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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacattacatgagatcactggtttcatgtatctgtgtatgtaacctctcttggggttctacttctggaaagattttaaacagttaattgtgaaaattagtcattgatcatgtcatgcatttggaagtcactctatttgttgcacgtaaattcatgctgacagtgagggttcttgttttcgacatgcagGGAGAGTGAGTCTATGACTTCCAAGAATCTCAGAAGCAATGCTGAGAAGTTTGAGTTCCAAGCTGAAGTCTCAAGGTTGATGGATATCATCATCCACTCT

Basic information

species Physcomitrella patens
transcript PP1S126_38V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S126_38V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 2
gtacattacatgagatcactggtttcatgtatctgtgtatgtaacctctcttggggttctacttctggaaagattttaaacagttaattgtgaaaattagtcattgatcatgtcatgcatttggaagtcactctatttgttgcacgtaaattcatgctgacagtgagggttcttgttttcgacatgcagGGAGAGTGAGTCTATGACTTCCAAGAA---TCTCAGAAGCAATGCTGAGAAGTTTGAGTTCCAAGCTGAAGTCTCAAGGTTGATGGATATCATCATCCACTCT
                                                                                                              |||      ||||        | | | | |||  |     ||  || || |     |    | |||| | |  ||     | ||||  |  |  ||  || ||||    |||| | |||||||| |||||||||||||||||||| ||||| ||| || | |||||||| |||||| | || 
------------------------------------------------------------------------------------------------------------ggtgtgcgttgtttgatttctcttttttctattgttctcttgtttctggtgtctaaacgcacgcgtgttgttgtgattgcaaGGGAGTCGGAGT-CGATCTCGAAGAGATCTCTCCGGAGCAATGCGGAGAAGTTTGAGTTCCAAGCGGAAGTGTCACGGCTTATGGATATTATCATCAATTC-

upper sequence: PP1S126_38V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA14G40320.4 (Glycine max), 3'ss of exon 2
gtacattacatgagatcactggtttcatgtatctgtgtatgtaacctctcttggggttctacttctggaaagattttaaacagttaattgtgaaaattagtcattgatcatgtcatgcatttggaagtcactctatttgttgcacgtaaattcatgctgacagtgagggttcttgttttcgacatgcagGGAGAGTGAGTCTATGACTTCCAAGAATCTCAGAAGCAATGCTGAGAAGTTTGAGTTCCAAGCTGAAGTCTCAAGGTTGATGGATATCATCATCCACTCT
                                                                                  ||   ||||   | ||     ||  || |||  |    ||         | | ||| |||   ||| |  | ||       || | ||| ||||  |    |   ||||||   ||||| ||  |    |    |||| | ||||| || |||||||||||||||||||| ||||| ||  || | ||||||||||||||| | |||
----------------------------------------------------------------------------------gtgcgttgtttgatttccctttttctcttgttctcttgtt---------ttttttttttgtgtgtataaacgtg-------tgcgtgttgttgtgatttgaa---agGGAGGCGGAGTCGATCTCGAAGAGATCTCTCCGGAGCAACGCGGAGAAGTTTGAGTTCCAAGCGGAAGTGTCGCGGCTTATGGATATCATCATCAATTCT

upper sequence: PP1S126_38V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA14G40320.2 (Glycine max), 3'ss of exon 2
gtacattacatgagatcactggtttcatgtatctgtgtatgtaacctctcttggggttctacttctggaaagattttaaacagttaattgtgaaaattagtcattgatcatgtcatgcatttggaagtcactctatttgttgcacgtaaattcatgctgacagtgagggttcttgttttcgacatgcagGGAGAGTGAGTCTATGACTTCCAAGAATCTCAGAAGCAATGCTGAGAAGTTTGAGTTCCAAGCTGAAGTCTCAAGGTTGATGGATATCATCATCCACTCT
                                                                                         |||    ||  |   |   | | |    | | |     |   | | ||| |||   ||| |  | ||       || | ||| ||||  |    |   ||||||   ||||| ||  |    |    |||| | ||||| || |||||||||||||||||||| ||||| ||  || | ||||||||||||||| | |||
-----------------------------------------------------------------------------------------gtgtgcgttgtttgatttccctttttctcttgttctcttgttttttttttttgtgtgtataaacgtg-------tgcgtgttgttgtgatttgaa---agGGAGGCGGAGTCGATCTCGAAGAGATCTCTCCGGAGCAACGCGGAGAAGTTTGAGTTCCAAGCGGAAGTGTCGCGGCTTATGGATATCATCATCAATTCT

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|18367288|gb|BJ199370.1|BJ199370
EST:     CTTGGGGCTGTGCCTGCTGGTTCCACCACTGATTCTGAAGTTGTTAAAAG                         GGAGAGTGAGTCTATGACTTCCAAGAATCTCAGAAGCAATGCTGAGAAGTT
genomic: CTTGGGGCTGTGCCTGCTGGTTCCACCACTGATTCTGAAGTTGTTAAAAGgtacattaca ... cgacatgcagGGAGAGTGAGTCTATGACTTCCAAGAATCTCAGAAGCAATGCTGAGAAGTT
EST: gi|18372090|gb|BJ203692.1|BJ203692
EST:     CTTGGGGCTGTGCCTGCTGGTTCCACCACTGATTCTGAAGTTGTTAAAAG                         GGAGAGTGAGTCTATGACTTCCAAGAATCTCAGAAGCAATGCTGAGAAGTT
genomic: CTTGGGGCTGTGCCTGCTGGTTCCACCACTGATTCTGAAGTTGTTAAAAGgtacattaca ... cgacatgcagGGAGAGTGAGTCTATGACTTCCAAGAATCTCAGAAGCAATGCTGAGAAGTT
EST: gi|18346979|gb|BJ179025.1|BJ179025
EST:     CTTGGGGCTGTGCCTGCTGGTTCCACCACTGATTCTGAAGTTGTTAAAAG                         GGAGAGTGAGTCTATGACTTCCAAGAATCTCAGAAGCAATGCTGAGAAGTT
genomic: CTTGGGGCTGTGCCTGCTGGTTCCACCACTGATTCTGAAGTTGTTAAAAGgtacattaca ... cgacatgcagGGAGAGTGAGTCTATGACTTCCAAGAATCTCAGAAGCAATGCTGAGAAGTT
EST: gi|18352909|gb|BJ184964.1|BJ184964
EST:     CTTGGGGCTGTGCCTGCTGGTTCCACCACTGATTCTGAAGTTGTTAAAAG                         GGAGAGTGAGTCTATGACTTCCAAGAATCTCAGAAGCAATGCTGAGAAGTT
genomic: CTTGGGGCTGTGCCTGCTGGTTCCACCACTGATTCTGAAGTTGTTAAAAGgtacattaca ... cgacatgcagGGAGAGTGAGTCTATGACTTCCAAGAATCTCAGAAGCAATGCTGAGAAGTT
EST: gi|18346023|gb|BJ178066.1|BJ178066
EST:     CTTGGGGCTGTGCCTGCTGGTTCCACCACTGATTCTGAAGTTGTTAAAAG                         GGAGAGTGAGTCTATGACTTCCAAGAATCTCAGAAGCAATGCTGAGAAGTT
genomic: CTTGGGGCTGTGCCTGCTGGTTCCACCACTGATTCTGAAGTTGTTAAAAGgtacattaca ... cgacatgcagGGAGAGTGAGTCTATGACTTCCAAGAATCTCAGAAGCAATGCTGAGAAGTT
EST: gi|18354827|gb|BJ186886.1|BJ186886
EST:     CTTGGGGCTGTGCCTGCTGGTTCCACCACTGATTCTGAAGTTGTTAAAAG                         GGAGAGTGAGTCTATGACTTCCAAGAATCTCAGAAGCAATGCTGAGAAGTT
genomic: CTTGGGGCTGTGCCTGCTGGTTCCACCACTGATTCTGAAGTTGTTAAAAGgtacattaca ... cgacatgcagGGAGAGTGAGTCTATGACTTCCAAGAATCTCAGAAGCAATGCTGAGAAGTT
EST: gi|18352804|gb|BJ184859.1|BJ184859
EST:     CTTGGGGCTGTGCCTGCTGGTTCCACCACTGATTCTGAAGTTGTTAAAAG                         GGAGAGTGAGTCTATGACTTCCAAGAATCTCAGAAGCAATGCTGAGAAGTT
genomic: CTTGGGGCTGTGCCTGCTGGTTCCACCACTGATTCTGAAGTTGTTAAAAGgtacattaca ... cgacatgcagGGAGAGTGAGTCTATGACTTCCAAGAATCTCAGAAGCAATGCTGAGAAGTT
EST: gi|18357801|gb|BJ189860.1|BJ189860
EST:     CTTGGGGCTGTGCCTGCTGGTTCCACCACTGATTCTGAAGTTGTTAAAAG                         GGAGAGTGAGTCTATGACTTCCAAGAATCTCAGAAGCAATGCTGAGAAGTT
genomic: CTTGGGGCTGTGCCTGCTGGTTCCACCACTGATTCTGAAGTTGTTAAAAGgtacattaca ... cgacatgcagGGAGAGTGAGTCTATGACTTCCAAGAATCTCAGAAGCAATGCTGAGAAGTT
EST: gi|18329083|gb|BJ161089.1|BJ161089
EST:     CTTGGGGCTGTGCCTGCTGGTTCCACCACTGATTCTGAAGTTGTTAAAAG                         GGAGAGTGAGTCTATGACTTCCAAGAATCTCAGAAGCAATGCTGAGAAGTT
genomic: CTTGGGGCTGTGCCTGCTGGTTCCACCACTGATTCTGAAGTTGTTAAAAGgtacattaca ... cgacatgcagGGAGAGTGAGTCTATGACTTCCAAGAATCTCAGAAGCAATGCTGAGAAGTT
EST: gi|18343471|gb|BJ175509.1|BJ175509
EST:     CTTGGGGCTGTGCCTGCTGGTTCCACCACTGATTCTGAAGTTGTTAAAAG                         GGAGAGTGAGTCTATGACTTCCAAGAATCTCAGAAGCAATGCTGAGAAGTT
genomic: CTTGGGGCTGTGCCTGCTGGTTCCACCACTGATTCTGAAGTTGTTAAAAGgtacattaca ... cgacatgcagGGAGAGTGAGTCTATGACTTCCAAGAATCTCAGAAGCAATGCTGAGAAGTT
EST: gi|18331239|gb|BJ163248.1|BJ163248
EST:     CTTGGGGCTGTGCCTGCTGGTTCCACCACTGATTCTGAAGTTGTTAAAAG                         GGAGAGTGAGTCTATGACTTCCAAGAATCTCAGAAGCAATGCTGAGAAGTT
genomic: CTTGGGGCTGTGCCTGCTGGTTCCACCACTGATTCTGAAGTTGTTAAAAGgtacattaca ... cgacatgcagGGAGAGTGAGTCTATGACTTCCAAGAATCTCAGAAGCAATGCTGAGAAGTT
EST: gi|18332430|gb|BJ164443.1|BJ164443
EST:     CTTGGGGCTGTGCCTGCTGGTTCCACCACTGATTCTGAAGTTGTTAAAAG                         GGAGAGTGAGTCTATGACTTCCAAGAATCTCAGAAGCAATGCTGAGAAGTT
genomic: CTTGGGGCTGTGCCTGCTGGTTCCACCACTGATTCTGAAGTTGTTAAAAGgtacattaca ... cgacatgcagGGAGAGTGAGTCTATGACTTCCAAGAATCTCAGAAGCAATGCTGAGAAGTT
EST: gi|18344948|gb|BJ176989.1|BJ176989
EST:     CTTGGGGCTGTGCCTGCTGGTTCCACCACTGATTCTGAAGTTGTTAAAAG                         GGAGAGTGAGTCTATGACTTCCAAGAATCTCAGAAGCAATGCTGAGAAGTT
genomic: CTTGGGGCTGTGCCTGCTGGTTCCACCACTGATTCTGAAGTTGTTAAAAGgtacattaca ... cgacatgcagGGAGAGTGAGTCTATGACTTCCAAGAATCTCAGAAGCAATGCTGAGAAGTT
EST: gi|18375456|gb|BJ207034.1|BJ207034
EST:     CTTGGGGCTGTGCCTGCTGGTTCCACCACTGATTCTGAAGTTGTTAAAAG                         GGAGAGTGAGTCTATGACTTCCAAGAATCTCAGAAGCAATGCTGAGAAGTT
genomic: CTTGGGGCTGTGCCTGCTGGTTCCACCACTGATTCTGAAGTTGTTAAAAGgtacattaca ... cgacatgcagGGAGAGTGAGTCTATGACTTCCAAGAATCTCAGAAGCAATGCTGAGAAGTT
EST: gi|18347429|gb|BJ179475.1|BJ179475
EST:     CTTGGGGCTGTGCCTGCTGGTTCCACCACTGATTCTGAAGTTGTTAAAAG                         GGAGAGTGAGTCTATGACTTCCAAGAATCTCAGAAGCAATGCTGAGAAGTT
genomic: CTTGGGGCTGTGCCTGCTGGTTCCACCACTGATTCTGAAGTTGTTAAAAGgtacattaca ... cgacatgcagGGAGAGTGAGTCTATGACTTCCAAGAATCTCAGAAGCAATGCTGAGAAGTT
EST: gi|100406123|gb|BY991551.1|BY991551
EST:     CTTGGGGCTGTGCCTGCTGGTTCCACCACTGATTCTGAAGTTGTTAAAAG                         GGAGAGTGAGTCTATGACTTCCAAGAATCTCAGAAGCAATGCTGAGAAGTT
genomic: CTTGGGGCTGTGCCTGCTGGTTCCACCACTGATTCTGAAGTTGTTAAAAGgtacattaca ... cgacatgcagGGAGAGTGAGTCTATGACTTCCAAGAATCTCAGAAGCAATGCTGAGAAGTT
EST: gi|18373407|gb|BJ204985.1|BJ204985
EST:     CTTGGGGCTGTGCCTGCTGGTTCCACCACTGATTCTGAAGTTGTTAAAAG                         GGAGAGTGAGTCTATGACTTCCAAGAATCTCAGAAGCAATGCTGAGAAGTT
genomic: CTTGGGGCTGTGCCTGCTGGTTCCACCACTGATTCTGAAGTTGTTAAAAGgtacattaca ... cgacatgcagGGAGAGTGAGTCTATGACTTCCAAGAATCTCAGAAGCAATGCTGAGAAGTT
EST: gi|18360762|gb|BJ192825.1|BJ192825
EST:     CTTGGGGCTGTGCCTGCTGGTTCCACCACTGATTCTGAAGTTGTTAAAAG                         GGAGAGTGAGTCTATGACTTCCAAGAATCTCAGAAGCAATGCTGAGAAGTT
genomic: CTTGGGGCTGTGCCTGCTGGTTCCACCACTGATTCTGAAGTTGTTAAAAGgtacattaca ... cgacatgcagGGAGAGTGAGTCTATGACTTCCAAGAATCTCAGAAGCAATGCTGAGAAGTT
EST: gi|18364379|gb|BJ196452.1|BJ196452
EST:     CTTGGGGCTGTGCCTGCTGGTTCCACCACTGATTCTGAAGTTGTTAAAAG                         GGAGAGTGAGTCTATGACTTCCAAGAATCTCAGAAGCAATGCTGAGAAGTT
genomic: CTTGGGGCTGTGCCTGCTGGTTCCACCACTGATTCTGAAGTTGTTAAAAGgtacattaca ... cgacatgcagGGAGAGTGAGTCTATGACTTCCAAGAATCTCAGAAGCAATGCTGAGAAGTT
EST: gi|18327014|gb|BJ159015.1|BJ159015
EST:     CTTGGGGCTGTGCCTGCTGGTTCCACCACTGATTCTGAAGTTGTTAAAAG                         GGAGAGTGAGTCTATGACTTCCAAGAATCTCAGAAGCAATGCTGAGAAGTT
genomic: CTTGGGGCTGTGCCTGCTGGTTCCACCACTGATTCTGAAGTTGTTAAAAGgtacattaca ... cgacatgcagGGAGAGTGAGTCTATGACTTCCAAGAATCTCAGAAGCAATGCTGAGAAGTT
EST: gi|67719606|gb|BJ969865.1|BJ969865
EST:     CTTGGGGCTGTGCCTGCTGGTTCCACCACTGATTCTGAAGTTGTTAAAAG                         GGAGAGTGAGTCTATGACTTCCAAGAATCTCAGAAGCAATGCTGAGAAGTT
genomic: CTTGGGGCTGTGCCTGCTGGTTCCACCACTGATTCTGAAGTTGTTAAAAGgtacattaca ... cgacatgcagGGAGAGTGAGTCTATGACTTCCAAGAATCTCAGAAGCAATGCTGAGAAGTT
EST: gi|18343482|gb|BJ175520.1|BJ175520
EST:     CTTGGGGCTGTGCCTGCTGGTTCCACCACTGATTCTGAAGTTGTTAAAAG                         GGAGAGTGAGTCTATGACTTCCAAGAATCTCAGAAGCAATGCTGAGAAGTT
genomic: CTTGGGGCTGTGCCTGCTGGTTCCACCACTGATTCTGAAGTTGTTAAAAGgtacattaca ... cgacatgcagGGAGAGTGAGTCTATGACTTCCAAGAATCTCAGAAGCAATGCTGAGAAGTT

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), 25 (downstream exon)
Score: 29

AGGAAGAATCGAAAATAGATGATGGAGCTCTCCCAAAGTTGGAAGAGAACCTTGGGGCTGTGCCTGCTGGTTCCACCACTGATTCTGAAGTTGTTAAAAGgtacattaca ... cgacatgcagGGAGAGTGAGTCTATGACTTCCAAGAATCTCAGAAGCAATGCTGAGAAGTTTGAGTTCCAAGCTGAAGTCTCAAGGTTGATGGATATCATCATCCACTCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttgttgcacgtaaattcatgctgacagtgagggttcttgttttcgacatgcagGGAGAGTGAGTCTATGACTTCCAAGAATCTCAGAAGCAATGCTGAGAAGTTTGAGTTCCAAGCTGAAGTCTCAAGGTTGATGGATATCATCATCCACTCT
                    tgctgac  putative branch site (score: 29)
                                   ttcttgttttc  putative PPT
            taaattcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacattacatgagatcactggtttcatgtatctgtgtatgtaacctctcttggggttctacttctggaaagattttaaacagttaattgtgaaaattagtcattgatcatgtcatgcatttggaagtcactctatttgttgcacgtaaattcatgctgacagtgagggttcttgttttcgacatgcagGGAGAGTGAGTCTATGACTTCCAAGAATCTCAGAAGCAATGCTGAGAAGTTTGAGTTCCAAGCTGAAGTCTCAAGGTTGATGGATATCATCATCCACTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA