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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggtttggcggtaatcatcgtagtcgcattttctgatgataaactgttatcagGCTGATATCGGTCTTTCAATGGGCATCCAAGGGACCGAGGTGGCCAAAGAAAGCTCAGACATTATAATTCTGGATGACAACTTTGCATCTGTTGTCAAG

Basic information

species Selaginella moellendorffii
transcript EFJ22392
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ22392 (Selaginella moellendorffii), 3'ss of exon 21
lower sequence: LOC_Os08g40530.1 (Oryza sativa), 3'ss of exon 10
----------------------------------------------------------gtgggtttggcggtaatcatcgtagtcgcattttctgatgataaactg-ttat-cagGCTGATATCGGTCTTTCAATGGGCATCCAAGGGACCGAGGTGGCCAAAGAAAGCTCAGACATTATAATTCTGGATGACAACTTTGCATCTGTTGTCAAG
                                                           |       | | | |||||| |  ||  |||   ||    |  | |  || |  |||| ||||| ||||| |||||||||||   |||||| || || ||||||||||| || |||||||||||  |||||||||||||  |||| ||||| |||
gtctcaactctcaagtgcatatctctcatgatattgatgaactctccctttgttctcttttatcacagagattatcatcttgttcttattccttgtcattccatttcttgtgtagGCCGATATAGGTCTCTCAATGGGCATTTCAGGGACAGAAGTTGCCAAAGAAAGTTCTGACATTATAATCTTGGATGACAACTTCACATCAGTTGTGAAG

upper sequence: EFJ22392 (Selaginella moellendorffii), 3'ss of exon 21
lower sequence: LOC_Os02g08010.1 (Oryza sativa), 3'ss of exon 8
----------------------------------------------------------------------gtgggtttgg-cggtaatcatcgtagtcgcat-tttctgatgataaactgttatc-----------agGCTGATATCGGTCTTTCAATGGGCATCCAAGGGACCGAGGTGGCCAAAGAAAGCTCAGACATTATAATTCTGGATGACAACTTTGCATCTGTTGTCAAG
                                                                       ||        || | ||    || |  |||  ||||| ||  | | || ||||            |||| || || |||||| | ||||| |||||||| || || || || |||||||||||||| || || |||||||||||||| ||||| || ||||| |||
gtacatacataattgggaattttgttttgaacaaataaaaggataaacataatggttttatttcaatcagatgaagacaatcgatcatgcatgttgatgcacatttctaattttgatctcttattcctcctaatttagGCAGACATTGGTCTTGCTATGGGTATCCAAGGAACAGAAGTAGCTAAAGAAAGCTCAGATATAATTATTCTGGATGACAATTTTGCTTCAGTTGTAAAG

upper sequence: EFJ22392 (Selaginella moellendorffii), 3'ss of exon 21
lower sequence: GRMZM5G893864_T01 (Zea mays), 3'ss of exon 4
----------------------------------------------------------------------------------------------gtgggtttggcggtaatcatcgtagtcgcattttctgatgataaactgttatcagGCTGATATCGGTCTTTCAATGGGCATCCAAGGGACCGAGGTGGCCAAAGAAAGCTCAGACATTATAATTCTGGATGACAACTTTGCATCTGTTGTCAAG
                                                                                                    |||  | |  |   | |  ||  || || | || ||   |  ||||||||| ||||| |||||||| |||||||||||||| || || || |||||||| ||||||||||| ||||||||||||||||| ||| | |||||||| |||
gtacattcaatttgggagttcatattttaaatgaatacaagaattcaacatgcatgtgattatatgaagcactatttggtaatacagcacttctaacatgttgaggtttcttccccttctca-atcttatcattattcccacttatcagGCAGATATTGGTCTTTCTATGGGCATCCAAGGAACAGAAGTAGCCAAAGAGAGCTCAGACATAATAATTCTGGATGACAATTTTTCTTCTGTTGTGAAG

upper sequence: EFJ22392 (Selaginella moellendorffii), 3'ss of exon 21
lower sequence: GRMZM2G340139_T01 (Zea mays), 3'ss of exon 25
--------------gtgggtttggcggtaatcatc--gtagtcgcatt-ttctgatgataaa----ctgttat-cagGCTGATATCGGTCTTTCAATGGGCATCCAAGGGACCGAGGTGGCCAAAGAAAGCTCAGACATTATAATTCTGGATGACAACTTTGCATCTGTTGTCAAG
               |    ||     || ||| |  | | |  | || | || ||  | ||     ||| ||  |||||||||| |||||||||||||| ||   ||| || || || ||||| ||||||||||||||||||||  |||||||  ||||  | ||||| ||||||
gtcagtccaaacttttatcattccttatagtcaacctgcaataaccttctcctaatcctgaaatttttgtcatatagGCTGATATAGGTCTTTCAATGGGAATATCAGGAACAGAAGTTGCCAAGGAAAGCTCAGACATTATAATCTTGGATGATGACTTCACCTCTGTGGTCAAG

upper sequence: EFJ22392 (Selaginella moellendorffii), 3'ss of exon 21
lower sequence: GRMZM2G132712_T03 (Zea mays), 3'ss of exon 26
-------------------------------------------------------------gtgggtttggcggtaatcatcgtagtcgcattttctgatgataaactgttatcagGCTGATATCGGTCTTTCAATGGGCATCCAAGGGACCGAGGTGGCCAAAGAAAGCTCAGACATTATAATTCTGGATGACAACTTTGCATCTGTTGTCAAG
                                                              || | ||  || |  | || |  | |   ||  ||  | ||    |||  | |||| ||||| |||||||||||||||||    ||||| || || || ||||||||||| |||||||||||  |||||||  ||||  | || |||||||||
gtgacatgttcagctcaagacattgatgaggcattacatattgcaccttttctttgcattgatgagcttaccgtttctaattgctgcc---ttgcctcttcatttgttgtcct-agGCCGATATAGGTCTTTCAATGGGCATTTCCGGGACAGAAGTTGCTAAAGAAAGCTCTGACATTATAATCTTGGATGATGACTTCACGTCAGTTGTCAAG

upper sequence: EFJ22392 (Selaginella moellendorffii), 3'ss of exon 21
lower sequence: GLYMA07G00630.2 (Glycine max), 3'ss of exon 24
--------------------------------------gtgggtttggcggtaatcatcgtagtcgcattt--tctgatgataaactgttat------cagGCTGATATCGGTCTTTCAATGGGCATCCAAGGGACCGAGGTGGCCAAAGAAAGCTCAGACATTATAATTCTGGATGACAACTTTGCATCTGTTGTCAAG
                                          ||||      ||  ||| | ||   | ||  |||  || |  ||| || |       |||||||||| |||||||| |||||||||||||| || || || || |||||||||||||| |||||||| || || || ||||||||||| || || |||
catctgtttggttgtcatgttccatttattaaaataattcctgtttactaaaaagaatctt-gttatagttaatctcgtgctttactattttgaattttagGCTGATATTGGTCTTTCTATGGGCATCCAAGGAACTGAAGTTGCAAAAGAAAGCTCAGATATTATAATCCTAGACGATAACTTTGCATCAGTGGTAAAG

upper sequence: EFJ22392 (Selaginella moellendorffii), 3'ss of exon 21
lower sequence: GLYMA15G00340.1 (Glycine max), 3'ss of exon 26
------------------------------------------gtgggtttggcggtaatc-atcgtagtc---gcattttctgatgataaactgttatcagGCTGATATCGGTCTTTCAATGGGCATCCAAGGGACCGAGGTGGCCAAAGAAAGCTCAGACATTATAATTCTGGATGACAACTTTGCATCTGTTGTCAAG
                                          ||   |||  |  |  |  ||  ||||     || | | | |  || |  |  | | |||| ||||| |||||||| |||||||||||||| || || || || |||||||| ||||| ||||||||  ||||||| ||||||||||| || || |||
gggtaccaaatccgaaactggaaataaactgggatcaaaaatgtaattttaccatttttttattatagtttatacaatgttttactattatgtaat-ttagGCAGATATTGGTCTTTCTATGGGCATCCAAGGAACAGAAGTTGCAAAAGAAAGTTCAGATATTATAATCTTGGATGATAACTTTGCATCAGTAGTAAAG

upper sequence: EFJ22392 (Selaginella moellendorffii), 3'ss of exon 21
lower sequence: GLYMA13G44990.1 (Glycine max), 3'ss of exon 26
--------------------------------gtgggtttggcggtaat-----catcgtagtcgcattt--tctgatgataaactgttat------cagGCTGATATCGGTCTTTCAATGGGCATCCAAGGGACCGAGGTGGCCAAAGAAAGCTCAGACATTATAATTCTGGATGACAACTTTGCATCTGTTGTCAAG
                                  | ||||  |  | ||       || |  |   | ||  |    || |  ||| ||||       |||| ||||| |||||||| |||||||||||||| || || || || |||||||| ||||| ||||||||  ||||||| ||||||||||| || || |||
aaagttgaaatttaaaattcattattaaaacctagagtttatcaattatattaatttccttattatagttgatacagtgctttactattatgtaatttagGCAGATATTGGTCTTTCTATGGGCATCCAAGGAACAGAAGTTGCAAAAGAAAGTTCAGATATTATAATCTTGGATGATAACTTTGCATCAGTAGTAAAG

upper sequence: EFJ22392 (Selaginella moellendorffii), 3'ss of exon 21
lower sequence: GLYMA08G23760.1 (Glycine max), 3'ss of exon 27
-------------------------------------gtgggtttggcggtaatcatcgtagtcgcattt--tctgatgataaactgttat------cagGCTGATATCGGTCTTTCAATGGGCATCCAAGGGACCGAGGTGGCCAAAGAAAGCTCAGACATTATAATTCTGGATGACAACTTTGCATCTGTTGTCAAG
                                      |    ||  |   ||  ||| | ||   | ||  |||  || |  ||| || |       |||| ||||| |||||||| |||||||||   || || || || || |||||||||||||| |||||||| || || |||||||||||||| || || |||
attggttgtcatgctccattctctaatattaaaataattcctgtttactaaaaagatccttgttatagttaatcttgtgctttactattttgtattttagGCAGATATTGGTCTTTCTATGGGCATCTCCGGAACTGAAGTTGCAAAAGAAAGCTCAGATATTATAATCCTAGACGACAACTTTGCATCAGTAGTAAAG

upper sequence: EFJ22392 (Selaginella moellendorffii), 3'ss of exon 21
lower sequence: AT4G29900.1 (Arabidopsis thaliana), 3'ss of exon 26
----------------------------gtggg-tttggcggta----atcatcgtag-tcgcattttctga--tgataaactgttatcagGCTGATATCGGTCTTTCAATGGGCATCCAAGGGACCGAGGTGGCCAAAGAAAGCTCAGACATTATAATTCTGGATGACAACTTTGCATCTGTTGTCAAG
                            ||  | |||     ||     | || |  | || || ||||||   ||     |   | |||||| ||||| |||||  ||||||| |||||||| ||||| || || || ||||  |||||||| || ||  ||||||||||||||| ||| ||||| |||
gttcaatacatttacattcctcgtatgtgtaagctttaaaaatacactgttattgaggatcacactttctgtgttgccccccaactttcagGCAGATATAGGTCTCGCAATGGGTATCCAAGGCACCGAAGTTGCAAAGGAAAAGTCAGACATCATTATCTTGGATGACAACTTTGAATCCGTTGTGAAG

upper sequence: EFJ22392 (Selaginella moellendorffii), 3'ss of exon 21
lower sequence: Vv09s0018g02130.t01 (Vitis vinifera), 3'ss of exon 26
---------------------------------------gtgggtt--tggcggtaat-catcgtagtcgcattttctgatg-ataaactgttat--cagGCTGATATCGGTCTTTCAATGGGCATCCAAGGGACCGAGGTGGCCAAAGAAAGCTCAGACATTATAATTCTGGATGACAACTTTGCATCTGTTGTCAAG
                                       |  ||||  |   | |  | | | ||| |      |   | || || |  |  |||   |||| ||||| ||||| || |||||||| ||||| || || || || ||||||||||||||||| || ||  ||||||| |||||||| || ||||| |||
ttatggctgtagagtttggatgttgtttttccatcttcagcaggttcataatgttgtttctttgtaatgattgatcaggttgtatcattttctattgtagGCAGATATAGGTCTCTCTATGGGCATTCAAGGAACTGAAGTTGCAAAAGAAAGCTCAGACATCATTATCTTGGATGATAACTTTGCCTCAGTTGTAAAG

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|169101664|gb|FE501208.1|FE501208
EST:     TTGTTGCAGTCACAGGAGACGGGACAAATGACGCTCCAGCGTTGCACGAG                         GCTGATATCGGTCTTTCAATGGGCATCCAAGGGACCGAGGTGGCCAAAGAA
genomic: TTGTTGCAGTCACAGGAGACGGGACAAATGACGCTCCAGCGTTGCACGAGgtgggtttgg ... ctgttatcagGCTGATATCGGTCTTTCAATGGGCATCCAAGGGACCGAGGTGGCCAAAGAA
EST: gi|169108170|gb|FE512543.1|FE512543
EST:     TTGTTGCAGTCACAGGAGACGGGACAAATGACGCTCCAGCGTTGCACGAG                         GCTGATATCGGTCTTTCAATGGGCATCCAAGGGACCGAGGTGGCCAAAGAA
genomic: TTGTTGCAGTCACAGGAGACGGGACAAATGACGCTCCAGCGTTGCACGAGgtgggtttgg ... ctgttatcagGCTGATATCGGTCTTTCAATGGGCATCCAAGGGACCGAGGTGGCCAAAGAA
EST: gi|169075222|gb|FE484104.1|FE484104
EST:     TTGTTGCAGTCACAGGAGACGGGACAAATGACGCTCCAGCGTTGCACGAG                         GCTGATATCGGTCTTTCAATGGGCATCCAAGGGACCGAGGTGGCCAAAGAA
genomic: TTGTTGCAGTCACAGGAGACGGGACAAATGACGCTCCAGCGTTGCACGAGgtgggtttgg ... ctgttatcagGCTGATATCGGTCTTTCAATGGGCATCCAAGGGACCGAGGTGGCCAAAGAA

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: 24 (upstream exon), 35 (downstream exon)
Score: 21

ACCAATGGATAAGCTGCTACTTGTGAAAACCCTTCGCAGCATGAACGACGTTGTTGCAGTCACAGGAGACGGGACAAATGACGCTCCAGCGTTGCACGAGgtgggtttgg ... ctgttatcagGCTGATATCGGTCTTTCAATGGGCATCCAAGGGACCGAGGTGGCCAAAGAAAGCTCAGACATTATAATTCTGGATGACAACTTTGCATCTGTTGTCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgggtttggcggtaatcatcgtagtcgcattttctgatgataaactgttatcagGCTGATATCGGTCTTTCAATGGGCATCCAAGGGACCGAGGTGGCCAAAGAAAGCTCAGACATTATAATTCTGGATGACAACTTTGCATCTGTTGTCAAG
                                ttctgat  putative branch site (score: 21)
                                     atgataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggtttggcggtaatcatcgtagtcgcattttctgatgataaactgttatcagGCTGATATCGGTCTTTCAATGGGCATCCAAGGGACCGAGGTGGCCAAAGAAAGCTCAGACATTATAATTCTGGATGACAACTTTGCATCTGTTGTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA