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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattaatcaaacttcaactttgttgttccttctgcatgaaggatcagtgttgactattgacaaatttcaatggtgcttgttcgtctgacattttatcggtttaggtgagttctgttccacatggatgcagtgacgataatgttgtaaaaatgttgtgcttcagAGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGT

Basic information

species Physcomitrella patens
transcript PP1S1_300V6.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S1_300V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: LOC_Os05g36270.1 (Oryza sativa), 3'ss of exon 9
gtattaatcaaacttcaactttgttgttccttctgcatgaaggatcagtgttgactattgacaaatttcaatggtgcttgttcgtctgacattttatcggtttaggtgagttctgttccacatggatgcagtgacgataatgttgtaaaaatgttgtgcttcagAGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGT
                                                                           |  || |  |   || | | | | |   ||||    |          |  ||| ||    | | | |||    | |||| |     ||| ||||||||||| || ||||| ||||| |||||| ||||||||||||| || ||| | || || ||||| || || 
---------------------------------------------------------------------------gtatgctgatgcaac-tctgaactgcaaaggtagagta--------gtaaatgtag-attgctgaagttcgctacatgtggcatggcagTGTTCTGTACGAAGTGTTCCCAATGTCATTCTTGATGGAGCAAGCTGGAGGACAAGCTTTCACAGGCAAACAACGG

upper sequence: PP1S1_300V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: LOC_Os01g64660.4 (Oryza sativa), 3'ss of exon 8
gtattaatcaaacttcaactttgttgttccttctgcatgaaggatcagtgttgactattgacaaatttcaatggtgcttgttcgtctgacattttatcggtttaggtgagttctgttccacatggatgcagtgacgataatgttgtaaaaatgttgtgcttcagAGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGT
                                                                 |    ||   || |  ||     |  |    ||| ||  |||   | |  || || || |||  |   |   | |  |    |||   | |   | ||| |||||||| || |||||||||||||| ||| || ||||||| ||||| ||||| || || || |||||  | || 
----------------------------------------------------------------gtacacattaagcctactctcggcatctcacttcgcttatggtacttccaatttcatattgata-aacaattctgaattcaccaaatcttggaattacagTGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGGCCAGTCTTTCACAGGCAAAGAACGG
















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:     GGTATCTTTATGTACCCTGGTGACAAGAAAAGCCCCAAAGGAAAGCTCAG                         AGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGG
genomic: GGTATCTTTATGTACCCTGGTGACAAGAAAAGCCCCAAAGGAAAGCTCAGgtattaatca ... tgtgcttcagAGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGG
EST: gi|162278601|gb|FC454999.1|FC454999
EST:     GGTATCTTTATGTACCCTGGTGACAAGAAAAGCCCCAAAGGAAAGCTCAG                         AGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGG
genomic: GGTATCTTTATGTACCCTGGTGACAAGAAAAGCCCCAAAGGAAAGCTCAGgtattaatca ... tgtgcttcagAGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGG
EST: gi|208365212|gb|DC950739.1|DC950739
EST:     GGTATCTTTATGTACCCTGGTGACAAGAAAAGCCCCAAAGGAAAGCTCAG                         AGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGG
genomic: GGTATCTTTATGTACCCTGGTGACAAGAAAAGCCCCAAAGGAAAGCTCAGgtattaatca ... tgtgcttcagAGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGG
EST: gi|162193915|gb|FC371728.1|FC371728
EST:     GGTATCTTTATGTACCCTGGTGACAAGAAAAGCCCCAAAGGAAAGCTCAG                         AGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGG
genomic: GGTATCTTTATGTACCCTGGTGACAAGAAAAGCCCCAAAGGAAAGCTCAGgtattaatca ... tgtgcttcagAGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGG
EST: gi|162171403|gb|FC346678.1|FC346678
EST:     GGTATCTTTATGTACCCTGGTGACAAGAAAAGCCCCAAAGGAAAGCTCAG                         AGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGG
genomic: GGTATCTTTATGTACCCTGGTGACAAGAAAAGCCCCAAAGGAAAGCTCAGgtattaatca ... tgtgcttcagAGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGG
EST: gi|208378504|gb|DC927201.1|DC927201
EST:     GGTATCTTTATGTACCCTGGTGACAAGAAAAGCCCCAAAGGAAAGCTCAG                         AGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGG
genomic: GGTATCTTTATGTACCCTGGTGACAAGAAAAGCCCCAAAGGAAAGCTCAGgtattaatca ... tgtgcttcagAGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGG
EST: gi|208396143|gb|DC924609.1|DC924609
EST:     GGTATCTTTATGTACCCTGGTGACAAGAAAAGCCCCAAAGGAAAGCTCAG                         AGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGG
genomic: GGTATCTTTATGTACCCTGGTGACAAGAAAAGCCCCAAAGGAAAGCTCAGgtattaatca ... tgtgcttcagAGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGG
EST: gi|208348185|gb|DC920976.1|DC920976
EST:     GGTATCTTTATGTACCCTGGTGACAAGAAAAGCCCCAAAGGAAAGCTCAG                         AGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGG
genomic: GGTATCTTTATGTACCCTGGTGACAAGAAAAGCCCCAAAGGAAAGCTCAGgtattaatca ... tgtgcttcagAGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGG
EST: gi|67698768|gb|BJ959001.1|BJ959001
EST:     AGAAAAGCCCCAAAGGAAAGCTCAG                         AGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGG
genomic: AGAAAAGCCCCAAAGGAAAGCTCAGgtattaatca ... tgtgcttcagAGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGG
EST: gi|162152140|gb|FC328730.1|FC328730
EST:     GGTATCTTTATGTACCCTGGTGACAAGAAAAGCCCCAAAGGAAAGCTCAG                         AGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGG
genomic: GGTATCTTTATGTACCCTGGTGACAAGAAAAGCCCCAAAGGAAAGCTCAGgtattaatca ... tgtgcttcagAGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGG
EST: gi|18333622|gb|BJ165637.1|BJ165637
EST:     GGTATCTTTATGTACCCTGGTGACAAGAAAAGCCCCAAAGGAAAGCTCAG                         AGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGG
genomic: GGTATCTTTATGTACCCTGGTGACAAGAAAAGCCCCAAAGGAAAGCTCAGgtattaatca ... tgtgcttcagAGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGG
EST: gi|208394809|gb|DC920152.1|DC920152
EST:     GATATCTTTATGTACCCTGGTGACAAGAAAAGCCCCAAAGGAAAGCTCAG                         AGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGTGGG
genomic: GGTATCTTTATGTACCCTGGTGACAAGAAAAGCCCCAAAGGAAAGCTCAGgtattaatca ... tgtgcttcagAGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGG
EST: gi|37834323|gb|BJ592335.1|BJ592335
EST:     GGTATCTTTATGTACCCTGGTGACAAGAAAAGCCCCAAAGGAAAGCTCAG                         AGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGG
genomic: GGTATCTTTATGTACCCTGGTGACAAGAAAAGCCCCAAAGGAAAGCTCAGgtattaatca ... tgtgcttcagAGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGG
EST: gi|208352801|gb|DC917765.1|DC917765
EST:     GGTATCTTTATGTACCCTGGTGACAAGAAAAGCCCCAAAGGAAAGCTCAG                         AGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGG
genomic: GGTATCTTTATGTACCCTGGTGACAAGAAAAGCCCCAAAGGAAAGCTCAGgtattaatca ... tgtgcttcagAGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGG
EST: gi|208385201|gb|DC923581.1|DC923581
EST:     GGTATCTTTATGTACCCTGGTGACAAGAAAAGCCCCAAAGGAAAGCTCAG                         AGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGNTGGGGG
genomic: GGTATCTTTATGTACCCTGGTGACAAGAAAAGCCCCAAAGGAAAGCTCAGgtattaatca ... tgtgcttcagAGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGG
EST: gi|208352520|gb|DC918229.1|DC918229
EST:     GGTATCTTTATGTACCCTGGTGACAAGAAAAGCCCCAAAGGAAAGCTCAG                         AGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGG
genomic: GGTATCTTTATGTACCCTGGTGACAAGAAAAGCCCCAAAGGAAAGCTCAGgtattaatca ... tgtgcttcagAGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGG
EST: gi|162171402|gb|FC346677.1|FC346677
EST:     GGTATCTTTATGTACCCTGGTGACAAGAAAAGCCCCAAAGGAAAGCTCAG                         AGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGG
genomic: GGTATCTTTATGTACCCTGGTGACAAGAAAAGCCCCAAAGGAAAGCTCAGgtattaatca ... tgtgcttcagAGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGG
EST: gi|208398545|gb|DC916516.1|DC916516
EST:     GGTATCTTTATGTACCCTGGTGACAAGAAAAGCCCCAAAGGAAAGCTCAG                         AGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGG
genomic: GGTATCTTTATGTACCCTGGTGACAAGAAAAGCCCCAAAGGAAAGCTCAGgtattaatca ... tgtgcttcagAGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGG
EST: gi|208358947|gb|DC946376.1|DC946376
EST:     GGTATCTTTATGTACCCTGGTGACAAGAAAAGCCCCAAAGGAAAGCTCAG                         AGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGG
genomic: GGTATCTTTATGTACCCTGGTGACAAGAAAAGCCCCAAAGGAAAGCTCAGgtattaatca ... tgtgcttcagAGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGG
EST: gi|18338549|gb|BJ170573.1|BJ170573
EST:     GGTATCTTTATGTACCCTGGTGACAAGAAAAGCCCCAAAGGAAAGCTCAG                         AGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGG
genomic: GGTATCTTTATGTACCCTGGTGACAAGAAAAGCCCCAAAGGAAAGCTCAGgtattaatca ... tgtgcttcagAGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGG
EST: gi|162278600|gb|FC454998.1|FC454998
EST:     GGTATCTTTATGTACCCTGGTGACAAGAAAAGCCCCAAAGGAAAGCTCAG                         AGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGG
genomic: GGTATCTTTATGTACCCTGGTGACAAGAAAAGCCCCAAAGGAAAGCTCAGgtattaatca ... tgtgcttcagAGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGG
EST: gi|208349119|gb|DC925902.1|DC925902
EST:     GGTATCTTTATGTACCCTGGTGACAAGAAAAGCCCCAAAGGAAAGCTCAG                         AGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGG
genomic: GGTATCTTTATGTACCCTGGTGACAAGAAAAGCCCCAAAGGAAAGCTCAGgtattaatca ... tgtgcttcagAGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGG
EST: gi|67694190|gb|BJ954423.1|BJ954423
EST:     GGTATCTTTATGTACCCTGGTGACAAGAAAAGCCCCAAAGGAAAGCTCAG                         AGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGG
genomic: GGTATCTTTATGTACCCTGGTGACAAGAAAAGCCCCAAAGGAAAGCTCAGgtattaatca ... tgtgcttcagAGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGG

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: 20

TATGGTAGCAGACGTCCACAGAACTCTACTTTACGGAGGTATCTTTATGTACCCTGGTGACAAGAAAAGCCCCAAAGGAAAGCTCAGgtattaatca ... tgtgcttcagAGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttctgttccacatggatgcagtgacgataatgttgtaaaaatgttgtgcttcagAGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGT
                           ataatgttgtaaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattaatcaaacttcaactttgttgttccttctgcatgaaggatcagtgttgactattgacaaatttcaatggtgcttgttcgtctgacattttatcggtttaggtgagttctgttccacatggatgcagtgacgataatgttgtaaaaatgttgtgcttcagAGTTCTGTACGAGGTTTTCCCCATGTCTTTCTTGGTGGAGCAAGCTGGGGGCCAATCCTTTACTGGCAAGCAGCGT

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