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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaagagttcatagaatgttgacatgtagctagtcgtatgctgaggtttgattctcgctccagttctgatgtattaacttttgtttatgttcaaatcgtagTTCCTAGGAACTTTCGCCTTCTCGAAGAACTTGAGAGGGGAGAGAAAGGTATTGGCGATGGCACCGTCAGCTATGGCATGGACGATGGTGATGACGTATT

Basic information

species Physcomitrella patens
transcript PP1S490_20V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S490_20V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA10G09280.2 (Glycine max), 3'ss of exon 1
----gaagagttcatagaatgttgacatg-tagctagtcgtatgctgaggtttgattctcgctccagttctgatgtattaacttttgtttatgttcaaatcgtagTTCCTAGGAACTTTCGCCTTCTCGAAGAACTTGAGAGGGGAGAGAAAGGTATTGGCGATGGCACCGTCAGCTATGGCATGGACGATGGTGATGACGTATT
     || |  ||||  | || |  ||   | ||||||   ||  ||   ||  | |          || || | | |||| | || | |||||| ||   | |||||||||||||||  |  | || || || |||||  | ||||| ||||| ||||| |||||||| || |||||||| ||||| |||||||||||| | | 
ttatcaatatgtcatgcattgatcccacaatggctagttacattgtgttattcaaataaaaaagt--ttgtgttttgttaaatatt-tgtatgttaaa--tgcagTTCCTAGGAACTTCAGATTGCTGGAGGAGCTTGAACGTGGAGAAAAAGGAATTGGAGATGGCACAGTTAGCTATGGAATGGATGATGGTGATGACATTTA

upper sequence: PP1S490_20V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA02G35990.1 (Glycine max), 3'ss of exon 1
--gaagagt----tcatagaatgttgacatg-tagctagtcgtatgctgaggtttgattctcgctccagttctgatgtattaacttttgtttatgttcaaatcgtagTTCCTAGGAACTTTCGCCTTCTCGAAGAACTTGAGAGGGGAGAGAAAGGTATTGGCGATGGCACCGTCAGCTATGGCATGGACGATGGTGATGACGTATT
    | | |    ||||  | || |  ||   | ||||||   ||| |      | |     | |   |||||| |     ||  |||||  ||||| |||| | |||||||||||||||  |  | || || || |||||  | || || ||||| ||||| |||||||| || |||||||| ||||| |||||||||||| | | 
gtagatattcttgtcatgaattgatcccacaatggctagttacatgttttcaaataaaaaatgtttgtgttctgtta----aatatttgt--atgtttaaat-gcagTTCCTAGGAACTTCAGATTGCTGGAGGAGCTTGAACGTGGTGAAAAAGGAATTGGAGATGGCACAGTTAGCTATGGAATGGATGATGGTGATGACATTTA

upper sequence: PP1S490_20V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA19G38450.1 (Glycine max), 3'ss of exon 1
gaagagttcatagaatgttgacat--gtagctagtcgtatgctgaggtttgattctcgctccagttctgatgtattaacttttgtttatgttcaaatcgtagTTCCTAGGAACTTTCGCCTTCTCGAAGAACTTGAGAGGGGAGAGAAAGGTATTGGCGATGGCACCGTCAGCTATGGCATGGACGATGGTGATGACGTATT
 || |  |  | ||| | | | ||  ||||| | || |    |    |     |       ||||     ||| |          ||    |  ||| | |||||| ||||||||  |  | || || || ||||||| |||||| ||||| || || |||||||| || || ||||| ||||| |||||||||||| | | 
-aaaatatggtggaaggattatatatgtagccattcttgatatttattgaagatacaatgtcagtatgagtgtgtagtaaggcaattgcactttaat-gcagTTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAATAGGAGATGGCACAGTTAGTTATGGAATGGATGATGGTGATGACATTTA

upper sequence: PP1S490_20V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT2G36060.3 (Arabidopsis thaliana), 3'ss of exon 1
gaagagttcatagaatgttgacatgtagctagtcgtatgctgaggtttgattctcgctccagttctgatgtattaa-cttttgtttatgttcaaatcgtagTTCCTAGGAACTTTCGCCTTCTCGAAGAACTTGAGAGGGGAGAGAAAGGTATTGGCGATGGCACCGTCAGCTATGGCATGGACGATGGTGATGACGTATT
  ||| |   |  ||  |       | |||     |||   |    ||  |  | | | |  |    |   ||| | || ||   | |  | ||     |||||| ||||| || ||  | || || || |||||  | ||||||||||||||||| ||||| || || |||||||| ||||| ||||| |||||| | | 
-tagattgttttcaagctcagtgctttgcttagaatatagagcttatttgtgttagtttccttcactaaaaattgagctgtttgatgttgttaatgtaaagTTCCGAGGAATTTCCGGTTGCTGGAGGAGCTTGAACGTGGAGAGAAAGGTATTGGAGATGGAACTGTGAGCTATGGAATGGATGATGGAGATGACATTTA

upper sequence: PP1S490_20V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT1G23260.1 (Arabidopsis thaliana), 3'ss of exon 1
gaagagttcatagaatgttgacatgtagctagtcgtatgctgaggtttgattctcgctccagttctgatg---tattaacttttgtttatgttcaaatcgtagTTCCTAGGAACTTTCGCCTTCTCGAAGAACTTGAGAGGGGAGAGAAAGGTATTGGCGATGGCACCGTCAGCTATGGCATGGACGATGGTGATGACGTATT
    |  | || | ||             |||   |||     | | ||      | |    ||  |  |   |||| |     | ||   ||      |||||||| ||||||||| |  |  | ||||| ||||| || || |||||||||||||| ||||| || || |||||||| ||||| |||| ||||||  | | 
--gaatgtgatcggatccatggtctcgattaggtatatatct-gatctgtaaaatgatttgatttgggggcgatatttataagagcttgattttgtgatgtagTTCCGAGGAACTTTAGATTGTTGGAAGAGCTTGAAAGAGGTGAGAAAGGTATTGGAGATGGTACTGTTAGCTATGGAATGGATGATGCTGATGATATTTA

upper sequence: PP1S490_20V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT3G52560.4 (Arabidopsis thaliana), 3'ss of exon 1
gaagagttcatagaatgttgacatgtagctagtcgtatgctgaggtttgattctcgctccagttctgatgtattaac-ttttgtttatgttcaaatcgtagTTCCTAGGAACTTTCGCCTTCTCGAAGAACTTGAGAGGGGAGAGAAAGGTATTGGCGATGGCACCGTCAGCTATGGCATGGACGATGGTGATGACGTATT
  |   |   |    |  |    | |   ||     | |     | ||| ||     | | | | |||  | ||    ||  | || |  |   |   ||||||| ||||| |||||  |  | || || |||||  | || |||||||||||||| ||||| || || |||||||| ||||| ||||| |||||| | | 
atatgatatgttctgttctctgctttgattaaaaaaa-gtgattgcttgttttcatttactgatatgaattgtttttgttacgcttgttattgcaatatagTTCCGAGGAATTTTCGGTTGTTGGAGGAGCTTGAACGTGGGGAGAAAGGTATTGGGGATGGAACTGTGAGCTATGGAATGGATGATGGAGATGACATCTA

upper sequence: PP1S490_20V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv08s0007g02580.t01 (Vitis vinifera), 3'ss of exon 1
--gaagagttcatagaatgttgacatgtagctagtcgtatgctga-ggtttgattctcgctccagttctgatgtattaacttttgtttatgttcaaatcgtagTTCCTAGGAACTTTCGCCTTCTCGAAGAACTTGAGAGGGGAGAGAAAGGTATTGGCGATGGCACCGTCAGCTATGGCATGGACGATGGTGATGACGTATT
  |       | |||  | |||| || ||    | | ||| | ||   ||| |||     || || | ||  | | |      | | |   ||   || | ||| ||| | |||||  |  | || || ||||||||  | ||||| || |||||||| ||||| || ||||||||||| ||||| ||||| |||||| | | 
tggtctgaagcttagcct-ttgatatttaaggcgccttattcagacaattttattaattttcaagatttg-cgcacttttaagtctctgcatttccat-gcagTCCCTCGAAACTTCAGATTGCTTGAGGAACTTGAACGTGGAGAAAAGGGTATTGGAGATGGTACTGTCAGCTATGGAATGGATGATGGAGATGACATTTA

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|208365088|gb|DC947324.1|DC947324
EST:     AAGGCTGCAGAAGGGGCTAACTGAGATGATTTCAGGAGGCTCTGTAGTTG                         TTCCTAGGAACTTTCGCCTTCTCGAAGAACTTGAGAGGGGAGAGAAAGGTA
genomic: AAGGCTGCAGAAGGGGCTAACTGAGATGATTTCAGGAGGCTCTGTAGTTGgtaagcttgt ... caaatcgtagTTCCTAGGAACTTTCGCCTTCTCGAAGAACTTGAGAGGGGAGAGAAAGGTA
EST: gi|162211664|gb|FC387952.1|FC387952
EST:     AAGGCTGCAGAAGGGGCTAACTGAGATGATTACAGGAGGCTCTGTAGTTG                         TTCCTAGGAACTTTCGCCTTCTCGAAGAACTTGAGAGGGGAGAGAAAGGTA
genomic: AAGGCTGCAGAAGGGGCTAACTGAGATGATTTCAGGAGGCTCTGTAGTTGgtaagcttgt ... caaatcgtagTTCCTAGGAACTTTCGCCTTCTCGAAGAACTTGAGAGGGGAGAGAAAGGTA
EST: gi|18348930|gb|BJ180979.1|BJ180979
EST:     AAGGCTGCAGAAGGGGCTAACTGAGATGATTTCAGGAGGCTCTGTAGTTG                         TTCCTAGGAACTTTCGCCTTCTCGAAGAACTTGAGAGGGGAGAGAAAGGTA
genomic: AAGGCTGCAGAAGGGGCTAACTGAGATGATTTCAGGAGGCTCTGTAGTTGgtaagcttgt ... caaatcgtagTTCCTAGGAACTTTCGCCTTCTCGAAGAACTTGAGAGGGGAGAGAAAGGTA
EST: gi|162248628|gb|FC424481.1|FC424481
EST:     AAGGCTGCAGAAGGGGCTAACTGAGATGATTACAGGAGGCTCTGTAGTTG                         TTCCTAGGAACTTTCGCCTTCTCGAAGAACTTGAGAGGGGAGAGAAAGGTA
genomic: AAGGCTGCAGAAGGGGCTAACTGAGATGATTTCAGGAGGCTCTGTAGTTGgtaagcttgt ... caaatcgtagTTCCTAGGAACTTTCGCCTTCTCGAAGAACTTGAGAGGGGAGAGAAAGGTA
EST: gi|67573475|gb|BJ946299.1|BJ946299
EST:     AAGGCTGCAGAAGGGGCTAACTGAGATGATTTCAGGAGGCTCTGTAGTTG                         TTCCTAGGAACTTTCGCCTTCTCGAAGAACTTGAGAGGGGAGAGAAAGGTA
genomic: AAGGCTGCAGAAGGGGCTAACTGAGATGATTTCAGGAGGCTCTGTAGTTGgtaagcttgt ... caaatcgtagTTCCTAGGAACTTTCGCCTTCTCGAAGAACTTGAGAGGGGAGAGAAAGGTA
EST: gi|162176507|gb|FC352976.1|FC352976
EST:     AAGGCTGCAGAAGGGGCTAACTGAGATGATTACAGGAGGCTCTGTAGTTG                         TTCCTAGGAACTTTCGCCTTCTCGAAGAACTTGAGAGGGGAGAGAAAGGTA
genomic: AAGGCTGCAGAAGGGGCTAACTGAGATGATTTCAGGAGGCTCTGTAGTTGgtaagcttgt ... caaatcgtagTTCCTAGGAACTTTCGCCTTCTCGAAGAACTTGAGAGGGGAGAGAAAGGTA
EST: gi|67696855|gb|BJ957088.1|BJ957088
EST:     GGCTGCAGAAGGGGCTAACTGAGATGATTTCAGGAGGCTCTGTAGTTG                         TTCCTAGGAACTTTCGCCTTCTCGAAGAACTTGAGAGGGGAGAGAAAGGTA
genomic: GGCTGCAGAAGGGGCTAACTGAGATGATTTCAGGAGGCTCTGTAGTTGgtaagcttgt ... caaatcgtagTTCCTAGGAACTTTCGCCTTCTCGAAGAACTTGAGAGGGGAGAGAAAGGTA
EST: gi|100447101|gb|CJ971400.1|CJ971400
EST:     AAGGCTGCAGAAGGGGCTAACTGAGATGATTTCAGGAGGCTCTGTAGTTG                         TTCCTAGGAACTTTCGCCTTCTCGAAGAACTTGAGAGGGGAGAGAAAGGTA
genomic: AAGGCTGCAGAAGGGGCTAACTGAGATGATTTCAGGAGGCTCTGTAGTTGgtaagcttgt ... caaatcgtagTTCCTAGGAACTTTCGCCTTCTCGAAGAACTTGAGAGGGGAGAGAAAGGTA
EST: gi|37821329|gb|BJ579395.1|BJ579395
EST:     AAGGCTGCAGAAGGGGCTAACTGAGATGATTTCAGGAGGCTCTGTAGTTG                         TTCCTAGGAACTTTCGCCTTCTCGAAGAACTTGAGAGGGGAGAGAAAGGTA
genomic: AAGGCTGCAGAAGGGGCTAACTGAGATGATTTCAGGAGGCTCTGTAGTTGgtaagcttgt ... caaatcgtagTTCCTAGGAACTTTCGCCTTCTCGAAGAACTTGAGAGGGGAGAGAAAGGTA
EST: gi|208388041|gb|DC941694.1|DC941694
EST:     AAGGCTGCAGAAGGGGCTAACTGAGATGATTTCAGGAGGCTCTGTAGTTG                         TTCCTAGGAACTTTCGCCTTCTCGAGGAACTTGAGAGGGGAGAGAAAGGTA
genomic: AAGGCTGCAGAAGGGGCTAACTGAGATGATTTCAGGAGGCTCTGTAGTTGgtaagcttgt ... caaatcgtagTTCCTAGGAACTTTCGCCTTCTCGAAGAACTTGAGAGGGGAGAGAAAGGTA
EST: gi|18353181|gb|BJ185236.1|BJ185236
EST:     AAGGCTGCAGAAGGGGCTAACTGAGATGATTTCAGGAGGCTCTGTAGTTG                         TTCCTAGGAACTTTCGCCTTCTCGAAGAACTTGAGAGGGGAGAGAAAGGTA
genomic: AAGGCTGCAGAAGGGGCTAACTGAGATGATTTCAGGAGGCTCTGTAGTTGgtaagcttgt ... caaatcgtagTTCCTAGGAACTTTCGCCTTCTCGAAGAACTTGAGAGGGGAGAGAAAGGTA
EST: gi|100446255|gb|CJ970554.1|CJ970554
EST:     AAGGCTGCAGAAGGGGCTAACTGAGATGATTTCAGGAGGCTCTGTAGTTG                         TTCCTAGGAACTTTCGCCTTCTCGAAGAACTTGAGAGGGGAGAGAAAGGTA
genomic: AAGGCTGCAGAAGGGGCTAACTGAGATGATTTCAGGAGGCTCTGTAGTTGgtaagcttgt ... caaatcgtagTTCCTAGGAACTTTCGCCTTCTCGAAGAACTTGAGAGGGGAGAGAAAGGTA
EST: gi|100440583|gb|BY962270.1|BY962270
EST:     AAGGCTGCAGAAGGGGCTAACTGAGATGATTTCAGGAGGCTCTGTAGTTG                         TTCCTAGGAACTTTCGCCTTCTCGAAGAACTTGAGAGGGGAGAGAAAGGTA
genomic: AAGGCTGCAGAAGGGGCTAACTGAGATGATTTCAGGAGGCTCTGTAGTTGgtaagcttgt ... caaatcgtagTTCCTAGGAACTTTCGCCTTCTCGAAGAACTTGAGAGGGGAGAGAAAGGTA
EST: gi|208388103|gb|DC933181.1|DC933181
EST:     AAGGCTGCAGAAGGGGCTAACTGAGATGATTTCAGGAGGCTCTGTAGTTG                         TTCCTAGGAACTTTCGCCTTCTCGAAGAACTTGAGAGGGGAGAGAAAGGTA
genomic: AAGGCTGCAGAAGGGGCTAACTGAGATGATTTCAGGAGGCTCTGTAGTTGgtaagcttgt ... caaatcgtagTTCCTAGGAACTTTCGCCTTCTCGAAGAACTTGAGAGGGGAGAGAAAGGTA
EST: gi|18355140|gb|BJ187199.1|BJ187199
EST:     AAGGCTGCAGAAGGGGCTAACTGAGATGATTTCAGGAGGCTCTGTAGTTG                         TTCCTAGGAACTTTCGCCTTCTCGAAGAACTTGAGAGGGGAGAGAAAGGTA
genomic: AAGGCTGCAGAAGGGGCTAACTGAGATGATTTCAGGAGGCTCTGTAGTTGgtaagcttgt ... caaatcgtagTTCCTAGGAACTTTCGCCTTCTCGAAGAACTTGAGAGGGGAGAGAAAGGTA
EST: gi|18372883|gb|BJ204485.1|BJ204485
EST:     AAGGCTGCAGAAGGGGCTAACTGAGATGATTTCAGGAGGCTCTGTAGTTG                         TTCCTAGGAACTTTCGCCTTCTCGAAGAACTTGAGAGGGGAGAGAAAGGTA
genomic: AAGGCTGCAGAAGGGGCTAACTGAGATGATTTCAGGAGGCTCTGTAGTTGgtaagcttgt ... caaatcgtagTTCCTAGGAACTTTCGCCTTCTCGAAGAACTTGAGAGGGGAGAGAAAGGTA
EST: gi|67575457|gb|BJ948281.1|BJ948281
EST:     AAGGCTGCAGAAGGGGCTAACTGAGATGATTTCAGGAGGCTCTGTAGTTG                         TTCCTAGGAACTTTCGCCTTCTCGAAGAACTTGAGAGGGGAGAGAAAGGTA
genomic: AAGGCTGCAGAAGGGGCTAACTGAGATGATTTCAGGAGGCTCTGTAGTTGgtaagcttgt ... caaatcgtagTTCCTAGGAACTTTCGCCTTCTCGAAGAACTTGAGAGGGGAGAGAAAGGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgattctcgctccagttctgatgtattaacttttgtttatgttcaaatcgtagTTCCTAGGAACTTTCGCCTTCTCGAAGAACTTGAGAGGGGAGAGAAAGGTATTGGCGATGGCACCGTCAGCTATGGCATGGACGATGGTGATGACGTATT
                         tattaac  putative branch site (score: 1)
                         tattaacttttgttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaagagttcatagaatgttgacatgtagctagtcgtatgctgaggtttgattctcgctccagttctgatgtattaacttttgtttatgttcaaatcgtagTTCCTAGGAACTTTCGCCTTCTCGAAGAACTTGAGAGGGGAGAGAAAGGTATTGGCGATGGCACCGTCAGCTATGGCATGGACGATGGTGATGACGTATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA