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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGTCAGGACAAGGACAGAGGCCGAATCAGTTTGTCCACCAAGAAGCTTGAGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAGgttaatcatttacgttcaaaagccttatcttctttgtaatgcactgacattttcgcattttggttgtaccgaaaatgaaccacaaagtaacgaattcaag...

Basic information

species Physcomitrella patens
transcript PP1S40_14V6.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S40_14V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: GRMZM5G862107_T01 (Zea mays), 5'ss of exon 5
GAGTCAGGACAAGGACAGAGGCCGAATCAGTTTGTCCACCAAGAAGCTTGAGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAGgttaatcatttacgttcaaaagccttatcttctttgtaatgcactgacattttcgcattttggttgtaccgaaaatgaaccacaaagtaacgaattcaag
||| || |||   || ||||||||| ||||  | || || |||||||||||||||||||||||||||||| | || || ||  |  | || | ||||||||| |       |    |||||||   || ||||     |||  ||||    |  || ||  |   | | |  | ||           |    || | |  
GAGCCATGACCGTGAAAGAGGCCGAGTCAGCCTTTCTACTAAGAAGCTTGAGCCAACACCTGGTGACATGATCCGCAATCCCAAGCTTGTGTTTGAGAAGgtaaga-----ataaacaaaagcaacattttctc----atgtgctgaa---tatgctttaggtaagcaactgacatatggtttcttttgctcaaattag-

upper sequence: PP1S40_14V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: AT5G30510.1 (Arabidopsis thaliana), 5'ss of exon 5
GAGTCAGGACAAGGACAGAGGCCGAATCAGTTTGTCCACCAAGAAGCTTGAGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAGgttaatc-atttacgttcaaaag------ccttatcttctttgtaatgcactgacattttcgcattttggttgtaccgaaaatgaaccacaaagtaacgaattcaag
|||||| |||   ||||||||  || | ||| | ||||| |||||||| ||||||||||||||||| ||| | ||||||||| || | || |  |||||||| | || |||| | |||||||       || ||| |||||| ||   | |   ||||| |   |||  | |||  | |                            
GAGTCACGACCGTGACAGAGGAAGAGTAAGTCTCTCCACAAAGAAGCTGGAGCCAACACCTGGTGATATGATTCGTAACCCAAAACTTGTGTTCGAGAAGgtaactctatttccattcaaaaaaactttccctattttcttt-tatgtctcaatcatttgctactttctgctgtctcaag---------------------------
















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|162190539|gb|FC366177.1|FC366177
EST:     AGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAG                         GCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAGgttaatcatt ... tgcactgcagGCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCA
EST: gi|162276038|gb|FC452314.1|FC452314
EST:     AGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAG                         GCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAGgttaatcatt ... tgcactgcagGCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCA
EST: gi|162204488|gb|FC381716.1|FC381716
EST:     AGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAG                         GCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAGgttaatcatt ... tgcactgcagGCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCA
EST: gi|67699996|gb|BJ960229.1|BJ960229
EST:     AGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAG                         GNTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAGgttaatcatt ... tgcactgcagGCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCA
EST: gi|67693939|gb|BJ954172.1|BJ954172
EST:     AGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAG                         GCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAGgttaatcatt ... tgcactgcagGCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCA
EST: gi|162191409|gb|FC368179.1|FC368179
EST:     AGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAG                         GCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAGgttaatcatt ... tgcactgcagGCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCA
EST: gi|37837429|gb|BJ595437.1|BJ595437
EST:     AGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAG                         GCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAGgttaatcatt ... tgcactgcagGCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCA
EST: gi|162276039|gb|FC452315.1|FC452315
EST:     AGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAG                         GCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAGgttaatcatt ... tgcactgcagGCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCA
EST: gi|162204214|gb|FC379687.1|FC379687
EST:     AGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAG                         GCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAGgttaatcatt ... tgcactgcagGCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCA
EST: gi|208358113|gb|DC946741.1|DC946741
EST:     AGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAG                         GCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAGgttaatcatt ... tgcactgcagGCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCA
EST: gi|18341604|gb|BJ173639.1|BJ173639
EST:     AGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAG                         GCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAGgttaatcatt ... tgcactgcagGCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCA
EST: gi|7648089|gb|AW739072.1|AW739072
EST:     AGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAG                         GCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAGgttaatcatt ... tgcactgcagGCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCA
EST: gi|162186279|gb|FC361587.1|FC361587
EST:     AGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAG                         GCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAGgttaatcatt ... tgcactgcagGCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCA
EST: gi|162191408|gb|FC368178.1|FC368178
EST:     AGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAG                         GCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAGgttaatcatt ... tgcactgcagGCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCA
EST: gi|162186278|gb|FC361586.1|FC361586
EST:     AGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAG                         GCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAGgttaatcatt ... tgcactgcagGCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCA
EST: gi|18339226|gb|BJ171253.1|BJ171253
EST:     AGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAG                         GCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAGgttaatcatt ... tgcactgcagGCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCA
EST: gi|162206261|gb|FC382331.1|FC382331
EST:     AGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAG                         GCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAGgttaatcatt ... tgcactgcagGCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCA
EST: gi|162279658|gb|FC455384.1|FC455384
EST:     AGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAG                         GCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAGgttaatcatt ... tgcactgcagGCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCA
EST: gi|37826197|gb|BJ584209.1|BJ584209
EST:     AGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAG                         GCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAGgttaatcatt ... tgcactgcagGCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCA
EST: gi|18336148|gb|BJ168170.1|BJ168170
EST:     AGCCAACACCTGGTGACATGTTGCGTAANCCACAATTGGTTTATNAGAAG                         GCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAGgttaatcatt ... tgcactgcagGCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCA
EST: gi|162205698|gb|FC381900.1|FC381900
EST:     AGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAG                         GCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAGgttaatcatt ... tgcactgcagGCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCA
EST: gi|208382842|gb|DC923889.1|DC923889
EST:     AGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAG                         GCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAGgttaatcatt ... tgcactgcagGCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCA
EST: gi|162167193|gb|FC342758.1|FC342758
EST:     AGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAG                         GCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAGgttaatcatt ... tgcactgcagGCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCA
EST: gi|162205699|gb|FC381901.1|FC381901
EST:     AGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAG                         GCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAGgttaatcatt ... tgcactgcagGCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCA

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: 33 (upstream exon), 34 (downstream exon)
Score: 23

GAGTCAGGACAAGGACAGAGGCCGAATCAGTTTGTCCACCAAGAAGCTTGAGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAGgttaatcatt ... tgcactgcagGCTGATGAGATGGCTAAGACCTTCAGGCAAAGGGTTGCTCAAGCCGAGGCAGCTGCTAGGGCAGAAGAATTGCGACTTCAGCAGTTTCAAGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGTCAGGACAAGGACAGAGGCCGAATCAGTTTGTCCACCAAGAAGCTTGAGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGGTTTATGAGAAGgttaatcatttacgttcaaaagccttatcttctttgtaatgcactgacattttcgcattttggttgtaccgaaaatgaaccacaaagtaacgaattcaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaatgaa