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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagctttttctactgatctcgatttaatttgatgtgttcctgtgcttgcagATTGCCTCGGATGGTCTCAAAGGGCGTGTCTTCGAAGTGTCGCTGGCGGACTTGCAGAATGACGAGGATCACGCCTTCCGGAAGATCAAGCTCAGGGCCG

Basic information

species Selaginella moellendorffii
transcript EFJ09763
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ09763 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S80_120V6.1 (Physcomitrella patens), 3'ss of exon 2
---------------------------------------------------------------------------------------gtgagctttttctactgatc-tcgatttaatttgatgtgt-tcctgtgc----ttgcagATTGCCTCGGATGGTCTCAAAGGGCGTGTCTTCGAAGTGTCGCTGGCGGACTTGCAGAATGACGAGGATCACGCCTTCCGGAAGATCAAGCTCAGGGCCG
                                                                                       | ||   |  |  |   ||  | |  || |   || | || |   |||        |||||||| || |||||  | || ||||| || ||||| ||||||||||||||||||||||| |||||||| || || ||||||||||||||||| ||||| |
gtaagagcatgctgctgggtgggtcggggtgtgtgcatggtggcggtgaattgagtggacgtagggtgcacgcagcattgattgggtgcgaatgtggtggaagaattgtggggttgacgagaggggtgttgcgtggggcgcaacagATTGCGTCCGATGGGTTGAAGGGGCGCGTGTTCGAGGTGTCGCTGGCGGACTTGCAGAACGACGAGGACCAGGCTTTCCGGAAGATCAAGCTGAGGGCGG

upper sequence: EFJ09763 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S179_15V6.1 (Physcomitrella patens), 3'ss of exon 2
--------------------------------------------------------------------------------------gtgagctttttctactgatctc-gatttaatttgatgtgttcctgtgcttgcagATTGCCTCGGATGGTCTCAAAGGGCGTGTCTTCGAAGTGTCGCTGGCGGACTTGCAGAATGACGAGGATCACGCCTTCCGGAAGATCAAGCTCAGGGCCG
                                                                                      |||   || |   | |    || |||   |  |  ||| |   || | || |||||||| || |||||| | ||||| ||||| ||||| || ||  |||| ||| ||||||||||||| ||||| |||||||| ||||| ||||| ||||| |
gtgcgagggtttgattgtttgtttgtttttatttatttgtttgtttattaaagttgggtttatctctgacctggtatggttatactgtgcatttctgtaattagcttctgatgagaggttttgtttgtttgggttt-cagATTGCTTCCGATGGTTTGAAAGGTCGTGTGTTCGAGGTCTCTTTGGCTGACCTGCAGAATGACGAAGATCAGGCCTTCCGCAAGATTAAGCTTAGGGCTG

upper sequence: EFJ09763 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S174_49V6.1 (Physcomitrella patens), 3'ss of exon 2
----------------------------------------------------gtgagctttttctac-tgatctcgatttaatttgatgtgttcctg-tgcttgcagATTGCCTCGGATGGTCTCAAAGGGCGTGTCTTCGAAGTGTCGCTGGCGGACTTGCAGAATGACGAGGATCACGCCTTCCGGAAGATCAAGCTCAGGGCCG--------------------------------------
                                                     | |  ||| || |  || | |     |||  | | |||| |  | || |  |||||||| || |||||  | |  || ||||| ||||| || |   |||| || ||||||||||||||||| || || ||||| ||||||||||| ||||| |                                      
gtgcgaaggttttggatttttttcatcatgtgtgtgtgtgtgtgtttttatttttatttttgtcaatgtggtttgttgctaacatcaggtgtgctggatgttaccagattgcttccgatggcttaaggggccgtgtgttcgaggtctaattggctgatttgcagAATGACGAGGACCAGGCTTTCCGCAAGATCAAGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACGAATTTTTGG

upper sequence: EFJ09763 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S219_50V6.1 (Physcomitrella patens), 3'ss of exon 2
--------------------------------------gtgagctttttctactgatctcgat--------ttaatttgatgtgttcctgtgcttg-cagATTGCCTCGGATGGTCTCAAAGGGCGTGTCTTCGAAGTGTCGCTGGCGGACTTGCAGAATGACGAGGATCACGCCTTCCGGAAGATCAAGCTCAGGGCCG
                                      | |   || | || |  ||    |         | ||||| |    |   ||     | ||||||||||| |||||  | || || ||||| ||||| || ||| | || |||||||||||||| || ||||| || ||||| || |||||||| |||||||
ttttaaaagaataggtctgtgtttaataagcttattttgcgtttttctgcttccaattgaaagcgagcatatgaatttaactcctgtttggatgcgacagATTGCCTCCGATGGGTTGAAGGGACGTGTGTTCGAGGTCTCGTTAGCCGACTTGCAGAATGATGAAGATCAGGCTTTCCGCAAAATCAAGCTGAGGGCCG

upper sequence: EFJ09763 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S17_306V6.1 (Physcomitrella patens), 3'ss of exon 2
-------------------------------------------------------------------------gtgagctttttctactga-tctcgatttaatttgatgtgttcct-----gtgcttgcagATTGCCTCGGATGGTCTCAAAGGGCGTGTCTTCGAAGTGTCGCTGGCGGACTTGCAGAATGACGAGGATCACGCCTTCCGGAAGATCAAGCTCAGGGCCG
                                                                         ||   ||||    || || ||   |  | ||   | ||  | ||     ||  |  ||||||||||| || ||  | || || ||||| ||||| || ||  |||| || |||||||||||||| ||||| || ||||| ||||| ||||| |||||||
gtattgagggttgagttttttatttttattttttatttatgggatgggtgtcgctttattgctggagcgcgctgtccactttgctcacggaatcgatagctgataaaaggttctacttgatggtcttatcagATTGCCTCCGACGGGTTGAAGGGTCGTGTGTTCGAGGTCTCCTTGGCTGATTTGCAGAATGACGAAGATCAGGCTTTCCGCAAGATTAAGCTGAGGGCCG

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|169054227|gb|FE463168.1|FE463168
EST:     ATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGAACAAAG                         ATTGCCTCGGATGGTCTCAAAGGGCGTGTCTTCGAAGTGTCGCTGGCGGAC
genomic: ATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGAACAAAGgtgagctttt ... gtgcttgcagATTGCCTCGGATGGTCTCAAAGGGCGTGTCTTCGAAGTGTCGCTGGCGGAC
EST: gi|169098886|gb|FE502283.1|FE502283
EST:     ATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGAACAAAG                         ATTGCCTCGGATGGTCTCAAAGGGCGTGTCTTCGAAGTGTCGCTGGCGGAC
genomic: ATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGAACAAAGgtgagctttt ... gtgcttgcagATTGCCTCGGATGGTCTCAAAGGGCGTGTCTTCGAAGTGTCGCTGGCGGAC
EST: gi|169022541|gb|FE429425.1|FE429425
EST:     ATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGAACAAAG                         ATTGCCTCGGATGGTCTCAAAGGGCGTGTCTTCGAAGTGTCGCTGGCGGAC
genomic: ATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGAACAAAGgtgagctttt ... gtgcttgcagATTGCCTCGGATGGTCTCAAAGGGCGTGTCTTCGAAGTGTCGCTGGCGGAC
EST: gi|169020263|gb|FE430340.1|FE430340
EST:     ATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGAACAAAG                         ATTGCCTCGGATGGTCTCAAAGGGCGTGTGTTCGAAGTGTCGCTGGCGGAC
genomic: ATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGAACAAAGgtgagctttt ... gtgcttgcagATTGCCTCGGATGGTCTCAAAGGGCGTGTCTTCGAAGTGTCGCTGGCGGAC
EST: gi|169020264|gb|FE430341.1|FE430341
EST:     ATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGAACAAAG                         ATTGCCTCGGATGGTCTCAAAGGGCGTGTGTTCGAAGTGTCGCTGGCGGAC
genomic: ATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGAACAAAGgtgagctttt ... gtgcttgcagATTGCCTCGGATGGTCTCAAAGGGCGTGTCTTCGAAGTGTCGCTGGCGGAC
EST: gi|169051171|gb|FE460252.1|FE460252
EST:     ATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGAACAAAG                         ATTGCCTCGGATGGTCTCAAAGGGCGTGTCTTCGAAGTGTCGCTGGCGGAC
genomic: ATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGAACAAAGgtgagctttt ... gtgcttgcagATTGCCTCGGATGGTCTCAAAGGGCGTGTCTTCGAAGTGTCGCTGGCGGAC
EST: gi|169065307|gb|FE473208.1|FE473208
EST:     ATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGAACAAAG                         ATTGCCTCGGATGGTCTCAAAGGGCGTGTCTTCGAAGTGTCGCTGGCGGAC
genomic: ATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGAACAAAGgtgagctttt ... gtgcttgcagATTGCCTCGGATGGTCTCAAAGGGCGTGTCTTCGAAGTGTCGCTGGCGGAC
EST: gi|169022540|gb|FE429424.1|FE429424
EST:     ATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGAACAAAG                         ATTGCCTCGGATGGTCTCAAAGGGCGTGTCTTCGAAGTGTCGCTGGCGGAC
genomic: ATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGAACAAAGgtgagctttt ... gtgcttgcagATTGCCTCGGATGGTCTCAAAGGGCGTGTCTTCGAAGTGTCGCTGGCGGAC
EST: gi|169103224|gb|FE505628.1|FE505628
EST:     AGGGAACAAAG                         ATTGCCTCGGATGGTCTCAAAGGGCGTGTCTTCGAAGTGTCGCTGGCGGAC
genomic: AGGGAACAAAGgtgagctttt ... gtgcttgcagATTGCCTCGGATGGTCTCAAAGGGCGTGTCTTCGAAGTGTCGCTGGCGGAC
EST: gi|169097436|gb|FE499022.1|FE499022
EST:     ATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGAACAAAG                         ATTGCCTCGGATGGTCTCAAAGGGCGTGTCTTCGAAGTGTCGCTGGCGGAC
genomic: ATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGAACAAAGgtgagctttt ... gtgcttgcagATTGCCTCGGATGGTCTCAAAGGGCGTGTCTTCGAAGTGTCGCTGGCGGAC
EST: gi|169104851|gb|FE508722.1|FE508722
EST:     ATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGAACAAAG                         ATTGCCTCGGATGGTCTCAAAGGGCGTGTCTTCGAAGTGTCGCTTGCGGAC
genomic: ATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGAACAAAGgtgagctttt ... gtgcttgcagATTGCCTCGGATGGTCTCAAAGGGCGTGTCTTCGAAGTGTCGCTGGCGGAC
EST: gi|169103249|gb|FE504821.1|FE504821
EST:     ATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGAACAAAG                         ATTGCCTCGGATGGTCTCAAAGGGCGTGTCTTCGAAGTGTCGCTGGCGGAC
genomic: ATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGAACAAAGgtgagctttt ... gtgcttgcagATTGCCTCGGATGGTCTCAAAGGGCGTGTCTTCGAAGTGTCGCTGGCGGAC
EST: gi|169097435|gb|FE499021.1|FE499021
EST:     ATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGAACAAAG                         ATTGCCTCGGATGGTCTCAAAGGGCGTGTCTTCGAAGTGTCGCTGGCGGAC
genomic: ATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGAACAAAGgtgagctttt ... gtgcttgcagATTGCCTCGGATGGTCTCAAAGGGCGTGTCTTCGAAGTGTCGCTGGCGGAC
EST: gi|169055047|gb|FE462962.1|FE462962
EST:     ATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGAACAAAG                         ATTGCCTCGGATGGTCTCAAAGGGCGTGTGTTCGAAGTGTCGCTGGCGGAC
genomic: ATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGAACAAAGgtgagctttt ... gtgcttgcagATTGCCTCGGATGGTCTCAAAGGGCGTGTCTTCGAAGTGTCGCTGGCGGAC
EST: gi|169098885|gb|FE502282.1|FE502282
EST:     ATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGAACAAAG                         ATTGCCTCGGATGGTCTCAAAGGGCGTGTCTTCGAAGTGTCGCTGGCGGAC
genomic: ATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGAACAAAGgtgagctttt ... gtgcttgcagATTGCCTCGGATGGTCTCAAAGGGCGTGTCTTCGAAGTGTCGCTGGCGGAC
EST: gi|169065308|gb|FE473209.1|FE473209
EST:     ATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGAACAAAG                         ATTGCCTCGGATGGTCTCAAAGGGCGTGTCTTCGAAGTGTCGCTGGCGGAC
genomic: ATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGAACAAAGgtgagctttt ... gtgcttgcagATTGCCTCGGATGGTCTCAAAGGGCGTGTCTTCGAAGTGTCGCTGGCGGAC
EST: gi|169103251|gb|FE505629.1|FE505629
EST:     ATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGAACAAAG                         ATTGCCTCGGATGGTCTCAAAGGGCGTGTCTTCGAAGTGTCGCTGGCGGAC
genomic: ATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGAACAAAGgtgagctttt ... gtgcttgcagATTGCCTCGGATGGTCTCAAAGGGCGTGTCTTCGAAGTGTCGCTGGCGGAC
EST: gi|169033920|gb|FE441952.1|FE441952
EST:     ATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGAACAAAG                         ATTGCCTCGGATGGTCTCAAAGGGCGTGTCTTCGAAGTGTCGCTGGCGGAC
genomic: ATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGAACAAAGgtgagctttt ... gtgcttgcagATTGCCTCGGATGGTCTCAAAGGGCGTGTCTTCGAAGTGTCGCTGGCGGAC
EST: gi|169056009|gb|FE466185.1|FE466185
EST:     ATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGAACAAAG                         ATTGCCTCGGATGGTCTCAAAGGGCGTGTCTTCGAAGTGTCGCTTGCGGAC
genomic: ATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGAACAAAGgtgagctttt ... gtgcttgcagATTGCCTCGGATGGTCTCAAAGGGCGTGTCTTCGAAGTGTCGCTGGCGGAC
EST: gi|169069101|gb|FE476740.1|FE476740
EST:     ATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGAACAAAG                         ATTGCCTCGGATGGTCTCAAAGGGCGTGTCTTCGAAGTGTCGCTGGCGGAC
genomic: ATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGAACAAAGgtgagctttt ... gtgcttgcagATTGCCTCGGATGGTCTCAAAGGGCGTGTCTTCGAAGTGTCGCTGGCGGAC
EST: gi|169056434|gb|FE467013.1|FE467013
EST:     ATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGAACAAAG                         ATTGCCTCGGATGGTCTCAAAGGGCGTGTCTTCGAAGTGTCGCTTGCGGAC
genomic: ATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGAACAAAGgtgagctttt ... gtgcttgcagATTGCCTCGGATGGTCTCAAAGGGCGTGTCTTCGAAGTGTCGCTGGCGGAC

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), 34 (downstream exon)
Score: 182

CCCTTTCTCGAAGAAGGATTGGTACGATGTCAAGGCCATGTCCACTTTCAATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGAACAAAGgtgagctttt ... gtgcttgcagATTGCCTCGGATGGTCTCAAAGGGCGTGTCTTCGAAGTGTCGCTGGCGGACTTGCAGAATGACGAGGATCACGCCTTCCGGAAGATCAAGCTCAGGGCCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgagctttttctactgatctcgatttaatttgatgtgttcctgtgcttgcagATTGCCTCGGATGGTCTCAAAGGGCGTGTCTTCGAAGTGTCGCTGGCGGACTTGCAGAATGACGAGGATCACGCCTTCCGGAAGATCAAGCTCAGGGCCG
                                         ttcctgt  CT-rich tract
                         atttaatttgatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagctttttctactgatctcgatttaatttgatgtgttcctgtgcttgcagATTGCCTCGGATGGTCTCAAAGGGCGTGTCTTCGAAGTGTCGCTGGCGGACTTGCAGAATGACGAGGATCACGCCTTCCGGAAGATCAAGCTCAGGGCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA