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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCTTGACTTACCGAGAGGTGGTCGCAATCGTGATGCAAAAGCTCATCTCGATTGATGGCAAGGTCCGGACGGACAAGTGCTATCCCGCTGGATTCATGGgtaagttctcgatttcttttcctctcttacccgactgacttgcttgtttcgcttttctag

Basic information

species Selaginella moellendorffii
transcript EFJ14824
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ14824 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: PP1S81_172V6.1 (Physcomitrella patens), 5'ss of exon 3
GCCTTGACTTACCGAGAGGTGGTCGCAATCGTGATGCAAAAGCTCATCTCGATTGATGGCAAGGTCCGGACGGACAAGTGCTATCCCGCTGGATTCATGGgtaagtt--ctcgatttcttttcctctcttacccgactgacttgcttgtttcgcttttctag--------------------------------------
|| ||||| ||||| || || || || ||||| |||||    |||||||| ||||||||||||||||| || ||||||||||| || || || |||||||||| |||  || |  | |  |  ||  |       | || ||| ||  ||       | | |                                      
GCTTTGACCTACCGCGAAGTAGTTGCCATCGTTATGCAGCGCCTCATCTCCATTGATGGCAAGGTCCGCACTGACAAGTGCTACCCTGCAGGTTTCATGGgtacgttatcttgcatacagtcacttgcactgtgcaatgtctttctaattctctacatgttgtaatcgtaaagatgattagtgctttgcgtaagacgcgc

upper sequence: EFJ14824 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: PP1S461_1V6.1 (Physcomitrella patens), 5'ss of exon 3
GCCTTGACTTACCGAGAGGTGGTCGCAATCGTGATGCAAAAGCTCATCTCGATTGATGGCAAGGTCCGGACGGACAAGTGCTATCCCGCTGGATTCATGGgtaagttctc--gatttcttttcctctcttacccgactgacttgcttgtttcgcttttctag--------------------------------------------------------------------------------------------------------------------------------
|| ||||| |||||||| || || || || || |||||    |||||||| ||||||||||||||||| || ||||| ||||| || || || |||||||||||||| |   |   |||| |      || |      ||  |     ||| |   |  |                                                                                                                                  
GCATTGACCTACCGAGAAGTAGTAGCCATTGTCATGCAGCGCCTCATCTCTATTGATGGCAAGGTCCGCACTGACAAATGCTACCCTGCAGGTTTCATGGgtaagtttttttgcagtcttattgaaagtttctttttagatatatgctttttggaatcatgaatgtttgtttttatgaatttatgtatggggataaacttgggtcatgcagactgatcgtcttttactcatacacgatttgaagcgtagtctcgtagcactggataacccgtttcatgctctcaatacag

upper sequence: EFJ14824 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: PP1S2_16V6.1 (Physcomitrella patens), 5'ss of exon 3
GCCTTGACTTACCGAGAGGTGGTCGCAATCGTGATGCAAAAGCTCATCTCGATTGATGGCAAGGTCCGGACGGACAAGTGCTATCCCGCTGGATTCATGGgtaagttc-tcgatttcttttcctctcttacccgactgacttgcttgtttcgcttttctag-----------------------------------------------------------------------------------------------------------------
|| ||||| ||||| || || || || || || ||||||   || || || ||||||||||||||||| || ||||||||||| || || || ||||||||| |||    |     |         |  ||     |  |||| |      |  |    |                                                                                                                  
GCGTTGACCTACCGTGAAGTTGTTGCTATTGTCATGCAACGCCTTATTTCCATTGATGGCAAGGTCCGTACTGACAAGTGCTACCCAGCAGGGTTCATGGgtgagtaaaccagcggcgcaaaaatgcccacgtttttagcttgttatcaatgtctcgtgaatgatatagtaagtattggcttttcaaagagtttttttcggatataggtcatgtcctgtagtgtactgctgtctcccttcggctcctgagtactctcatctcatcctttgctag

upper sequence: EFJ14824 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: PP1S282_25V6.1 (Physcomitrella patens), 5'ss of exon 3
GCCTTGACTTACCGAGAGGTGGTCGCAATCGTGATGCAAAAGCTCATCTCGATTGATGGCAAGGTCCGGACGGACAAGTGCTATCCCGCTGGATTCATGGgtaagt----tctcgatt-tcttttcctctcttacccgactgacttgcttgtttcgcttttctag-------------------------------------------------------------------------------------------------------------
||||| || ||||| || ||||| || |||||||||||    |||||||| |||||||| ||||| || || ||||||||||| || || || ||||||||| |||    | | |||  |||||    |  |       |  || | |  |     ||||| ||                                                                                                              
GCCTTAACCTACCGCGAAGTGGTTGCCATCGTGATGCAGCGCCTCATCTCCATTGATGGAAAGGTTCGAACTGACAAGTGCTACCCTGCCGGTTTCATGGgtgagtaacatttagatcatctttattgccatcgtagcgccaacattcgagccggccttttttattcttgacaatctcggaaccaaagtccacacattgcgtgttttaacctctttaatggagccataaagttttcttacaagatcaggtttatcatctgataaaaaaatgcag

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|169039300|gb|FE448858.1|FE448858
EST:     GATTGATGGCAAGGTCCGGACGGACAAGTGCTATCCCGCTGGATTCATGG                         ATGTGTTGACGGTCGGCAAGGTGGATGAGAACTACCGTCTCCTCTATGACA
genomic: GATTGATGGCAAGGTCCGGACGGACAAGTGCTATCCCGCTGGATTCATGGgtaagttctc ... gcttttctagATGTGTTGACGGTCGGCAAGGTGGATGAGAACTACCGTCTCCTCTATGACA
EST: gi|169073370|gb|FE481121.1|FE481121
EST:     GATTGATGGCAAGGTCCGGACGGACAAGTGCTATCCCGCTGGATTCATGG                         ATGTGTTGACGGTCGGCAAGGTGGATGAGAACTACCGTCTCCTCTATGACA
genomic: GATTGATGGCAAGGTCCGGACGGACAAGTGCTATCCCGCTGGATTCATGGgtaagttctc ... gcttttctagATGTGTTGACGGTCGGCAAGGTGGATGAGAACTACCGTCTCCTCTATGACA
EST: gi|169053556|gb|FE463325.1|FE463325
EST:     GATTGATGGCAAGGTCCGGACGGACAAGTGCTATCCCGCTGGATTCATGG                         ATGTGTTGACGGTCGGCAAGGTGGATGAGAACTACCGTCTCCTCTATGACA
genomic: GATTGATGGCAAGGTCCGGACGGACAAGTGCTATCCCGCTGGATTCATGGgtaagttctc ... gcttttctagATGTGTTGACGGTCGGCAAGGTGGATGAGAACTACCGTCTCCTCTATGACA
EST: gi|169073371|gb|FE481122.1|FE481122
EST:     GATTGATGGCAAGGTCCGGACGGACAAGTGCTATCCCGCTGGATTCATGG                         ATGTGTTGACGGTCGGCAAGGTGGATGAGAACTACCGTCTCCTCTATGACA
genomic: GATTGATGGCAAGGTCCGGACGGACAAGTGCTATCCCGCTGGATTCATGGgtaagttctc ... gcttttctagATGTGTTGACGGTCGGCAAGGTGGATGAGAACTACCGTCTCCTCTATGACA
EST: gi|169100977|gb|FE500604.1|FE500604
EST:     GATTGATGGCAAGGTCCGGACGGACAAGTGCTATCCCGCTGGATTCATGG                         ATGTGTTGACGGTCGGCAAGGTGGATGAGAACTACCGTCTCCTCTATGACA
genomic: GATTGATGGCAAGGTCCGGACGGACAAGTGCTATCCCGCTGGATTCATGGgtaagttctc ... gcttttctagATGTGTTGACGGTCGGCAAGGTGGATGAGAACTACCGTCTCCTCTATGACA
EST: gi|169057772|gb|FE465266.1|FE465266
EST:     GATTGATGGCAAGGTCCGGACGGACAAATGCTATCCCGCTGGATTCATGG                         ATGTGTTGACGGTCGGCAAGGTGGATGAGAACTACCGTCTCCTCTATGACA
genomic: GATTGATGGCAAGGTCCGGACGGACAAGTGCTATCCCGCTGGATTCATGGgtaagttctc ... gcttttctagATGTGTTGACGGTCGGCAAGGTGGATGAGAACTACCGTCTCCTCTATGACA
EST: gi|169114018|gb|FE516489.1|FE516489
EST:     GATTGATGGCAAGGTCCGGACGGACAAATGCTATCCCGCTGGATTCATGG                         ATGTGTTGACGGTCGGCAAGGTGGATGAGAACTACCGTCTCCTCTATGACA
genomic: GATTGATGGCAAGGTCCGGACGGACAAGTGCTATCCCGCTGGATTCATGGgtaagttctc ... gcttttctagATGTGTTGACGGTCGGCAAGGTGGATGAGAACTACCGTCTCCTCTATGACA
EST: gi|169053555|gb|FE463324.1|FE463324
EST:     GATTGATGGCAAGGTCCGGACGGACAAGTGCTATCCCGCTGGATTCATGG                         ATGTGTTGACGGTCGGCAAGGTGGATGAGAACTACCGTCTCCTCTATGACA
genomic: GATTGATGGCAAGGTCCGGACGGACAAGTGCTATCCCGCTGGATTCATGGgtaagttctc ... gcttttctagATGTGTTGACGGTCGGCAAGGTGGATGAGAACTACCGTCTCCTCTATGACA
EST: gi|169054328|gb|FE460773.1|FE460773
EST:     GATTGATGGCAAGGTCCGGACGGACAAATGCTATCCCGCTGGATTCATGG                         ATGTGTTGACGGTCGGCAAGGTGGATGAGAACTACCGTCTCCTCTATGACA
genomic: GATTGATGGCAAGGTCCGGACGGACAAGTGCTATCCCGCTGGATTCATGGgtaagttctc ... gcttttctagATGTGTTGACGGTCGGCAAGGTGGATGAGAACTACCGTCTCCTCTATGACA
EST: gi|169074638|gb|FE481193.1|FE481193
EST:     GATTGATGGCAAGGTCCGGACGGACAAGTGCTATCCCGCTGGATTCATGG                         ATGTGTTGACGGTCGGCAAGGTGGATGAGAACTACCGTCTCCTCTATGACA
genomic: GATTGATGGCAAGGTCCGGACGGACAAGTGCTATCCCGCTGGATTCATGGgtaagttctc ... gcttttctagATGTGTTGACGGTCGGCAAGGTGGATGAGAACTACCGTCTCCTCTATGACA
EST: gi|169042741|gb|FE451560.1|FE451560
EST:     GATTGATGGCAAGGTCCGGACGGACAAGTGCTATCCCGCTGGATTCATGG                         ATGTGTTGACGGTCGGCAAGGTGGATGAGAACTACCGTCTCCTCTATGACA
genomic: GATTGATGGCAAGGTCCGGACGGACAAGTGCTATCCCGCTGGATTCATGGgtaagttctc ... gcttttctagATGTGTTGACGGTCGGCAAGGTGGATGAGAACTACCGTCTCCTCTATGACA
EST: gi|169053335|gb|FE460426.1|FE460426
EST:     GATTGATGGCAAGGTCCGGACGGACAAATGCTATCCCGCTGGATTCATGG                         ATGTGTTGACGGTCGGCAAGGTGGATGAGAACTACCGTCTCCTCTATGACA
genomic: GATTGATGGCAAGGTCCGGACGGACAAGTGCTATCCCGCTGGATTCATGGgtaagttctc ... gcttttctagATGTGTTGACGGTCGGCAAGGTGGATGAGAACTACCGTCTCCTCTATGACA
EST: gi|169041716|gb|FE449287.1|FE449287
EST:     GATTGATGGCAAGGTCCGGACGGACAAGTGCTATCCCGCTGGATTCATGG                         ATGTGTTGACGGTCGGCAAGGTGGATGAGAACTACCGTCTCCTCTATGACA
genomic: GATTGATGGCAAGGTCCGGACGGACAAGTGCTATCCCGCTGGATTCATGGgtaagttctc ... gcttttctagATGTGTTGACGGTCGGCAAGGTGGATGAGAACTACCGTCTCCTCTATGACA
EST: gi|169097355|gb|FE498486.1|FE498486
EST:     GATTGATGGCAAGGTCCGGACGGACAAGTGCTATCCCGCTGGATTCATGG                         ATGTGTTGACGGTCGGCAAGGTGGATGAGAACTACCGTCTCCTCTATGACA
genomic: GATTGATGGCAAGGTCCGGACGGACAAGTGCTATCCCGCTGGATTCATGGgtaagttctc ... gcttttctagATGTGTTGACGGTCGGCAAGGTGGATGAGAACTACCGTCTCCTCTATGACA
EST: gi|169074639|gb|FE481194.1|FE481194
EST:     GATTGATGGCAAGGTCCGGACGGACAAGTGCTATCCCGCTGGATTCATGG                         ATGTGTTGACGGTCGGCAAGGTGGATGAGAACTACCGTCTCCTCTATGACA
genomic: GATTGATGGCAAGGTCCGGACGGACAAGTGCTATCCCGCTGGATTCATGGgtaagttctc ... gcttttctagATGTGTTGACGGTCGGCAAGGTGGATGAGAACTACCGTCTCCTCTATGACA
EST: gi|169041419|gb|FE448977.1|FE448977
EST:     GATTGATGGCAAGGTCCGGACGGACAAATGCTATCCCGCTGGATTCATGG                         ATGTGTTGACGGTCGGCAAGGTGGATGAGAACTACCGTCTCCTCTATGACA
genomic: GATTGATGGCAAGGTCCGGACGGACAAGTGCTATCCCGCTGGATTCATGGgtaagttctc ... gcttttctagATGTGTTGACGGTCGGCAAGGTGGATGAGAACTACCGTCTCCTCTATGACA

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: 35 (upstream exon), 28 (downstream exon)
Score: 22

GCCTTGACTTACCGAGAGGTGGTCGCAATCGTGATGCAAAAGCTCATCTCGATTGATGGCAAGGTCCGGACGGACAAGTGCTATCCCGCTGGATTCATGGgtaagttctc ... gcttttctagATGTGTTGACGGTCGGCAAGGTGGATGAGAACTACCGTCTCCTCTATGACAGCAAGGGCCGATTCACCTTGCACTCGATCAACTCCGAGGAGGCCAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCTTGACTTACCGAGAGGTGGTCGCAATCGTGATGCAAAAGCTCATCTCGATTGATGGCAAGGTCCGGACGGACAAGTGCTATCCCGCTGGATTCATGGgtaagttctcgatttcttttcctctcttacccgactgacttgcttgtttcgcttttctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA