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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgcttgtgtgcactgttatcatcgtcttgctcaaagcacattttatgaacatatgctacggggcttttctgtcatttcgacacagcgatgcattgataaatttgcttggggatcgctgcctgtatgactgaaattttgtgtcgcagGTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGTGGTGCGCCTAATGAAGAAGAAACCCTTCACTTTGCACGTGCCCTAATTG

Basic information

species Physcomitrella patens
transcript PP1S7_156V6.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S7_156V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GRMZM2G107082_T01 (Zea mays), 3'ss of exon 7
gtactgcttgtgtgcactgttatcatcgtcttgctcaaagca-cattttatgaacatatgctacggggcttttctgtcatttcgacacagcgatgcattgataaatttgcttggggatcgctgcctgtatgactgaaatttt----gtgtcgcagGTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGTGGTGCGCCTAATGAAGAAGAAACCCTTCACTTTGCACGTGCCCTAATTG
                                     ||||| || ||| |    | |    |   |  |||     ||| | ||  ||        || |   |||  | |     | ||||||   ||||    ||||       | |  |||||||||||||| || | |||    ||||| || |||||||| |||||||||||||| |||||||| || ||    ||  | | | |  | |   |  |||
-----------------------------------gtaagcatcaatttgtatttacacataaaaagatttt-----catgttgatgca------tgttaaactattcacctatatttagctgccatgatgaaatcaattcctcccatttaccagGTTGGAGACTTGGGATATGCATCAGAGCTTGGAAACTATGCAGAGTATAGTGGTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTTCTTG
















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|208394814|gb|DC920157.1|DC920157
EST:     TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACG                         GTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
genomic: TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACGgtactgcttg ... tgtgtcgcagGTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
EST: gi|67699027|gb|BJ959260.1|BJ959260
EST:     TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACG                         GTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
genomic: TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACGgtactgcttg ... tgtgtcgcagGTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
EST: gi|162274022|gb|FC450369.1|FC450369
EST:     TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACG                         GTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
genomic: TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACGgtactgcttg ... tgtgtcgcagGTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
EST: gi|208374183|gb|DC945229.1|DC945229
EST:     TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACG                         GTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
genomic: TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACGgtactgcttg ... tgtgtcgcagGTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
EST: gi|208371001|gb|DC944376.1|DC944376
EST:     TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACG                         GTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
genomic: TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACGgtactgcttg ... tgtgtcgcagGTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
EST: gi|208362836|gb|DC950636.1|DC950636
EST:     TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACG                         GTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
genomic: TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACGgtactgcttg ... tgtgtcgcagGTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
EST: gi|162270681|gb|FC446294.1|FC446294
EST:     TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACG                         GTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
genomic: TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACGgtactgcttg ... tgtgtcgcagGTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
EST: gi|208369217|gb|DC956050.1|DC956050
EST:     TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACG                         GTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
genomic: TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACGgtactgcttg ... tgtgtcgcagGTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
EST: gi|208367644|gb|DC955003.1|DC955003
EST:     TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACG                         GTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
genomic: TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACGgtactgcttg ... tgtgtcgcagGTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
EST: gi|37846179|gb|BJ604187.1|BJ604187
EST:     TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACG                         GTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
genomic: TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACGgtactgcttg ... tgtgtcgcagGTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
EST: gi|162203672|gb|FC378547.1|FC378547
EST:     TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACG                         GTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
genomic: TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACGgtactgcttg ... tgtgtcgcagGTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
EST: gi|67701044|gb|BJ961277.1|BJ961277
EST:     TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACG                         GTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
genomic: TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACGgtactgcttg ... tgtgtcgcagGTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
EST: gi|208374459|gb|DC948435.1|DC948435
EST:     TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACG                         GTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
genomic: TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACGgtactgcttg ... tgtgtcgcagGTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
EST: gi|208366133|gb|DC955234.1|DC955234
EST:     TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACG                         GTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
genomic: TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACGgtactgcttg ... tgtgtcgcagGTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
EST: gi|162198094|gb|FC372121.1|FC372121
EST:     TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACG                         GTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
genomic: TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACGgtactgcttg ... tgtgtcgcagGTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
EST: gi|67724921|gb|BJ975180.1|BJ975180
EST:     TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACG                         GTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGCAGTATAGT
genomic: TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACGgtactgcttg ... tgtgtcgcagGTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
EST: gi|208386150|gb|DC949061.1|DC949061
EST:     TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACG                         GTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
genomic: TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACGgtactgcttg ... tgtgtcgcagGTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
EST: gi|208364385|gb|DC950686.1|DC950686
EST:     TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCNGATACG                         GTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
genomic: TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACGgtactgcttg ... tgtgtcgcagGTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
EST: gi|208390780|gb|DC945853.1|DC945853
EST:     TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACG                         GTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
genomic: TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACGgtactgcttg ... tgtgtcgcagGTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
EST: gi|37851290|gb|BJ609298.1|BJ609298
EST:     TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACG                         GTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
genomic: TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACGgtactgcttg ... tgtgtcgcagGTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
EST: gi|208386182|gb|DC949093.1|DC949093
EST:     TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACG                         GTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
genomic: TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACGgtactgcttg ... tgtgtcgcagGTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
EST: gi|37845304|gb|BJ603312.1|BJ603312
EST:     TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACG                         GTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
genomic: TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACGgtactgcttg ... tgtgtcgcagGTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
EST: gi|208370928|gb|DC944303.1|DC944303
EST:     TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACG                         GTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
genomic: TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACGgtactgcttg ... tgtgtcgcagGTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
EST: gi|162184487|gb|FC359961.1|FC359961
EST:     TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACG                         GTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
genomic: TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACGgtactgcttg ... tgtgtcgcagGTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
EST: gi|208379626|gb|DC927123.1|DC927123
EST:     TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACG                         GTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
genomic: TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACGgtactgcttg ... tgtgtcgcagGTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
EST: gi|18341274|gb|BJ173308.1|BJ173308
EST:     TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACG                         GTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
genomic: TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACGgtactgcttg ... tgtgtcgcagGTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
EST: gi|67725040|gb|BJ975299.1|BJ975299
EST:     TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACG                         GTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
genomic: TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACGgtactgcttg ... tgtgtcgcagGTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
EST: gi|208364465|gb|DC958034.1|DC958034
EST:     TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACG                         GTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
genomic: TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACGgtactgcttg ... tgtgtcgcagGTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
EST: gi|162198093|gb|FC372120.1|FC372120
EST:     TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACG                         GTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
genomic: TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACGgtactgcttg ... tgtgtcgcagGTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
EST: gi|208384409|gb|DC928160.1|DC928160
EST:     TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACG                         GTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
genomic: TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACGgtactgcttg ... tgtgtcgcagGTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
EST: gi|67720385|gb|BJ970644.1|BJ970644
EST:     TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACG                         GTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAATATAGT
genomic: TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACGgtactgcttg ... tgtgtcgcagGTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
EST: gi|208354287|gb|DC957465.1|DC957465
EST:     TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACG                         GTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
genomic: TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACGgtactgcttg ... tgtgtcgcagGTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
EST: gi|208360305|gb|DC950250.1|DC950250
EST:     TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACG                         GTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
genomic: TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACGgtactgcttg ... tgtgtcgcagGTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
EST: gi|67691916|gb|BJ952149.1|BJ952149
EST:     ACCATNGTCGCTGGGGGAGGTGCAAGTGTTATTTACTCTGATACG                         GTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
genomic: ACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACGgtactgcttg ... tgtgtcgcagGTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
EST: gi|208379943|gb|DC927669.1|DC927669
EST:     TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACG                         GTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT
genomic: TCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACGgtactgcttg ... tgtgtcgcagGTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgataaatttgcttggggatcgctgcctgtatgactgaaattttgtgtcgcagGTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGTGGTGCGCCTAATGAAGAAGAAACCCTTCACTTTGCACGTGCCCTAATTG
 cattgat  putative branch site (score: 4)
                                     tgaaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactgcttgtgtgcactgttatcatcgtcttgctcaaagcacattttatgaacatatgctacggggcttttctgtcatttcgacacagcgatgcattgataaatttgcttggggatcgctgcctgtatgactgaaattttgtgtcgcagGTTGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGTGGTGCGCCTAATGAAGAAGAAACCCTTCACTTTGCACGTGCCCTAATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA