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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttttgtgtccaggattttctctgaatcagttgaagttcgctcactcttatcagcactaagttttggttgcctgatcttttacattctttgtgttacagATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTGACATGAAGTTATGGCCATTCAAGATTACTCCTGGACCGGGAGAGAAGCC

Basic information

species Physcomitrella patens
transcript PP1S97_279V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S97_279V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA18G52650.1 (Glycine max), 3'ss of exon 1
---at-ttttgtgtccaggattttctctgaatca-gttgaagttcgctcactcttatcagcactaagttttggttgcctgatcttttacattctttgtgttacagATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTGACATGAAGTTATGGCCATTCAAGATTACTCCTGGACCGGGAGAGAAGCC
   || |   ||||  | | |||||  |  ||   | || | || |       ||       ||  || | | |||  ||||   |     |  |    || ||||||| || ||| ||||||| ||| |  |||||||  | |||||||| ||||| |||||||| |||||||||||| ||||| ||||  | || || || ||
tatatgtacagtgtggaaggttttcattctattgtggtgtaatttgtgag---ttgatgatgcttggtgt-gattgt-tgataactgggggttgtcactttgcagATGCGAAGAGGTTGATTGGTAGGAGAGTTAGCGACCCTTCTGTTCAGAGTGATATGAAGTTGTGGCCATTCAAGGTTACTGCTGGTGCTGGTGAAAAACC
















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|18331530|gb|BJ163541.1|BJ163541
EST:     GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTG                         ATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
genomic: GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTGgtgagttttt ... tgtgttacagATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
EST: gi|100424971|gb|BY976907.1|BY976907
EST:     GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTG                         ATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
genomic: GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTGgtgagttttt ... tgtgttacagATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
EST: gi|162255690|gb|FC431688.1|FC431688
EST:     GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTG                         ATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
genomic: GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTGgtgagttttt ... tgtgttacagATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
EST: gi|18365801|gb|BJ197879.1|BJ197879
EST:     GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTG                         ATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
genomic: GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTGgtgagttttt ... tgtgttacagATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
EST: gi|18341955|gb|BJ173990.1|BJ173990
EST:     GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTG                         ATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
genomic: GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTGgtgagttttt ... tgtgttacagATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
EST: gi|208362173|gb|DC935615.1|DC935615
EST:     GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTG                         ATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
genomic: GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTGgtgagttttt ... tgtgttacagATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
EST: gi|67716911|gb|BJ967170.1|BJ967170
EST:     GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTG                         ATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
genomic: GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTGgtgagttttt ... tgtgttacagATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
EST: gi|18327726|gb|BJ159729.1|BJ159729
EST:     GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTG                         ATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
genomic: GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTGgtgagttttt ... tgtgttacagATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
EST: gi|18372614|gb|BJ204216.1|BJ204216
EST:     GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTG                         ATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
genomic: GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTGgtgagttttt ... tgtgttacagATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
EST: gi|67702399|gb|BJ962632.1|BJ962632
EST:     GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTG                         ATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
genomic: GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTGgtgagttttt ... tgtgttacagATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
EST: gi|18344663|gb|BJ176704.1|BJ176704
EST:     GGACGCCGCTAAGAATCANGTGGCAATGAACCCCACCAACACCGTGTTTG                         ATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
genomic: GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTGgtgagttttt ... tgtgttacagATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
EST: gi|67718916|gb|BJ969175.1|BJ969175
EST:     GGACGCCGCTAGGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTG                         ATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
genomic: GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTGgtgagttttt ... tgtgttacagATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
EST: gi|18363163|gb|BJ195235.1|BJ195235
EST:     GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTG                         ATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
genomic: GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTGgtgagttttt ... tgtgttacagATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
EST: gi|162260168|gb|FC436303.1|FC436303
EST:     GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTG                         ATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
genomic: GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTGgtgagttttt ... tgtgttacagATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
EST: gi|67717923|gb|BJ968182.1|BJ968182
EST:     GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTG                         ATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
genomic: GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTGgtgagttttt ... tgtgttacagATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
EST: gi|67716427|gb|BJ966687.1|BJ966687
EST:     GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTG                         ATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
genomic: GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTGgtgagttttt ... tgtgttacagATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
EST: gi|18356733|gb|BJ188792.1|BJ188792
EST:     GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTG                         ATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
genomic: GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTGgtgagttttt ... tgtgttacagATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
EST: gi|162277742|gb|FC453581.1|FC453581
EST:     GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTG                         ATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
genomic: GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTGgtgagttttt ... tgtgttacagATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
EST: gi|67701875|gb|BJ962108.1|BJ962108
EST:     GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTG                         ATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
genomic: GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTGgtgagttttt ... tgtgttacagATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
EST: gi|18327245|gb|BJ159247.1|BJ159247
EST:     GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTG                         ATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
genomic: GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTGgtgagttttt ... tgtgttacagATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
EST: gi|18331414|gb|BJ163425.1|BJ163425
EST:     GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTG                         ATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
genomic: GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTGgtgagttttt ... tgtgttacagATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
EST: gi|18331177|gb|BJ163185.1|BJ163185
EST:     GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTG                         ATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
genomic: GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTGgtgagttttt ... tgtgttacagATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
EST: gi|162276624|gb|FC452202.1|FC452202
EST:     GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTG                         ATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
genomic: GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTGgtgagttttt ... tgtgttacagATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
EST: gi|18329996|gb|BJ162002.1|BJ162002
EST:     GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTG                         ATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
genomic: GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTGgtgagttttt ... tgtgttacagATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
EST: gi|208352962|gb|DC913846.1|DC913846
EST:     GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTG                         ATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
genomic: GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTGgtgagttttt ... tgtgttacagATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
EST: gi|162210920|gb|FC387018.1|FC387018
EST:     GCAATGAACCCCACCAACACCGTGTTTG                         ATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
genomic: GCAATGAACCCCACCAACACCGTGTTTGgtgagttttt ... tgtgttacagATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
EST: gi|162256823|gb|FC432717.1|FC432717
EST:     GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTG                         ATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
genomic: GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTGgtgagttttt ... tgtgttacagATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
EST: gi|100379130|gb|BY986590.1|BY986590
EST:     GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTG                         ATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
genomic: GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTGgtgagttttt ... tgtgttacagATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
EST: gi|67717155|gb|BJ967414.1|BJ967414
EST:     GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTG                         ATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
genomic: GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTGgtgagttttt ... tgtgttacagATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
EST: gi|208384527|gb|DC914999.1|DC914999
EST:     GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTG                         ATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
genomic: GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTGgtgagttttt ... tgtgttacagATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
EST: gi|100365514|gb|BY966634.1|BY966634
EST:     GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTG                         ATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG
genomic: GGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTGgtgagttttt ... tgtgttacagATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTG

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: 34 (upstream exon), 31 (downstream exon)
Score: 16

AGGACCACCCCCAGTTATGTCGCATTCACCGACACGGAGCGACTCATTGGGGACGCCGCTAAGAATCAGGTGGCAATGAACCCCACCAACACCGTGTTTGgtgagttttt ... tgtgttacagATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTGACATGAAGTTATGGCCATTCAAGATTACTCCTGGACCGGGAGAGAAGCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcttatcagcactaagttttggttgcctgatcttttacattctttgtgttacagATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTGACATGAAGTTATGGCCATTCAAGATTACTCCTGGACCGGGAGAGAAGCC
                         gcctgat  putative branch site (score: 16)
                               tcttttacattcttt  CT-rich tract
                                 ttttacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttttgtgtccaggattttctctgaatcagttgaagttcgctcactcttatcagcactaagttttggttgcctgatcttttacattctttgtgttacagATGCTAAAAGGCTGATTGGAAGGCGTTTTAGCGATGCATCTGTTCAAAGTGACATGAAGTTATGGCCATTCAAGATTACTCCTGGACCGGGAGAGAAGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC