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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caatgtactatttcgaaagcttgactcagaaacgtaaccgacactgatgtttcggtttcgatcatcttactgatactgttgcaatggactggttttgcagCACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCACTCCGACCAGTCGTGCACTCTCAGACCTTGAAGTACAACTCTAAGATCCG

Basic information

species Physcomitrella patens
transcript PP1S58_38V6.1
intron # 2
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|162278221|gb|FC454456.1|FC454456
EST:     TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgtaactatag ... ggttttgcagCACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
EST: gi|162229091|gb|FC404775.1|FC404775
EST:     TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgtaactatag ... ggttttgcagCACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
EST: gi|162212016|gb|FC388126.1|FC388126
EST:     TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgtaactatag ... ggttttgcagCACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
EST: gi|67569177|gb|BJ942001.1|BJ942001
EST:     TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgtaactatag ... ggttttgcagCACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
EST: gi|162230248|gb|FC406604.1|FC406604
EST:     TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgtaactatag ... ggttttgcagCACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
EST: gi|37832289|gb|BJ590301.1|BJ590301
EST:     TGTGAGGACNTGGTTCAACCAGCCCGCCCACAAGAAAAGAAGAAGAACGG                         CACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCNTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgtaactatag ... ggttttgcagCACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
EST: gi|19788486|gb|BQ040777.1|BQ040777
EST:     TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGTTGTACCAC
genomic: TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgtaactatag ... ggttttgcagCACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
EST: gi|162214883|gb|FC391018.1|FC391018
EST:     TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgtaactatag ... ggttttgcagCACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
EST: gi|162184451|gb|FC359197.1|FC359197
EST:     TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgtaactatag ... ggttttgcagCACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
EST: gi|18366625|gb|BJ198704.1|BJ198704
EST:     TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgtaactatag ... ggttttgcagCACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
EST: gi|18374966|gb|BJ206544.1|BJ206544
EST:     TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgtaactatag ... ggttttgcagCACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
EST: gi|208346451|gb|DC917404.1|DC917404
EST:     TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgtaactatag ... ggttttgcagCACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
EST: gi|208349479|gb|DC905617.1|DC905617
EST:     TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgtaactatag ... ggttttgcagCACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
EST: gi|162214882|gb|FC391017.1|FC391017
EST:     TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgtaactatag ... ggttttgcagCACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
EST: gi|162209537|gb|FC385633.1|FC385633
EST:     TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgtaactatag ... ggttttgcagCACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
EST: gi|18327512|gb|BJ159515.1|BJ159515
EST:     TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgtaactatag ... ggttttgcagCACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
EST: gi|67692422|gb|BJ952655.1|BJ952655
EST:     TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgtaactatag ... ggttttgcagCACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
EST: gi|162271775|gb|FC448908.1|FC448908
EST:     TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgtaactatag ... ggttttgcagCACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
EST: gi|162201749|gb|FC377501.1|FC377501
EST:     CCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
genomic: CCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgtaactatag ... ggttttgcagCACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
EST: gi|162212397|gb|FC388125.1|FC388125
EST:     TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgtaactatag ... ggttttgcagCACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
EST: gi|162217291|gb|FC392031.1|FC392031
EST:     TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgtaactatag ... ggttttgcagCACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
EST: gi|162271774|gb|FC448907.1|FC448907
EST:     TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgtaactatag ... ggttttgcagCACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
EST: gi|37844654|gb|BJ602662.1|BJ602662
EST:     TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCNTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgtaactatag ... ggttttgcagCACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
EST: gi|208381498|gb|DC919500.1|DC919500
EST:     TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgtaactatag ... ggttttgcagCACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
EST: gi|162201750|gb|FC377502.1|FC377502
EST:     CCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
genomic: CCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgtaactatag ... ggttttgcagCACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
EST: gi|162222665|gb|FC397477.1|FC397477
EST:     TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgtaactatag ... ggttttgcagCACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
EST: gi|18355339|gb|BJ187398.1|BJ187398
EST:     TGTGAGGACCTGGTTCAACCAGCCCGCCCACAAGAAAAGAAGAAGAACGG                         CACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgtaactatag ... ggttttgcagCACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
EST: gi|162278222|gb|FC454457.1|FC454457
EST:     TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgtaactatag ... ggttttgcagCACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
EST: gi|162222664|gb|FC397476.1|FC397476
EST:     TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgtaactatag ... ggttttgcagCACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
EST: gi|208384998|gb|DC903505.1|DC903505
EST:     TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgtaactatag ... ggttttgcagCACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
EST: gi|162229991|gb|FC407353.1|FC407353
EST:     TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgtaactatag ... ggttttgcagCACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
EST: gi|18374111|gb|BJ205689.1|BJ205689
EST:     TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgtaactatag ... ggttttgcagCACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
EST: gi|22492659|gb|BU052582.1|BU052582
EST:     TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgtaactatag ... ggttttgcagCACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
EST: gi|67703647|gb|BJ963880.1|BJ963880
EST:     TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAANAAGAACGG                         CACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgtaactatag ... ggttttgcagCACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
EST: gi|162229992|gb|FC407354.1|FC407354
EST:     TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgtaactatag ... ggttttgcagCACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
EST: gi|162230249|gb|FC406605.1|FC406605
EST:     TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgtaactatag ... ggttttgcagCACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCAC

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), 34 (downstream exon)
Score: 35

CATAATAATGTTATCCCCAATGGTCACTTCAAGAAGGACTGGCAGAACTATGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgtaactatag ... ggttttgcagCACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCACTCCGACCAGTCGTGCACTCTCAGACCTTGAAGTACAACTCTAAGATCCG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgtttcggtttcgatcatcttactgatactgttgcaatggactggttttgcagCACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCACTCCGACCAGTCGTGCACTCTCAGACCTTGAAGTACAACTCTAAGATCCG
                      tactgat  putative branch site (score: 35)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caatgtactatttcgaaagcttgactcagaaacgtaaccgacactgatgtttcggtttcgatcatcttactgatactgttgcaatggactggttttgcagCACGTCAAAAGAAGGCTGTCGCTGTGTTTCCACGCCCTACTGCTGGACCACTCCGACCAGTCGTGCACTCTCAGACCTTGAAGTACAACTCTAAGATCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgca