG
genomic: TGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGGgtataatcat ... gtgtgtgcagTAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
EST: gi|18374703|gb|BJ206281.1|BJ206281
EST:     CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGG                         TAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
genomic: CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGGgtataatcat ... gtgtgtgcagTAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
EST: gi|162226145|gb|FC401605.1|FC401605
EST:     CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGG                         TAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
genomic: CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGGgtataatcat ... gtgtgtgcagTAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
EST: gi|162202712|gb|FC379018.1|FC379018
EST:     CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGG                         TAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
genomic: CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGGgtataatcat ... gtgtgtgcagTAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
EST: gi|67574049|gb|BJ946873.1|BJ946873
EST:     TCTTCTATCATGGGGCGCATGCACAGCTCTGG                         TAAGGGTATGATCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTT
genomic: TCTTCTATCATGGGGCGCATGCACAGCTCTGGgtataatcat ... gtgtgtgcagTAAGGGTATG-TCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTT
EST: gi|162274364|gb|FC450391.1|FC450391
EST:     CAATCTTCTATCATGGGGCGCATGCACAGCTCTGG                         TAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
genomic: CAATCTTCTATCATGGGGCGCATGCACAGCTCTGGgtataatcat ... gtgtgtgcagTAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
EST: gi|162216850|gb|FC393032.1|FC393032
EST:     CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGG                         TAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
genomic: CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGGgtataatcat ... gtgtgtgcagTAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
EST: gi|162223015|gb|FC399945.1|FC399945
EST:     CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGG                         TAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
genomic: CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGGgtataatcat ... gtgtgtgcagTAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
EST: gi|162277626|gb|FC453257.1|FC453257
EST:     CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGG                         TAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
genomic: CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGGgtataatcat ... gtgtgtgcagTAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
EST: gi|7147815|gb|AW509737.1|AW509737
EST:     CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGG                         TAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
genomic: CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGGgtataatcat ... gtgtgtgcagTAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
EST: gi|162257772|gb|FC434219.1|FC434219
EST:     CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGG                         TAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
genomic: CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGGgtataatcat ... gtgtgtgcagTAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
EST: gi|162228862|gb|FC405006.1|FC405006
EST:     CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGG                         TAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
genomic: CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGGgtataatcat ... gtgtgtgcagTAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
EST: gi|162244863|gb|FC425480.1|FC425480
EST:     CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGG                         TAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
genomic: CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGGgtataatcat ... gtgtgtgcagTAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
EST: gi|162260562|gb|FC436150.1|FC436150
EST:     ATCATGGGGCGCATGCACAGCTCTGG                         TAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
genomic: ATCATGGGGCGCATGCACAGCTCTGGgtataatcat ... gtgtgtgcagTAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
EST: gi|162249693|gb|FC426521.1|FC426521
EST:     CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGG                         TAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
genomic: CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGGgtataatcat ... gtgtgtgcagTAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
EST: gi|37848826|gb|BJ606834.1|BJ606834
EST:     CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGG                         TAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
genomic: CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGGgtataatcat ... gtgtgtgcagTAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
EST: gi|67697475|gb|BJ957708.1|BJ957708
EST:     CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGG                         TAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
genomic: CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGGgtataatcat ... gtgtgtgcagTAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
EST: gi|162224128|gb|FC399192.1|FC399192
EST:     CTTCTATCATGGGGCGCATGCACAGCTCTGG                         TAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
genomic: CTTCTATCATGGGGCGCATGCACAGCTCTGGgtataatcat ... gtgtgtgcagTAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
EST: gi|208364375|gb|DC950676.1|DC950676
EST:     CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGG                         TAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
genomic: CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGGgtataatcat ... gtgtgtgcagTAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
EST: gi|208391463|gb|DC937611.1|DC937611
EST:     CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGG                         TAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
genomic: CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGGgtataatcat ... gtgtgtgcagTAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
EST: gi|162243081|gb|FC417929.1|FC417929
EST:     CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGG                         TAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
genomic: CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGGgtataatcat ... gtgtgtgcagTAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
EST: gi|67572354|gb|BJ945178.1|BJ945178
EST:     CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGG                         TAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
genomic: CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGGgtataatcat ... gtgtgtgcagTAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
EST: gi|162260563|gb|FC436151.1|FC436151
EST:     CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGG                         TAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
genomic: CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGGgtataatcat ... gtgtgtgcagTAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
EST: gi|67695729|gb|BJ955962.1|BJ955962
EST:     CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGG                         TAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
genomic: CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGGgtataatcat ... gtgtgtgcagTAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
EST: gi|67575868|gb|BJ948692.1|BJ948692
EST:     CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGG                         TAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
genomic: CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGGgtataatcat ... gtgtgtgcagTAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
EST: gi|67573503|gb|BJ946327.1|BJ946327
EST:     CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGG                         TAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
genomic: CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGGgtataatcat ... gtgtgtgcagTAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
EST: gi|162257771|gb|FC434218.1|FC434218
EST:     ATCATGGGGCGCATGCACAGCTCTGG                         TAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
genomic: ATCATGGGGCGCATGCACAGCTCTGGgtataatcat ... gtgtgtgcagTAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
EST: gi|19782649|gb|BQ039884.1|BQ039884
EST:     CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGG                         TAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
genomic: CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGGgtataatcat ... gtgtgtgcagTAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
EST: gi|67697502|gb|BJ957735.1|BJ957735
EST:     CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGG                         TAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
genomic: CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGGgtataatcat ... gtgtgtgcagTAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
EST: gi|67574084|gb|BJ946908.1|BJ946908
EST:     CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGG                         TAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG
genomic: CCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGGgtataatcat ... gtgtgtgcagTAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTG

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: 30

GTCCCTTTTCAACGCACACAGTCTGGTGGCTTTCGCCTCCCGAGTCGGCTCCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGGgtataatcat ... gtgtgtgcagTAAGGGTATGTCCTCTTCGGCTCTGCCGTACAAGAGGAGCCCGCCATCTTGGTTGAAGATCACAACCGCCGAGGTTGAGGAGCACATCTGCAAGCTCGCT




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCCCTTTTCAACGCACACAGTCTGGTGGCTTTCGCCTCCCGAGTCGGCTCCAGCCTGCAACCATCAATCTTCTATCATGGGGCGCATGCACAGCTCTGGgtataatcatctctctttgttgccgcattccctcacacgcccttgctggacacgctcctgtaatggcagtggctggtgtctcttttccgtggttgatggggattagggttcagggttctggactttgacggcgtttttgttttgaggttttgttggattgaggtctgagattctttgtgtgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC