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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAATGAGCAGAGTAGATTTCCAGAGGCTCGTGGCGATCTCACAATCCTCCTTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAGgtatcgtcttcgtacttgcacaattttgcaacactatattcagtttgagatttcttagtctagttcccagtccctatcgggaagagtacattgtgctgga...

Basic information

species Physcomitrella patens
transcript PP1S1_300V6.2
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|100396704|gb|BY953785.1|BY953785
EST:     TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAG                         GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
genomic: TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAGgtatcgtctt ... tattccacagGCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
EST: gi|208350793|gb|DC913439.1|DC913439
EST:     TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAG                         GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
genomic: TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAGgtatcgtctt ... tattccacagGCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
EST: gi|18325673|gb|BJ157670.1|BJ157670
EST:     TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAG                         GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
genomic: TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAGgtatcgtctt ... tattccacagGCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
EST: gi|100372971|gb|BY949374.1|BY949374
EST:     TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAG                         GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
genomic: TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAGgtatcgtctt ... tattccacagGCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
EST: gi|18352888|gb|BJ184943.1|BJ184943
EST:     TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAG                         GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
genomic: TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAGgtatcgtctt ... tattccacagGCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
EST: gi|208376930|gb|DC910792.1|DC910792
EST:     TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAG                         GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
genomic: TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAGgtatcgtctt ... tattccacagGCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
EST: gi|100444333|gb|BY982362.1|BY982362
EST:     TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAG                         GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
genomic: TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAGgtatcgtctt ... tattccacagGCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
EST: gi|100385122|gb|BY987585.1|BY987585
EST:     TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAG                         GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
genomic: TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAGgtatcgtctt ... tattccacagGCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
EST: gi|100412529|gb|BY974779.1|BY974779
EST:     TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAG                         GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
genomic: TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAGgtatcgtctt ... tattccacagGCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
EST: gi|100450318|gb|CJ974203.1|CJ974203
EST:     TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAG                         GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
genomic: TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAGgtatcgtctt ... tattccacagGCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
EST: gi|100412577|gb|BY974803.1|BY974803
EST:     TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAG                         GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
genomic: TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAGgtatcgtctt ... tattccacagGCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
EST: gi|100423945|gb|BY976600.1|BY976600
EST:     TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAG                         GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
genomic: TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAGgtatcgtctt ... tattccacagGCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
EST: gi|208398969|gb|DC912128.1|DC912128
EST:     TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAG                         GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
genomic: TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAGgtatcgtctt ... tattccacagGCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
EST: gi|208347328|gb|DC909719.1|DC909719
EST:     TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAG                         GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
genomic: TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAGgtatcgtctt ... tattccacagGCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
EST: gi|100404176|gb|BY955293.1|BY955293
EST:     TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAG                         GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
genomic: TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAGgtatcgtctt ... tattccacagGCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
EST: gi|100445533|gb|CJ975682.1|CJ975682
EST:     TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAG                         GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
genomic: TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAGgtatcgtctt ... tattccacagGCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
EST: gi|100451052|gb|CJ974573.1|CJ974573
EST:     TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAG                         GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
genomic: TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAGgtatcgtctt ... tattccacagGCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
EST: gi|208393616|gb|DC904332.1|DC904332
EST:     TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAG                         GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
genomic: TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAGgtatcgtctt ... tattccacagGCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
EST: gi|100380980|gb|BY986828.1|BY986828
EST:     TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAG                         GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
genomic: TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAGgtatcgtctt ... tattccacagGCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
EST: gi|208391526|gb|DC937674.1|DC937674
EST:     TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAG                         GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGCGCAG
genomic: TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAGgtatcgtctt ... tattccacagGCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
EST: gi|100410811|gb|BY956199.1|BY956199
EST:     TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAG                         GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
genomic: TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAGgtatcgtctt ... tattccacagGCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
EST: gi|208373427|gb|DC931872.1|DC931872
EST:     TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAG                         GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
genomic: TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAGgtatcgtctt ... tattccacagGCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
EST: gi|100391045|gb|BY953055.1|BY953055
EST:     TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAG                         GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
genomic: TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAGgtatcgtctt ... tattccacagGCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
EST: gi|208352123|gb|DC906268.1|DC906268
EST:     TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAG                         GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
genomic: TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAGgtatcgtctt ... tattccacagGCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
EST: gi|100449051|gb|CJ973350.1|CJ973350
EST:     TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAG                         GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
genomic: TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAGgtatcgtctt ... tattccacagGCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
EST: gi|100451165|gb|CJ974629.1|CJ974629
EST:     TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAG                         GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
genomic: TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAGgtatcgtctt ... tattccacagGCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
EST: gi|100360619|gb|BY984209.1|BY984209
EST:     TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAG                         GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
genomic: TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAGgtatcgtctt ... tattccacagGCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
EST: gi|208380958|gb|DC903870.1|DC903870
EST:     TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAG                         GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
genomic: TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAGgtatcgtctt ... tattccacagGCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
EST: gi|100352928|gb|BY945520.1|BY945520
EST:     TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAG                         GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
genomic: TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAGgtatcgtctt ... tattccacagGCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
EST: gi|208378151|gb|DC902624.1|DC902624
EST:     TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAG                         GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
genomic: TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAGgtatcgtctt ... tattccacagGCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
EST: gi|208350215|gb|DC901599.1|DC901599
EST:     TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAG                         GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
genomic: TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAGgtatcgtctt ... tattccacagGCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
EST: gi|100448828|gb|CJ973127.1|CJ973127
EST:     TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAG                         GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
genomic: TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAGgtatcgtctt ... tattccacagGCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
EST: gi|100445852|gb|CJ970151.1|CJ970151
EST:     TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAG                         GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
genomic: TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAGgtatcgtctt ... tattccacagGCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
EST: gi|100362014|gb|BY947740.1|BY947740
EST:     TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAG                         GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
genomic: TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAGgtatcgtctt ... tattccacagGCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
EST: gi|67570889|gb|BJ943713.1|BJ943713
EST:     TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAG                         GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
genomic: TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAGgtatcgtctt ... tattccacagGCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
EST: gi|100353087|gb|BY945599.1|BY945599
EST:     TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAG                         GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
genomic: TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAGgtatcgtctt ... tattccacagGCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
EST: gi|100412457|gb|BY974743.1|BY974743
EST:     TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAG                         GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
genomic: TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAGgtatcgtctt ... tattccacagGCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
EST: gi|208384630|gb|DC907103.1|DC907103
EST:     TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAG                         GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
genomic: TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAGgtatcgtctt ... tattccacagGCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
EST: gi|162193916|gb|FC371729.1|FC371729
EST:     TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAG                         GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG
genomic: TTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAGgtatcgtctt ... tattccacagGCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG

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: 33 (upstream exon), 35 (downstream exon)
Score: 33

GAATGAGCAGAGTAGATTTCCAGAGGCTCGTGGCGATCTCACAATCCTCCTTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAGgtatcgtctt ... tattccacagGCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAATGAGCAGAGTAGATTTCCAGAGGCTCGTGGCGATCTCACAATCCTCCTTAACAACATCGTGCTGGGCTGCAAGTTCGTGTGCTCCTCCGTGAGCAAGgtatcgtcttcgtacttgcacaattttgcaacactatattcagtttgagatttcttagtctagttcccagtccctatcgggaagagtacattgtgctgga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG