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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcatacattgcggtacaattgaaaccacagtcttcaggtctttccataaaatattaattctgggattgaatttgaatgaatgggtgcaaatatgattcagAATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAAAGCATTCGAAGGTGTCCCTGCACCTTATGATAAGATGAAGAGGATGGTT

Basic information

species Physcomitrella patens
transcript PP1S63_162V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S63_162V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv07s0005g06490.t01 (Vitis vinifera), 3'ss of exon 1
tcatacattgcggtacaattgaaaccacagt-cttcaggtctttccata-aaatattaattctgggattgaatttgaatgaat-----gggtgcaaatatgattcagAATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAAAGCATTCGAAGGTGTCCCTGCACCTTATGATAAGATGAAGAGGATGGTT
      |||  ||| |   |       |    |||||     | ||||| | |  ||||||     | ||  ||| |||||||      |||     | |  |  || ||||| || |||||||||||| | || || || |||||||  || || || || |  || ||  ||||| |||| ||||||||||||||||||||||| 
------attttggtgcctgtacctttccttcacttcattaggtaccatacagagcttaatttcaacactgttttt-aatgaatttttttggttttgttttattgtagGATGATTCCGCACAAGACCAAGCGTGGAGCAGCAGCCCTTGCACGATTGAAGGCTTATGAGGGAATCCCTCCACCATATGATAAGATGAAGAGGATGGTC
















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|18353359|gb|BJ185414.1|BJ185414
EST:     CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGG                         AATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
genomic: CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGGgtaatctcgc ... tatgattcagAATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
EST: gi|162244373|gb|FC421025.1|FC421025
EST:     CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGG                         AATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
genomic: CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGGgtaatctcgc ... tatgattcagAATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
EST: gi|162205282|gb|FC380964.1|FC380964
EST:     CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGG                         AATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
genomic: CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGGgtaatctcgc ... tatgattcagAATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
EST: gi|208366844|gb|DC940158.1|DC940158
EST:     CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGG                         AATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
genomic: CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGGgtaatctcgc ... tatgattcagAATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
EST: gi|162225076|gb|FC401700.1|FC401700
EST:     CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGG                         AATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
genomic: CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGGgtaatctcgc ... tatgattcagAATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
EST: gi|162225077|gb|FC401701.1|FC401701
EST:     CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGG                         AATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
genomic: CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGGgtaatctcgc ... tatgattcagAATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
EST: gi|18342105|gb|BJ174140.1|BJ174140
EST:     CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGG                         AATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
genomic: CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGGgtaatctcgc ... tatgattcagAATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
EST: gi|162209015|gb|FC385567.1|FC385567
EST:     CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGG                         AATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
genomic: CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGGgtaatctcgc ... tatgattcagAATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
EST: gi|67728015|gb|BJ978274.1|BJ978274
EST:     CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGG                         AATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
genomic: CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGGgtaatctcgc ... tatgattcagAATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
EST: gi|162209016|gb|FC385568.1|FC385568
EST:     CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGG                         AATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
genomic: CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGGgtaatctcgc ... tatgattcagAATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
EST: gi|100368987|gb|BY984971.1|BY984971
EST:     CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGG                         AATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
genomic: CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGGgtaatctcgc ... tatgattcagAATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
EST: gi|162207199|gb|FC382521.1|FC382521
EST:     CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGG                         AATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
genomic: CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGGgtaatctcgc ... tatgattcagAATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
EST: gi|162225768|gb|FC400708.1|FC400708
EST:     CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGG                         AATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
genomic: CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGGgtaatctcgc ... tatgattcagAATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
EST: gi|18373903|gb|BJ205481.1|BJ205481
EST:     CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGG                         AATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
genomic: CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGGgtaatctcgc ... tatgattcagAATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
EST: gi|37821181|gb|BJ579247.1|BJ579247
EST:     CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGG                         AATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
genomic: CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGGgtaatctcgc ... tatgattcagAATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
EST: gi|208370695|gb|DC936845.1|DC936845
EST:     CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGG                         AATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
genomic: CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGGgtaatctcgc ... tatgattcagAATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
EST: gi|67726636|gb|BJ976895.1|BJ976895
EST:     CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGG                         AATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
genomic: CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGGgtaatctcgc ... tatgattcagAATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
EST: gi|18373813|gb|BJ205391.1|BJ205391
EST:     CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGG                         AATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
genomic: CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGGgtaatctcgc ... tatgattcagAATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
EST: gi|162242094|gb|FC419428.1|FC419428
EST:     CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGG                         AATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
genomic: CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGGgtaatctcgc ... tatgattcagAATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
EST: gi|100442597|gb|BY963291.1|BY963291
EST:     CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGG                         AATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
genomic: CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGGgtaatctcgc ... tatgattcagAATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
EST: gi|162205281|gb|FC380963.1|FC380963
EST:     CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGG                         AATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
genomic: CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGGgtaatctcgc ... tatgattcagAATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
EST: gi|67694236|gb|BJ954469.1|BJ954469
EST:     CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGG                         AATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
genomic: CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGGgtaatctcgc ... tatgattcagAATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
EST: gi|162211930|gb|FC387802.1|FC387802
EST:     CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGG                         AATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
genomic: CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGGgtaatctcgc ... tatgattcagAATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
EST: gi|67718147|gb|BJ968406.1|BJ968406
EST:     CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGG                         AATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
genomic: CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGGgtaatctcgc ... tatgattcagAATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
EST: gi|162220991|gb|FC396176.1|FC396176
EST:     CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGG                         AATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
genomic: CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGGgtaatctcgc ... tatgattcagAATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
EST: gi|162220990|gb|FC396175.1|FC396175
EST:     CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGG                         AATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
genomic: CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGGgtaatctcgc ... tatgattcagAATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
EST: gi|162242093|gb|FC419427.1|FC419427
EST:     CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGG                         AATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
genomic: CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGGgtaatctcgc ... tatgattcagAATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
EST: gi|67719750|gb|BJ970009.1|BJ970009
EST:     CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGG                         AATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
genomic: CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGGgtaatctcgc ... tatgattcagAATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
EST: gi|162211929|gb|FC387801.1|FC387801
EST:     ATGGAGGACCATCCGTGG                         AATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
genomic: ATGGAGGACCATCCGTGGgtaatctcgc ... tatgattcagAATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
EST: gi|37847760|gb|BJ605768.1|BJ605768
EST:     CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGG                         AATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
genomic: CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGGgtaatctcgc ... tatgattcagAATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
EST: gi|208394042|gb|DC957123.1|DC957123
EST:     CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGG                         AATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
genomic: CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGGgtaatctcgc ... tatgattcagAATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
EST: gi|67570934|gb|BJ943758.1|BJ943758
EST:     CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGG                         AATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
genomic: CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGGgtaatctcgc ... tatgattcagAATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
EST: gi|162225769|gb|FC400709.1|FC400709
EST:     CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGG                         AATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
genomic: CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGGgtaatctcgc ... tatgattcagAATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
EST: gi|15261557|gb|BI436867.1|BI436867
EST:     CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGG                         AATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA
genomic: CCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGGgtaatctcgc ... tatgattcagAATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAA

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: 68

AATACCTTAGGTTTTTGAGGAAGAGGATGAACACCAAGCCCAGCAAGGGTCCCATTCATTTCCGGTCCCCAGCACGCATCTTATGGAGGACCATCCGTGGgtaatctcgc ... tatgattcagAATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAAAGCATTCGAAGGTGTCCCTGCACCTTATGATAAGATGAAGAGGATGGTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataaaatattaattctgggattgaatttgaatgaatgggtgcaaatatgattcagAATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAAAGCATTCGAAGGTGTCCCTGCACCTTATGATAAGATGAAGAGGATGGTT
      tattaat  putative branch site (score: 68)
     atattaattct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcatacattgcggtacaattgaaaccacagtcttcaggtctttccataaaatattaattctgggattgaatttgaatgaatgggtgcaaatatgattcagAATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAAAGCATTCGAAGGTGTCCCTGCACCTTATGATAAGATGAAGAGGATGGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG