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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCATCCCCGTGAATCCGAAACCCTTTTTGAACGACTTGACAGGGAAGCCGGTGATCGTGAAACTGAAGTGGGGGATGGAATACAAAGgtgctctgttttgtttcttgtatttgtttttattttgctttgtttttgttagcaatatggtcttatggttttcgggttttccaggggttgattcctttgaatacatatgtatttgagggtaatacatttaatcgtggcagttgaatgtctggtgtggtgagaacag

Basic information

species Physcomitrella patens
transcript PP1S46_244V6.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S46_244V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: LOC_Os11g43620.1 (Oryza sativa), 5'ss of exon 2
ACCATCCCCGTGAATCCGAAACCCTTTTTGAACGACTTGACAGGGAAGCCGGTGATCGTGAAACTGAAGTGGGGGATGGAATACAAAGgtgctctgttttgtttcttgtatttgtttttattttgctttgtttttgttagcaatatggtcttatggttttcgggttttccaggggttgattcctttgaatacatatgtatttgagggtaatacatttaatcgtggcagttgaatgtctggtgtggtgagaacag
||  | || || || || ||||| || |||||| || ||||||||||||| || || || ||||| |||||||| |||||||||||||||  ||| |  | || | |   ||   || |  ||  |||  |   || |      |  |  | |   |||  |  |         |  |||| |    ||| |                                                              
ACTGTTCCAGTTAACCCAAAACCTTTCTTGAACAACCTGACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctatacttttacct---ttcacttcttcttcacttattacatgcttaagccagtgcttgaaaatttcagaatgaaatctctga-gatttcaggaaatcc--------------------------------------------------------------

upper sequence: PP1S46_244V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: LOC_Os02g08090.1 (Oryza sativa), 5'ss of exon 2
ACCATCCCCGTGAATCCGAAACCCTTTTTGAACGACTTGACAGGGAAGCCGGTGATCGTGAAACTGAAGTGGGGGATGGAATACAAAGgtgctctgttttgtttcttgtatttgtttttattttgctttgtttttgttagcaatatggtcttatggttttcgggttttccaggggttgattcctttgaatacatatgtatttgagggtaatacatttaatcgtggcagttgaatgtctggtgtggtgagaacag
||  | || || || ||||| || || |||||| || ||||||||||||| || || || ||||| |||||||| |||||||||||||||  ||| |  | || |  ||     ||| |    || | || ||  | |||  ||      ||  |  |      | |   |||  |      | |||||                                                                 
ACTGTGCCAGTTAACCCGAAGCCTTTCTTGAACAACCTGACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctatacttttacccgtcacattttattcactgatatgcttaggctagtgattgaaatttcagaatg--aaatctctgaggtttcaggaacattgaaa----------------------------------------------------------------

upper sequence: PP1S46_244V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA17G07060.1 (Glycine max), 5'ss of exon 2
ACCATCCCCGTGAATCCGAAACCCTTTTTGAACGACTTGACAGGGAAGCCGGTGATCGTGAAACTGAAGTGGGGGATGGAATACAAAGgtgctctgttttgtttcttgtatttgtttttattttgctttgtttttgttagcaatatggtcttatggttttcgggttttccaggggttgattcctttgaatacatatgtatttgagggtaatacatttaatcgtggcagttgaatgtctggtgtggtgagaacag
|| || || || ||||| || || || |||||| | ||||| |||||||| || || ||||||||||||||||| ||||| ||||| |||  |  || |  |   |||  | ||  |  ||| | ||    || |   |    ||   | | ||  ||  | | | ||     | || |||  |  |                                                                   
ACTATACCAGTTAATCCCAAGCCTTTCTTGAACAATTTGACTGGGAAGCCTGTAATTGTGAAACTGAAGTGGGGAATGGAGTACAAGGgta-tgagtatgatgctttgc-tatggatcaattgttctactgttattccactcttacactttcat--ttcgctgttatttt---gttttatttttcag-------------------------------------------------------------------

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|162270790|gb|FC446819.1|FC446819
EST:     GACAGGGAAGCCGGTGATCGTGAAACTGAAGTGGGGGATGGAATACAAAG                         GTTATTTGGTGTCGGTCGACTCATATATGAATCTCCAA
genomic: GACAGGGAAGCCGGTGATCGTGAAACTGAAGTGGGGGATGGAATACAAAGgtgctctgtt ... gtgagaacagGTTATTTGGTGTCGGTCGACTCATATATGAATCTCCAA
EST: gi|37850996|gb|BJ609004.1|BJ609004
EST:     GACAGGGAAGCCGGTGATCGTGAAACTGAAGTGGGGGATGGAATACAAAG                         GTTATTTGGTGTCGGTCGACTCATATATGAATCTCCAA
genomic: GACAGGGAAGCCGGTGATCGTGAAACTGAAGTGGGGGATGGAATACAAAGgtgctctgtt ... gtgagaacagGTTATTTGGTGTCGGTCGACTCATATATGAATCTCCAA
EST: gi|7067255|gb|AW497110.1|AW497110
EST:     GACAGGGAAGCCGGTGATCGTGAAACTGAAGTGGGGGATGGAATACAAAG                         GTTATTTGGTGTCGGTCGACTCATATATGAATCTCCAA
genomic: GACAGGGAAGCCGGTGATCGTGAAACTGAAGTGGGGGATGGAATACAAAGgtgctctgtt ... gtgagaacagGTTATTTGGTGTCGGTCGACTCATATATGAATCTCCAA
EST: gi|19790253|gb|BQ041775.1|BQ041775
EST:     GACAGGGAAGCCGGTGATCGTGAAACTGAAGTGGGGGATGGAATACAAAG                         GTTATTTGGTGTCGGTCGACTCATATATGAATCTCCAA
genomic: GACAGGGAAGCCGGTGATCGTGAAACTGAAGTGGGGGATGGAATACAAAGgtgctctgtt ... gtgagaacagGTTATTTGGTGTCGGTCGACTCATATATGAATCTCCAA
EST: gi|18370173|gb|BJ201775.1|BJ201775
EST:     GACAGGGAAGCCGGTGATCGTGAAACTGAAGTGGGGGATGGAATACAAAG                         GTTATTTGGTGTCGGTCGACTCATATATGAATCTCCAA
genomic: GACAGGGAAGCCGGTGATCGTGAAACTGAAGTGGGGGATGGAATACAAAGgtgctctgtt ... gtgagaacagGTTATTTGGTGTCGGTCGACTCATATATGAATCTCCAA
EST: gi|18360431|gb|BJ192493.1|BJ192493
EST:     GACAGGGAAGCCGGTGATCGTGAAACTGAAGTGGGGGATGGAATACAAAG                         GTTATTTGGTGTCGGTCGACTCATATATGAATCTCCAA
genomic: GACAGGGAAGCCGGTGATCGTGAAACTGAAGTGGGGGATGGAATACAAAGgtgctctgtt ... gtgagaacagGTTATTTGGTGTCGGTCGACTCATATATGAATCTCCAA
EST: gi|162270791|gb|FC446820.1|FC446820
EST:     GACAGGGAAGCCGGTGATCGTGAAACTGAAGTGGGGGATGGAATACAAAG                         GTTATTTGGTGTCGGTCGACTCATATATGAATCTCCAA
genomic: GACAGGGAAGCCGGTGATCGTGAAACTGAAGTGGGGGATGGAATACAAAGgtgctctgtt ... gtgagaacagGTTATTTGGTGTCGGTCGACTCATATATGAATCTCCAA
EST: gi|67507561|gb|BJ940443.1|BJ940443
EST:     GACAGGGAAGCCGGTGATCGTGAAACTGAAGTGGGGGATGGAATACAAAG                         GTTATTTGGTGTCGGTCGACTCATATATGAATCTCCAA
genomic: GACAGGGAAGCCGGTGATCGTGAAACTGAAGTGGGGGATGGAATACAAAGgtgctctgtt ... gtgagaacagGTTATTTGGTGTCGGTCGACTCATATATGAATCTCCAA
EST: gi|18360389|gb|BJ192451.1|BJ192451
EST:     GACAGGGAAGCCGGTGATCGTGAAACTGAAGTGGGGGATGGAATACAAAG                         GTTATTTGGTGTCGGTCGACTCATATATGAATCTCCAA
genomic: GACAGGGAAGCCGGTGATCGTGAAACTGAAGTGGGGGATGGAATACAAAGgtgctctgtt ... gtgagaacagGTTATTTGGTGTCGGTCGACTCATATATGAATCTCCAA
EST: gi|18363001|gb|BJ195073.1|BJ195073
EST:     GACAGGGAAGCCGGTGATCGTGAAACTGAAGTGGGGGATGGAATACAAAG                         GTTATTTGGTGTCGGTCGACTCATATATGAATCTCCAA
genomic: GACAGGGAAGCCGGTGATCGTGAAACTGAAGTGGGGGATGGAATACAAAGgtgctctgtt ... gtgagaacagGTTATTTGGTGTCGGTCGACTCATATATGAATCTCCAA
EST: gi|67508119|gb|BJ940990.1|BJ940990
EST:     GACAGGGAAGCCGGNGATCGTGAAACTGAAGTGGGGGATGGAATACAAAG                         GTTATTTGGTGTCGGTCGACTCATATATGAATCTCCAACTCGCAAGCA
genomic: GACAGGGAAGCCGGTGATCGTGAAACTGAAGTGGGGGATGGAATACAAAGgtgctctgtt ... gtgagaacagGTTATTTGGTGTCGGTCGACTCATATATGAATCTCCAACTCGCAAGCA
EST: gi|67569504|gb|BJ942328.1|BJ942328
EST:     GACAGGGAAGCCGGTGATCGTGAAACTGAAGTGGGGGATGGAATACAAAG                         GTTATTTGGTGTCGGTCGACTCATATATGAATCTCCAA
genomic: GACAGGGAAGCCGGTGATCGTGAAACTGAAGTGGGGGATGGAATACAAAGgtgctctgtt ... gtgagaacagGTTATTTGGTGTCGGTCGACTCATATATGAATCTCCAA
EST: gi|67692772|gb|BJ953005.1|BJ953005
EST:     GACAGGGAAGCCGGTGATCGTGAAACTGAAGTGGGGGATGGAATACAAAG                         GTTATTTGGTGTCGGTCGACTCATATATGAATCTCCAA
genomic: GACAGGGAAGCCGGTGATCGTGAAACTGAAGTGGGGGATGGAATACAAAGgtgctctgtt ... gtgagaacagGTTATTTGGTGTCGGTCGACTCATATATGAATCTCCAA
EST: gi|67691336|gb|BJ951569.1|BJ951569
EST:     GAAACTGAANTGGGNGGANGGGAATACAAAG                         GTTATTTGGTGTCGGTCGACTCATATATGAATCTCCAA
genomic: GAAACTGAAGTGGG-GGA-TGGAATACAAAGgtgctctgtt ... gtgagaacagGTTATTTGGTGTCGGTCGACTCATATATGAATCTCCAA
EST: gi|37838403|gb|BJ596411.1|BJ596411
EST:     GACAGGGAAGCCGGTGATCGTGAAACTGAAGTGGGGGATGGAATACAAAG                         GTTATTTGGTGTCGGTCGACTCATATATGAATCTCCAA
genomic: GACAGGGAAGCCGGTGATCGTGAAACTGAAGTGGGGGATGGAATACAAAGgtgctctgtt ... gtgagaacagGTTATTTGGTGTCGGTCGACTCATATATGAATCTCCAA

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: 32 (upstream exon), 31 (downstream exon)
Score: 12

ACCATCCCCGTGAATCCGAAACCCTTTTTGAACGACTTGACAGGGAAGCCGGTGATCGTGAAACTGAAGTGGGGGATGGAATACAAAGgtgctctgtt ... gtgagaacagGTTATTTGGTGTCGGTCGACTCATATATGAATCTCCAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACCATCCCCGTGAATCCGAAACCCTTTTTGAACGACTTGACAGGGAAGCCGGTGATCGTGAAACTGAAGTGGGGGATGGAATACAAAGgtgctctgttttgtttcttgtatttgtttttattttgctttgtttttgttagcaatatggtcttatggttttcgggttttccaggggttgattcctttgaatacatatgtatttgagggtaatacatttaatcgtggcagttgaatgtctggtgtggtgagaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA