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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAATGGTCAGCTTGAGTTCTACAATGTGGATGACCTGGAGACAATGGCGACAGCTGAGCACTTTATGGCCACGGATGTCGACTGGGATCCTACTGGCAGgcaagtgaaagtctcctggtgttgtttagggaactgttgtctgattttgaagtgaatgtttctggttttgttgtgaattaccacactaaagacgtatcaactttaactaatctattgctgggcatttttttgggtcggctagtaatattgggtgttcccattgttctgcag

Basic information

species Physcomitrella patens
transcript PP1S138_36V6.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S138_36V6.1 (Physcomitrella patens), 5'ss of exon 8
lower sequence: GRMZM2G174757_T01 (Zea mays), 5'ss of exon 9
ACAATGGTCAGCTTGAGTTCTACAATGTGGATGACCTGGAGACAATGGCGACAGCTGAGCACTTTATGGCCACGGATGTCGACTGGGATCCTACTGGCAGgcaagtgaaagtctcctggtgttgtttagggaactgttgtctgattttgaagtgaatgtttctggttttgttgtgaattaccacactaaagacgtatcaactttaactaatctattgctgggcatttttttgggtcggctagtaatattgggtgttcccattgttctgcag
 ||| || ||||| || ||||||||||| ||||| || ||||||||||| ||||  ||||| |||||||| || ||| ||   |||||||| ||||| |||  ||  |       |||||    |||||  |  |  ||  | |   |  | ||| || |  |     |  | |   | |  | ||  ||  |   |  ||  |  |  |||                                                           
TCAACGGGCAGCTGGAATTCTACAATGTTGATGAACTAGAGACAATGGCAACAGGAGAGCATTTTATGGCAACAGATATCATGTGGGATCCAACTGGGAGgtgagctag---tcactggt----tttagaaatttcctgattcaacat--actgactggtatta--cataatatagttaaaaatacctaatcca-gttgacacttgcagatc-----------------------------------------------------------

upper sequence: PP1S138_36V6.1 (Physcomitrella patens), 5'ss of exon 8
lower sequence: AT5G27640.1 (Arabidopsis thaliana), 5'ss of exon 10
ACAATGGTCAGCTTGAGTTCTACAATGTGGATGACCTGGAGACAATGGCGACAGCTGAGCACTTTATGGCCACGGATGTCGACTGGGATCCTACTGGCAGg--caagtgaaagtctcctggtgttgtttagggaactgttgtctgattttgaagtgaatgtttctggttttgttgtgaattaccacactaaagacgtatcaactttaactaatctattgctgggcatttttttgggtcggctagtaatattgggtgttcccattgttctgcag
 |||||| |||||||| || | ||| |||||||| || ||||||||||| |||||||| ||||| |||||||||||| |||| ||||| || ||||| |||  | | ||               |  || ||    |  | | || |      |   |||||  | |   | || |  |||  || |                                                                                      
TCAATGGCCAGCTTGAATTTTTCAACGTGGATGAGCTCGAGACAATGGCCACAGCTGAACACTTCATGGCCACGGATATCGAATGGGACCCGACTGGAAGgtcctactgtcttaactaaaccagtcctttggttgtttctatttgttccaattgctgatgttgtttgcactttttt--attttcaaag-------------------------------------------------------------------------------------

upper sequence: PP1S138_36V6.1 (Physcomitrella patens), 5'ss of exon 8
lower sequence: AT5G25780.1 (Arabidopsis thaliana), 5'ss of exon 9
ACAATGGTCAGCTTGAGTTCTACAATGTGGATGACCTGGAGACAATGGCGACAGCTGAGCACTTTATGGCCACGGATGTCGACTGGGATCCTACTGGCAGgcaagtgaaagtctcctggtgttgtttagggaactgttg-tctgattttgaagtgaatgtttctggttttgttgtgaattaccacactaaagacgtatcaactttaactaatctattgctgggcatttttttgggtcggctagtaatattgggtgttcccattgttctgcag
 |||||| |||||||| || | ||| |||||||| || ||||||||||| |||||||| ||||| |||||||| ||| |||| ||||| || ||||| ||| |    || ||||                 |   |||| | |   ||||         || ||| | ||||| || | |       ||    |  |                                                                           
TCAATGGCCAGCTTGAATTTTTCAACGTGGATGAGCTCGAGACAATGGCCACAGCTGAACACTTCATGGCCACAGATATCGAATGGGACCCAACTGGAAGgta--ctaatgtcttaaaaccaaaccagtccattggttggtttctctttgtttcaccaattgctgatgttgtt-tgcactttttttttattttcaaag--------------------------------------------------------------------------

upper sequence: PP1S138_36V6.1 (Physcomitrella patens), 5'ss of exon 8
lower sequence: EFJ13839 (Selaginella moellendorffii), 5'ss of exon 9
ACAATGGTCAGCTTGAGTTCTACAATGTGGATGACCTGGAGACAATGGCGACAGCTGAGCACTTTATGGCCACGGATGTCGACTGGGATCCTACTGGCAGgcaagtgaaagtctcctggtgttgtttagggaactgttgtctgattttgaagtgaatgtttctggttttgttgtgaattaccacactaaagacgtatcaactttaactaatctattgctgggcatttttttgggtcggctagtaatattgggtgttcccattgttctgcag
| || || ||||| |||||||||||||| ||||| || ||||| ||||| || || ||||| || ||||| || ||||| || ||||||||  |||| ||| |||      ||| |||         |  |||||  | ||    ||   |  |   ||||   |                                                                                                          
ATAACGGGCAGCTCGAGTTCTACAATGTTGATGATCTCGAGACTATGGCAACGGCAGAGCATTTCATGGCAACTGATGTGGATTGGGATCCCGCTGGAAGgtaagc-----tcttctga--------aacgaact--tatcc---ttaccaccggtcgtttgcag----------------------------------------------------------------------------------------------------------

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|162172465|gb|FC349134.1|FC349134
EST:     GGATGTCGACTGGGATCCTACTGGCAG                         GTTCTGTTCAACTTCAGTGACATCTGTTCACCAGATGGAGAACGGTTTCAA
genomic: GGATGTCGACTGGGATCCTACTGGCAGgcaagtgaaa ... tgttctgcagGTTCTGTTCAACTTCAGTGACATCTGTTCACCAGATGGAGAACGGTTTCAA
EST: gi|162213004|gb|FC389220.1|FC389220
EST:     ACAGCTGAGCACTTTATGGCCACGGATGTCGACTGGGATCCTACTGGCAG                         GTTCTGTTCAACTTCAGTGACATCTGTTCACCAGATGGAGAACGGTTTCAA
genomic: ACAGCTGAGCACTTTATGGCCACGGATGTCGACTGGGATCCTACTGGCAGgcaagtgaaa ... tgttctgcagGTTCTGTTCAACTTCAGTGACATCTGTTCACCAGATGGAGAACGGTTTCAA
EST: gi|162230690|gb|FC406113.1|FC406113
EST:     ACAGCTGAGCACTTTATGGCCACGGATGTCGACTGGGATCCTACTGGCAG                         GTTCTGTTCAACTTCAGTGACATCTGTTCACCAGATGGAGAACGGTTTCAA
genomic: ACAGCTGAGCACTTTATGGCCACGGATGTCGACTGGGATCCTACTGGCAGgcaagtgaaa ... tgttctgcagGTTCTGTTCAACTTCAGTGACATCTGTTCACCAGATGGAGAACGGTTTCAA
EST: gi|162171930|gb|FC349028.1|FC349028
EST:     GACTGGGATCCTACTGGCAG                         GTTCTGTTCAACTTCAGTGACATCTGTTCACCAGATGGAGAACGGTTTCAA
genomic: GACTGGGATCCTACTGGCAGgcaagtgaaa ... tgttctgcagGTTCTGTTCAACTTCAGTGACATCTGTTCACCAGATGGAGAACGGTTTCAA
EST: gi|162186684|gb|FC363656.1|FC363656
EST:     ACAGCTGAGCACTTTATGGCCACGGATGTCGACTGGGATCCTACTGGCAG                         GTTCTGTTCAACTTCAGTGACATCTGTTCACCAGATGGAGAACGGTTTCAA
genomic: ACAGCTGAGCACTTTATGGCCACGGATGTCGACTGGGATCCTACTGGCAGgcaagtgaaa ... tgttctgcagGTTCTGTTCAACTTCAGTGACATCTGTTCACCAGATGGAGAACGGTTTCAA
EST: gi|162190898|gb|FC368096.1|FC368096
EST:     ACAGCTGAGCACTTTATGGCCACGGATGTCGACTGGGATCCTACTGGCAG                         GTTCTGTTCAACTTCAGTGACATCTGTTCACCAGATGGAGAACGGTTTCAA
genomic: ACAGCTGAGCACTTTATGGCCACGGATGTCGACTGGGATCCTACTGGCAGgcaagtgaaa ... tgttctgcagGTTCTGTTCAACTTCAGTGACATCTGTTCACCAGATGGAGAACGGTTTCAA
EST: gi|37843508|gb|BJ601516.1|BJ601516
EST:     GTCGACTGGGATCCTACTGGCAG                         GTTCTGTTCAACTTCCAGTGACATCTGTTCACCAGATGGAGAACGGTTTCA
genomic: GTCGACTGGGATCCTACTGGCAGgcaagtgaaa ... tgttctgcagGTTCTGTTCAACTT-CAGTGACATCTGTTCACCAGATGGAGAACGGTTTCA
EST: gi|162212529|gb|FC388505.1|FC388505
EST:     TGTCGACTGGGATCCTACTGGCAG                         GTTCTGTTCAACTTCAGTGACATCTGTTCACCAGATGGAGAACGGTTTCAA
genomic: TGTCGACTGGGATCCTACTGGCAGgcaagtgaaa ... tgttctgcagGTTCTGTTCAACTTCAGTGACATCTGTTCACCAGATGGAGAACGGTTTCAA
EST: gi|67700220|gb|BJ960453.1|BJ960453
EST:     ACAGCTGAGCACNTTATGGCCACGGATGTCGACTGGGATCCTACTGGCAG                         GTTCTGTTCAACTTCAGTGACATCTGTTCACCAGATGGAGAACGGTTTCAA
genomic: ACAGCTGAGCACTTTATGGCCACGGATGTCGACTGGGATCCTACTGGCAGgcaagtgaaa ... tgttctgcagGTTCTGTTCAACTTCAGTGACATCTGTTCACCAGATGGAGAACGGTTTCAA
EST: gi|162170162|gb|FC347282.1|FC347282
EST:     TGGCCACGGATGTCGACTGGGATCCTACTGGCAG                         GTTCTGTTCAACTTCAGTGACATCTGTTCACCAGATGGAGAACGGTTTCAA
genomic: TGGCCACGGATGTCGACTGGGATCCTACTGGCAGgcaagtgaaa ... tgttctgcagGTTCTGTTCAACTTCAGTGACATCTGTTCACCAGATGGAGAACGGTTTCAA
EST: gi|162190899|gb|FC368097.1|FC368097
EST:     ACAGCTGAGCACTTTATGGCCACGGATGTCGACTGGGATCCTACTGGCAG                         GTTCTGTTCAACTTCAGTGACATCTGTTCACCAGATGGAGAACGGTTTCAA
genomic: ACAGCTGAGCACTTTATGGCCACGGATGTCGACTGGGATCCTACTGGCAGgcaagtgaaa ... tgttctgcagGTTCTGTTCAACTTCAGTGACATCTGTTCACCAGATGGAGAACGGTTTCAA
EST: gi|37850033|gb|BJ608041.1|BJ608041
EST:     CCACGGATGTCGACTGGGATCCTACTGGCAG                         GTTCTGTTCAACTTCAGTGACATCTGTTCACCAGATGGAGAACGGTTTCAA
genomic: CCACGGATGTCGACTGGGATCCTACTGGCAGgcaagtgaaa ... tgttctgcagGTTCTGTTCAACTTCAGTGACATCTGTTCACCAGATGGAGAACGGTTTCAA
EST: gi|162173039|gb|FC349171.1|FC349171
EST:     ACAGCTGAGCACTTTATGGCCACGGATGTCGACTGGGATCCTACTGGCAG                         GTTCTGTTCAACTTCAGTGACATCTGTTCACCAGATGGAGAACGGTTTCAA
genomic: ACAGCTGAGCACTTTATGGCCACGGATGTCGACTGGGATCCTACTGGCAGgcaagtgaaa ... tgttctgcagGTTCTGTTCAACTTCAGTGACATCTGTTCACCAGATGGAGAACGGTTTCAA
EST: gi|162262408|gb|FC439672.1|FC439672
EST:     ACAGCTGAGCACTTTATGGCCACGGATGTCGACTGGGATCCTACTGGCAG                         GTTCTGTTCAACTTCAGTGACATCTGTTCACCAGATGGAGAACGGTTTCAA
genomic: ACAGCTGAGCACTTTATGGCCACGGATGTCGACTGGGATCCTACTGGCAGgcaagtgaaa ... tgttctgcagGTTCTGTTCAACTTCAGTGACATCTGTTCACCAGATGGAGAACGGTTTCAA
EST: gi|37824388|gb|BJ582454.1|BJ582454
EST:     AGCTGAGCACTTTATGGCCACGGATGTCGACTGGGATCCTACTGGCAG                         GTTCTGTTCAACTTCAGTGACATCTGTTCACCAGATGGAGAACGGTTTCAA
genomic: AGCTGAGCACTTTATGGCCACGGATGTCGACTGGGATCCTACTGGCAGgcaagtgaaa ... tgttctgcagGTTCTGTTCAACTTCAGTGACATCTGTTCACCAGATGGAGAACGGTTTCAA
EST: gi|37838565|gb|BJ596573.1|BJ596573
EST:     GTCGACTGGGATCNTACTGGCAG                         GTTCTGTTCAACTTCAGTGACATCTGTTCACCAGATGGAGAACGGTTTCAA
genomic: GTCGACTGGGATCCTACTGGCAGgcaagtgaaa ... tgttctgcagGTTCTGTTCAACTTCAGTGACATCTGTTCACCAGATGGAGAACGGTTTCAA
EST: gi|37826309|gb|BJ584321.1|BJ584321
EST:     TGTCGACTGGGATCNTACTGGCAG                         GTTCTGTTCAACTTCCAGTGACATCTGTTCACCAGATGGAGAACGGTTTCA
genomic: TGTCGACTGGGATCCTACTGGCAGgcaagtgaaa ... tgttctgcagGTTCTGTTCAACTT-CAGTGACATCTGTTCACCAGATGGAGAACGGTTTCA
EST: gi|162207017|gb|FC383026.1|FC383026
EST:     ACAGCTGAGCACTTTATGGCCACGGATGTCGACTGGGATCCTACTGGCAG                         GTTCTGTTCAACTTCAGTGACATCTGTTCACCAGATGGAGAACGGTTTCAA
genomic: ACAGCTGAGCACTTTATGGCCACGGATGTCGACTGGGATCCTACTGGCAGgcaagtgaaa ... tgttctgcagGTTCTGTTCAACTTCAGTGACATCTGTTCACCAGATGGAGAACGGTTTCAA
EST: gi|162154475|gb|FC330477.1|FC330477
EST:     ACAGCTGAGCACTTTATGGCCACGGATGTCGACTGGGATCCTACTGGCAG                         GTTCTGTTCAACTTCAGTGACATCTGTTCACCAGATGGAGAACGGTTTCAA
genomic: ACAGCTGAGCACTTTATGGCCACGGATGTCGACTGGGATCCTACTGGCAGgcaagtgaaa ... tgttctgcagGTTCTGTTCAACTTCAGTGACATCTGTTCACCAGATGGAGAACGGTTTCAA
EST: gi|162173038|gb|FC349170.1|FC349170
EST:     ACAGCTGAGCACTTTATGGCCACGGATGTCGACTGGGATCNTACTGGCAG                         GTTCTGTTCAACTTCAGTGACATCTGTTCACCAGATGGAGAACGGTTTCAA
genomic: ACAGCTGAGCACTTTATGGCCACGGATGTCGACTGGGATCCTACTGGCAGgcaagtgaaa ... tgttctgcagGTTCTGTTCAACTTCAGTGACATCTGTTCACCAGATGGAGAACGGTTTCAA

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: 31 (upstream exon), 18 (downstream exon)
Score: 7

ACAATGGTCAGCTTGAGTTCTACAATGTGGATGACCTGGAGACAATGGCGACAGCTGAGCACTTTATGGCCACGGATGTCGACTGGGATCCTACTGGCAGgcaagtgaaa ... tgttctgcagGTTCTGTTCAACTTCAGTGACATCTGTTCACCAGATGGAGAACGGTTTCAATATATGGTCATTCCAAGGAAAGCTGTTGTACCGTCTGCCAAGGGACAGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACAATGGTCAGCTTGAGTTCTACAATGTGGATGACCTGGAGACAATGGCGACAGCTGAGCACTTTATGGCCACGGATGTCGACTGGGATCCTACTGGCAGgcaagtgaaagtctcctggtgttgtttagggaactgttgtctgattttgaagtgaatgtttctggttttgttgtgaattaccacactaaagacgtatcaactttaactaatctattgctgggcatttttttgggtcggctagtaatattgggtgttcccattgttctgcag

- - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA