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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGTgtaagtgttcaaatcttttttttaatagtggcgtttctaaatttcattaatggatgaattctttgtgatgattctcgaaaagtttattccacgtgtaaaa...

Basic information

species Physcomitrella patens
transcript PP1S1_300V6.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S1_300V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: LOC_Os05g36270.1 (Oryza sativa), 5'ss of exon 10
AGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGTgtaagtgttcaaatcttttttttaatagtggcgtttctaaatttca--ttaatggatgaattctttgtgatgattctcgaaaagtttattccacgtgtaaaa
 ||||||||||| || ||||| ||||| |||||| ||||||||||||| || ||| | || || ||||| || || || ||  |  |  ||  ||   |  |||| ||   |  |  || |   ||||   |  || | |      |   | ||  || |    |    |  | |   
TGTTCTGTACGAAGTGTTCCCAATGTCATTCTTGATGGAGCAAGCTGGAGGACAAGCTTTCACAGGCAAACAACGGgtgagc-tgaacttcacttcggttttagtagcacattcatcttacgatttaaccaaaaaaatgtactccctctgtttcacaatgcaagtcattctagcatt-

upper sequence: PP1S1_300V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: LOC_Os05g36270.3 (Oryza sativa), 5'ss of exon 9
------------------------AGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGTgtaagtgttcaaatcttttttttaatagtggcgtttctaaatttca--ttaatggatgaattctttgtgatgattctcgaaaagtttattccacgtgtaaaa
                         ||||||||||| || ||||| ||||| |||||| ||||||||||||| || ||| | || || ||||| || || || ||  |  |  ||  ||   |  |||| ||   |  |  || |   ||||   |  || | |      |   | ||  || |    |    |  | |   
AGTTCGCTACATGTGGCATGGCAGTGTTCTGTACGAAGTGTTCCCAATGTCATTCTTGATGGAGCAAGCTGGAGGACAAGCTTTCACAGGCAAACAACGGgtgagc-tgaacttcacttcggttttagtagcacattcatcttacgatttaaccaaaaaaatgtactccctctgtttcacaatgcaagtcattctagcatt-

upper sequence: PP1S1_300V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: LOC_Os01g64660.4 (Oryza sativa), 5'ss of exon 9
AGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGTgtaagtgtt--------caaatcttttttttaatagtggcgtttctaaatttcattaatggatgaattctttg-----tgatgattctcgaaaagtttattccacgtgtaaaa-----
 |||||||| || |||||||||||||| ||| || ||||||| ||||| ||||| || || || |||||  | || |||  | ||        ||  || | ||  | | |   || |   |   |   ||||     |  | |  |||     ||||   |     ||| ||  | | || |    ||     
TGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGGCCAGTCTTTCACAGGCAAAGAACGGgtacttatttcttcattcatttcatcttgattaaaacagcatgcatgtttagtattagcatcttgagttcttgaatcctgatacattgttcaaacttgttgctacattggcaatgcag

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|67694034|gb|BJ954267.1|BJ954267
EST:     CTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGT                         GCTCTCGAATTGGTCCCAGCACATATCCATGATAGATCACCCATTTTCTTG
genomic: CTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGTgtaagtgttc ... gattttgtagGCTCTCGAATTGGTCCCAGCACATATCCATGATAGATCACCCATTTTCTTG
EST: gi|162278601|gb|FC454999.1|FC454999
EST:     CTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGT                         GCTCTCGAATTGGTCCCAGCACATATCCATGATAGATCACCCATTTTCTTG
genomic: CTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGTgtaagtgttc ... gattttgtagGCTCTCGAATTGGTCCCAGCACATATCCATGATAGATCACCCATTTTCTTG
EST: gi|208365212|gb|DC950739.1|DC950739
EST:     CTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGT                         GCTCTCGAATTGGCCCCAGCACATATCCATGATAGATCACCCATTTTCTTG
genomic: CTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGTgtaagtgttc ... gattttgtagGCTCTCGAATTGGTCCCAGCACATATCCATGATAGATCACCCATTTTCTTG
EST: gi|162193915|gb|FC371728.1|FC371728
EST:     CTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGT                         GCTCTCGAATTGGTCCCAGCACATATCCATGATAGATCACCCATTTTCTTG
genomic: CTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGTgtaagtgttc ... gattttgtagGCTCTCGAATTGGTCCCAGCACATATCCATGATAGATCACCCATTTTCTTG
EST: gi|162171403|gb|FC346678.1|FC346678
EST:     CTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGT                         GCTCTCGAATTGGTCCCAGCACATATCCATGATAGATCACCCATTTTCTTG
genomic: CTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGTgtaagtgttc ... gattttgtagGCTCTCGAATTGGTCCCAGCACATATCCATGATAGATCACCCATTTTCTTG
EST: gi|208378504|gb|DC927201.1|DC927201
EST:     CTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGT                         GCTCTCGAATTGGTCCCAGCACATATCCATGATAGATCACCCATTTTCTTG
genomic: CTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGTgtaagtgttc ... gattttgtagGCTCTCGAATTGGTCCCAGCACATATCCATGATAGATCACCCATTTTCTTG
EST: gi|208396143|gb|DC924609.1|DC924609
EST:     CTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGT                         GCTCTCGAATTGGTCCCAGCACATATCCATGATAGATCACCCATTTTCTTG
genomic: CTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGTgtaagtgttc ... gattttgtagGCTCTCGAATTGGTCCCAGCACATATCCATGATAGATCACCCATTTTCTTG
EST: gi|208348185|gb|DC920976.1|DC920976
EST:     CTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGT                         GCTCTCGAATTGGTCCCAGCACATATCCATGATAGATCACCCATTTTCTTG
genomic: CTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGTgtaagtgttc ... gattttgtagGCTCTCGAATTGGTCCCAGCACATATCCATGATAGATCACCCATTTTCTTG
EST: gi|67698768|gb|BJ959001.1|BJ959001
EST:     CTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGT                         GCTCTCGAATTGGTCCCAGCACATATCCATGATAGATCACCCATTTTCTTG
genomic: CTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGTgtaagtgttc ... gattttgtagGCTCTCGAATTGGTCCCAGCACATATCCATGATAGATCACCCATTTTCTTG
EST: gi|162152140|gb|FC328730.1|FC328730
EST:     CTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGT                         GCTCTCGAATTGGTCCCAGCACATATCCATGATAGATCACCCATTTTCTTG
genomic: CTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGTgtaagtgttc ... gattttgtagGCTCTCGAATTGGTCCCAGCACATATCCATGATAGATCACCCATTTTCTTG
EST: gi|18333622|gb|BJ165637.1|BJ165637
EST:     CTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGT                         GCTCTCGAATTGGTCCCAGCACATATCCATGATAGATCACCCATTTTCTTG
genomic: CTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGTgtaagtgttc ... gattttgtagGCTCTCGAATTGGTCCCAGCACATATCCATGATAGATCACCCATTTTCTTG
EST: gi|208394809|gb|DC920152.1|DC920152
EST:     CTTTCTTGGTGGAGCAAGCTGTGGGCCAATCCTTTACTGGCAAGCAGCGT                         GCTCTCGAATTGGTCCCAGCACATATCCATGATAGATCACCCATTTTCTTG
genomic: CTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGTgtaagtgttc ... gattttgtagGCTCTCGAATTGGTCCCAGCACATATCCATGATAGATCACCCATTTTCTTG
EST: gi|37834323|gb|BJ592335.1|BJ592335
EST:     CTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGT                         GCTCTCGAATTGGTCCCAGCACATATCCATGATAGATCACCCATTTTCTTG
genomic: CTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGTgtaagtgttc ... gattttgtagGCTCTCGAATTGGTCCCAGCACATATCCATGATAGATCACCCATTTTCTTG
EST: gi|208352801|gb|DC917765.1|DC917765
EST:     CTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGT                         GCTCTCGAATTGGTCCCAGCACATATCCATGATAGATCACCCATTTTCTTG
genomic: CTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGTgtaagtgttc ... gattttgtagGCTCTCGAATTGGTCCCAGCACATATCCATGATAGATCACCCATTTTCTTG
EST: gi|208385201|gb|DC923581.1|DC923581
EST:     CTTTCTTGGTGGAGCAAGNTGGGGGCCAATCCTTTACTGGCAAGCAGCGT                         GCTCTCGAATTGGTCCCAGCACATATCCATGATAGATCACCCATTTTCTTG
genomic: CTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGTgtaagtgttc ... gattttgtagGCTCTCGAATTGGTCCCAGCACATATCCATGATAGATCACCCATTTTCTTG
EST: gi|208352520|gb|DC918229.1|DC918229
EST:     CTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGT                         GCTCTCGAATTGGTCCCAGCACATATCCATGATAGATCACCCATTTTCTTG
genomic: CTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGTgtaagtgttc ... gattttgtagGCTCTCGAATTGGTCCCAGCACATATCCATGATAGATCACCCATTTTCTTG
EST: gi|162171402|gb|FC346677.1|FC346677
EST:     CTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGT                         GCTCTCGAATTGGTCCCAGCACATATCCATGATAGATCACCCATTTTCTTG
genomic: CTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGTgtaagtgttc ... gattttgtagGCTCTCGAATTGGTCCCAGCACATATCCATGATAGATCACCCATTTTCTTG
EST: gi|208398545|gb|DC916516.1|DC916516
EST:     CTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGT                         GCTCTCGAATTGGTCCCAGCACATATCCATGATAGATCACCCATTTTCTTG
genomic: CTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGTgtaagtgttc ... gattttgtagGCTCTCGAATTGGTCCCAGCACATATCCATGATAGATCACCCATTTTCTTG
EST: gi|208358947|gb|DC946376.1|DC946376
EST:     CTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGT                         GCTCTCGAATTGGTCCCAGCACATATCCATGATAGATCACCCATTTTCTTG
genomic: CTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGTgtaagtgttc ... gattttgtagGCTCTCGAATTGGTCCCAGCACATATCCATGATAGATCACCCATTTTCTTG
EST: gi|18338549|gb|BJ170573.1|BJ170573
EST:     CTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGT                         GCTCTCGAATTGGTCCCAGCACATATCCATGATAGATCACCCATTTTCTTG
genomic: CTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGTgtaagtgttc ... gattttgtagGCTCTCGAATTGGTCCCAGCACATATCCATGATAGATCACCCATTTTCTTG
EST: gi|162278600|gb|FC454998.1|FC454998
EST:     CTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGT                         GCTCTCGAATTGGTCCCAGCACATATCCATGATAGATCACCCATTTTCTTG
genomic: CTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGTgtaagtgttc ... gattttgtagGCTCTCGAATTGGTCCCAGCACATATCCATGATAGATCACCCATTTTCTTG
EST: gi|208349119|gb|DC925902.1|DC925902
EST:     CTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGT                         GCTCTCGAATTGGTCCCAGCACATATCCATGATAGATCACCCATTTTCTTG
genomic: CTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGTgtaagtgttc ... gattttgtagGCTCTCGAATTGGTCCCAGCACATATCCATGATAGATCACCCATTTTCTTG
EST: gi|67694190|gb|BJ954423.1|BJ954423
EST:     CTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGT                         GCTCTCGAATTGGTCCCAGCACATATCCATGATAGATCACCCATTTTCTTG
genomic: CTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGTgtaagtgttc ... gattttgtagGCTCTCGAATTGGTCCCAGCACATATCCATGATAGATCACCCATTTTCTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGTgtaagtgttcaaatcttttttttaatagtggcgtttctaaatttcattaatggatgaattctttgtgatgattctcgaaaagtttattccacgtgtaaaa

- - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - -  AAGCTG