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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCGAGATTGATGTGCCCAACCTTCAGGTCATCAAGCTCATGCAGAGCTTCAAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTGgtaagctatgttcgtactttatgctcagtttggcatgtccttccttgttctggaaatcgtaggtatctttcttcttcttctccttctccttctttttctt...

Basic information

species Physcomitrella patens
transcript PP1S427_37V6.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S427_37V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: AC209215.4_FGT006 (Zea mays), 5'ss of exon 3
--------------------------------------------CCG-AGATTGATGTGCCCAACCTTC--------AGGTCATCAAGCTCATGCAGAGCTTCAAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTGgtaagctatgttcgtactttatgctcagtttggcatgtccttccttgttctggaaatcgtaggtatctttcttcttcttctccttctccttctttttctt
                                            ||| |||| |||||||||||||| |        |||| |||||||||||||||||||| |||||||||||||| || | ||||| |||| ||||||   |||| ||||  ||      || | |     | | |    |||                                                                    
AGGGCGTGCTGTATGCCAAGAAGGACTACAACCTGGCGAAGCACCCGCAGATCGATGTGCCCAACCTCCAGGACTCTAGgtgatcaagctcatgcagagctttaagtccaaggagtatgttagggagaccttctcctggcagtactactactacta------gtacctcaccaacgatggcattg--------------------------------------------------------------------

upper sequence: PP1S427_37V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: EDP00807 (Chlamydomonas reinhardtii), 5'ss of exon 2
CCGAGATT---GATGTGCCCAACCTTCAGGTCATCAAGCTCATGCAGAGCTTCAAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTGgtaagct----atgttcgtactttatgctcag----------tttggcatgtccttccttgttctg------------gaaatcgtaggtatctttcttcttcttctccttctccttctttttctt-------------------------------------------------------------------------
   ||||    |  ||||||||||| |||||||| |||||||||||||||||||||||| |||||   || |  |||  |||| ||||||||||||| ||||||| |||          |  ||     ||   |              ||  |     |  ||| ||             ||   || |   |  ||   || || | |||  | |    | |  | |                                                                         
---AGATCCCCGGCGTGCCCAACCTGCAGGTCATTAAGCTCATGCAGAGCTTCAAGTCCCAGGAGCTGGTGACTGAGCGCTTCTCCTGGCGCCACTACTACTGgtgagcgcgcggcacacacacacggggccgggggggggggcgccgagcgcgcggggcaatgtactaaccacgcagggcgacgccgcacacacattctctcgtcgtgtcccgcccagcatctaccgtcgcatccccactccccctcccgtccgcacaagcaccgacacacacgtatggtgttacatatctgcacatgtag
















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|162279758|gb|FC455666.1|FC455666
EST:     AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCGGGCGCCACTATTACTG                         GTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
genomic: AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTGgtaagctatg ... tgtcttgtagGTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
EST: gi|67709450|gb|BJ965266.1|BJ965266
EST:     AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTG                         GTACTTGACCAATGACGGCNTCGAGCATCTCCGGACATACCTCAACCTCCC
genomic: AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTGgtaagctatg ... tgtcttgtagGTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
EST: gi|18335075|gb|BJ167093.1|BJ167093
EST:     AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTG                         GTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
genomic: AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTGgtaagctatg ... tgtcttgtagGTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
EST: gi|208394676|gb|DC928836.1|DC928836
EST:     AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTG                         GTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
genomic: AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTGgtaagctatg ... tgtcttgtagGTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
EST: gi|67718975|gb|BJ969234.1|BJ969234
EST:     AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTG                         GNACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
genomic: AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTGgtaagctatg ... tgtcttgtagGTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
EST: gi|162268239|gb|FC444528.1|FC444528
EST:     AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTG                         GTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
genomic: AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTGgtaagctatg ... tgtcttgtagGTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
EST: gi|162239588|gb|FC414075.1|FC414075
EST:     AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTG                         GTACTTGACCAATGACGGCATCGAGCACCTCCGGACATACCTCAACCTCCC
genomic: AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTGgtaagctatg ... tgtcttgtagGTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
EST: gi|67725802|gb|BJ976061.1|BJ976061
EST:     AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTG                         GTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
genomic: AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTGgtaagctatg ... tgtcttgtagGTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
EST: gi|67574679|gb|BJ947503.1|BJ947503
EST:     AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTG                         GTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
genomic: AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTGgtaagctatg ... tgtcttgtagGTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
EST: gi|162268238|gb|FC444527.1|FC444527
EST:     AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTG                         GTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
genomic: AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTGgtaagctatg ... tgtcttgtagGTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
EST: gi|37823681|gb|BJ581747.1|BJ581747
EST:     AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTG                         GTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
genomic: AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTGgtaagctatg ... tgtcttgtagGTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
EST: gi|67718969|gb|BJ969228.1|BJ969228
EST:     AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTG                         GTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
genomic: AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTGgtaagctatg ... tgtcttgtagGTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
EST: gi|162207280|gb|FC383317.1|FC383317
EST:     AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTG                         GTACTTGACCAATGACGGCATCGAGCACCTCCGGACATACCTCAACCTCCC
genomic: AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTGgtaagctatg ... tgtcttgtagGTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
EST: gi|67702623|gb|BJ962856.1|BJ962856
EST:     AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTG                         GTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAAC
genomic: AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTGgtaagctatg ... tgtcttgtagGTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAAC
EST: gi|208385290|gb|DC915090.1|DC915090
EST:     AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTG                         GTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
genomic: AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTGgtaagctatg ... tgtcttgtagGTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
EST: gi|162202214|gb|FC378083.1|FC378083
EST:     AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTG                         GTACTTGACCAATGACGGCATCGAGCACCTCCGGACATACCTCAACCTCCC
genomic: AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTGgtaagctatg ... tgtcttgtagGTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
EST: gi|67576640|gb|BJ949464.1|BJ949464
EST:     AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTG                         GTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
genomic: AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTGgtaagctatg ... tgtcttgtagGTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
EST: gi|162202213|gb|FC378082.1|FC378082
EST:     AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTG                         GTACTTGACCAATGACGGCATCGAGCACCTCCGGACATACCTCAACCTCCC
genomic: AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTGgtaagctatg ... tgtcttgtagGTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
EST: gi|67717286|gb|BJ967545.1|BJ967545
EST:     AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTG                         GTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
genomic: AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTGgtaagctatg ... tgtcttgtagGTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
EST: gi|162239589|gb|FC414076.1|FC414076
EST:     AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTG                         GTACTTGACCAATGACGGCATCGAGCACCTCCGGACATACCTCAACCTCCC
genomic: AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTGgtaagctatg ... tgtcttgtagGTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
EST: gi|162270051|gb|FC446751.1|FC446751
EST:     AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTG                         GTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
genomic: AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTGgtaagctatg ... tgtcttgtagGTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
EST: gi|18344482|gb|BJ176522.1|BJ176522
EST:     AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTG                         GTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
genomic: AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTGgtaagctatg ... tgtcttgtagGTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
EST: gi|162199963|gb|FC376230.1|FC376230
EST:     AGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCCACTAT-ACTG                         GTACTTGACCAATGACGGCATCGAGCACCTCCGGACATACCCTCA-CCTCC
genomic: AGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCC-ACTATTACTGgtaagctatg ... tgtcttgtagGTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACC-TCAACCTCC
EST: gi|162207281|gb|FC383318.1|FC383318
EST:     AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTG                         GTACTTGACCAATGACGGCATCGAGCACCTCCGGACATACCTCAACCTCCC
genomic: AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTGgtaagctatg ... tgtcttgtagGTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
EST: gi|67700174|gb|BJ960407.1|BJ960407
EST:     AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTG                         GTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
genomic: AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTGgtaagctatg ... tgtcttgtagGTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
EST: gi|67702879|gb|BJ963112.1|BJ963112
EST:     AAATCCAAGGAGTACGCCAAGGAGAACTTCGCCTGGCGCCACTATTACTG                         GTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
genomic: AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTGgtaagctatg ... tgtcttgtagGTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
EST: gi|67704516|gb|BJ964749.1|BJ964749
EST:     ACTTCGCCTGGCGCCACTATTACTG                         GTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
genomic: ACTTCGCCTGGCGCCACTATTACTGgtaagctatg ... tgtcttgtagGTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
EST: gi|18367528|gb|BJ199611.1|BJ199611
EST:     AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTG                         GTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
genomic: AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTGgtaagctatg ... tgtcttgtagGTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
EST: gi|67724541|gb|BJ974800.1|BJ974800
EST:     AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTG                         GTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
genomic: AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTGgtaagctatg ... tgtcttgtagGTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
EST: gi|18331586|gb|BJ163597.1|BJ163597
EST:     AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTG                         GTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
genomic: AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTGgtaagctatg ... tgtcttgtagGTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
EST: gi|67712832|gb|BJ966281.1|BJ966281
EST:     AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTG                         GTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
genomic: AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTGgtaagctatg ... tgtcttgtagGTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
EST: gi|67698096|gb|BJ958329.1|BJ958329
EST:     AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTG                         GTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
genomic: AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTGgtaagctatg ... tgtcttgtagGTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
EST: gi|162279759|gb|FC455667.1|FC455667
EST:     AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTG                         GTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC
genomic: AAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTGgtaagctatg ... tgtcttgtagGTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCC

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), 35 (downstream exon)
Score: 52

CCGAGATTGATGTGCCCAACCTTCAGGTCATCAAGCTCATGCAGAGCTTCAAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTGgtaagctatg ... tgtcttgtagGTACTTGACCAATGACGGCATCGAGCATCTCCGGACATACCTCAACCTCCCCTCCGAGATTGTCCCTGCTACTTTGAAGAAGTCTGCTCGTCCTCCAAGC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCGAGATTGATGTGCCCAACCTTCAGGTCATCAAGCTCATGCAGAGCTTCAAGTCCAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTATTACTGgtaagctatgttcgtactttatgctcagtttggcatgtccttccttgttctggaaatcgtaggtatctttcttcttcttctccttctccttctttttctt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA