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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcttttgtctgatcattcgtacttgctaacgccccaagcttcacagATATTTCGCAAAGAACCATTCTTTTATGGCCATGACAATCACGATCAGCTGGTGAAGATTGCCAAG

Basic information

species Selaginella moellendorffii
transcript EFJ20478
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ20478 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: LOC_Os03g10940.1 (Oryza sativa), 3'ss of exon 5
------------------------------------------------------------gtgagtcttttgtct---gatcattcgtacttgcta------acgccccaagcttca--cagATATTTCGCAAAGAACCATTCTTTTATGGCCATGACAATCACGATCAGCTGGTGAAGATTGCCAAG
                                                            || | |   |||  |   ||    | | |  || ||      |    |     || |  |||||||||||||| ||||||||||| |||||||| || || || || ||||| || || || ||||||
gtgtgtttgccctcctatgattataaaataacctatcaaaattgccatggccttacttctgtaaattacttgcgtatagaaagatagcaactgttatgctttatttactgtttttgatgcagATATTTCGCAAGGAACCATTCTTCTATGGCCACGATAACCATGACCAGCTTGTCAAAATAGCCAAG

upper sequence: EFJ20478 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM2G141903_T01 (Zea mays), 3'ss of exon 5
-------------------------------------------------------------------------gtgagtctttt---gtctgatcattcgtacttgctaacgccccaagcttcacagATATTTCGCAAAGAACCATTCTTTTATGGCCATGACAATCACGATCAGCTGGTGAAGATTGCCAAG
                                                                         || |||  |||   || |  | |    ||  || |  |   |  |      |||||||||||||| |||||||||||||||||||||||||| || || || || ||||||||||| |||
gtatgtacatgtaaaaatgctctccctaccttaatactatcagacacaatttaggggggagggttgacattttgtcagtgctttcgtgtttttttacctatatatgtttgctgactgatggctgcagATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAG

upper sequence: EFJ20478 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM2G047855_T01 (Zea mays), 3'ss of exon 5
-------------------------------------------------------------------------------------------------------gtgagtcttttgtctgatcattcgtacttgctaacgccccaagcttcacagATATTTCGCAAAGAACCATTCTTTTATGGCCATGACAATCACGATCAGCTGGTGAAGATTGCCAAG
                                                                                                       |||  ||  | || |  | |  | ||  || |  |   |  |      |||||||||||||| |||||||||||||||||||||||||| || || || || ||||||||||| |||
gtatgtacacaaaagtgctgtctctaggttaatactattggacacaattgggtttgacattctgtaatactattggacacgatggggattgacattttgtcaagtgcttcagtggtttt-ttacccatatatgtttgctgactgattgctgcagATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAG

upper sequence: EFJ20478 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA01G39950.1 (Glycine max), 3'ss of exon 5
--------------------------------------------------------------------------------gtgagtcttt-tgtctgatcattcgtacttgctaacgccccaagcttcacagATATTTCGCAAAGAACCATTCTTTTATGGCCATGACAATCACGATCAGCTGGTGAAGATTGCCAAG
                                                                                 ||| |     |||  |||   | ||  |   |  |     |   ||   ||||||||||||||||||| ||||||||||| |||||||| || |||||||| || || || || |||
gtgtgaatcataactacaagtttctgattatatatggcatactcttgacatttatgcagatggtctaaatttgagcatacatgattaaaaatgtgagatt-ctggtcataattttcattgtactttttgtagATATTTCGCAAAGAACCTTTCTTTTATGGTCATGACAACCATGATCAGCTTGTCAAAATAGCTAAG

upper sequence: EFJ20478 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA11G05340.2 (Glycine max), 3'ss of exon 5
--------------------------------------------------------------------------------------gtgagtcttttgt-ctgatcattcgtacttgctaacgccccaagcttcacagATATTTCGCAAAGAACCATTCTTTTATGGCCATGACAATCACGATCAGCTGGTGAAGATTGCCAAG
                                                                                         | | |    | ||| ||||   |  ||  |    | |     ||   ||||||||||||||||||| ||||||||||| |||||||| || |||||||| || || || || |||
gtgtgaattataactataagttactggttatatatggcatactcttgacatttatgcagatggtctaaatttgagcgtacatgattaaaaatgtaaaattctggtcataatttgttcgttgtactct----tttgtagATATTTCGCAAAGAACCTTTCTTTTATGGTCATGACAACCATGATCAGCTTGTCAAAATAGCTAAG

upper sequence: EFJ20478 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA17G17790.1 (Glycine max), 3'ss of exon 5
---------------------------------------------------------------------------------------gtgagtcttttgtctgatcattcgtacttgctaacgccccaagcttcacagATATTTCGCAAAGAACCATTCTTTTATGGCCATGACAATCACGATCAGCTGGTGAAGATTGCCAAG
                                                                                           ||      ||   | ||||    ||   | |     |       |||||||||||||| ||||| || |||||||| || ||||| || |||||||| || || || || |||
gtgagaattatagctataggctacaacttactggttatatgtgacatacccttggcgttatttaatatgaagtctaattttgaatctacatgtacaaaatcgtgtaattctgggttatgatcattttacttaatgcagATATTTCGCAAGGAACCTTTTTTTTATGGTCACGACAACCATGATCAGCTTGTCAAAATAGCTAAG

upper sequence: EFJ20478 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: AT2G23070.1 (Arabidopsis thaliana), 3'ss of exon 5
-------------------------------------------------------------------------------------gtgagtctttt-gtctgatcattcgtacttgcta-acgccccaagcttcacagATATTTCGCAAAGAACCATTCTTTTATGGCCATGACAATCACGATCAGCTGGTGAAGATTGCCAAG
                                                                                        | || ||  ||  | | | | ||   |  |  |  | | |   ||  |||||||| ||||| || || ||||||||||||||||||||  | |||||  |||| || ||||| |||
gtaagcgttttaagctagaatttagttaacttggtttaagctgtaatggaatgacaagaattcgacagtacattttggttattttaccattccttaagttagttaagtggtgaatattgtatactctactgtttgcagATATTCCGCAAGGAGCCGTTCTTTTATGGCCATGACAACTATGATCAATTGGTCAAAATTGCGAAG

upper sequence: EFJ20478 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: Vv07s0129g00410.t01 (Vitis vinifera), 3'ss of exon 5
------------------------------------------------------------------gtgagtcttttgtctgatcattcgt---acttgctaacgccccaagcttcac--agATATTTCGCAAAGAACCATTCTTTTATGGCCATGACAATCACGATCAGCTGGTGAAGATTGCCAAG
                                                                  ||   | ||||   |     || ||   |||   ||     | |   || |   |||| |||||||| ||||||||||||||||| ||||||||||| |||||||| || ||||||||||||
gtgagatttactactactgttgatcttgaatcatttgaagggctgattgtgccatttacattttttgtatttattttaattatcattttgttttactcagtatacttctattatttatgtagATCTTTCGCAAGGAACCATTCTTTTATGGTCATGACAATCATGATCAGCTTGTCAAGATTGCCAAG

upper sequence: EFJ20478 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: Vv18s0001g09320.t01 (Vitis vinifera), 3'ss of exon 5
--------------------------------------------------gtgagtcttttgtctgatcatt---cgtacttgctaacgccccaa-----gcttc-------acagATATTTCGCAAAGAACCATTCTTTTATGGCCATGACAATCACGATCAGCTGGTGAAGATTGCCAAG
                                                      |   ||||||| |||| |    |||  |   |||  | |||     | ||        |||||| |||||||| || |||||||||||||| ||||| ||||| || ||||| || || |||||||||
gtaacagttacagtggcagttggtgttaattttcttttacatattacttgaaatgcagtttgtcttatcaataaatgtaactttcaactactcaatggaggtttttttcccaacagATTTTTCGCAAGGAGCCATTCTTTTATGGTCATGATAATCATGACCAGCTTGTAAAAATTGCCAAG

upper sequence: EFJ20478 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: PP1S63_208V6.1 (Physcomitrella patens), 3'ss of exon 6
----------------------------------------------------------------------gtgagtcttttgt-ctga--tcattcgtact-tgctaacgccccaagct--tcacagATATTTCGCAAAGAACCATTCTTTTATGGCCATGACAATCACGATCAGCTGGTGAAGATTGCCAAG
                                                                      | || | |||  | ||||  |  |||    | |||| | |        |  |  ||||| ||||| || || |||||||||||||| ||||||||| | |||||||| |||||||||||||||
gtaacgtatcctcgcagtttattttaacactaatctttcgttatttacagttttcccatgatgtgtatctgcgattttttcattctgaagtacttctcgttatgctgaagagattgcgtggttgcagATCTTTCGGAAGGAGCCATTCTTTTATGGACATGACAATTATGATCAGCTTGTGAAGATTGCCAAG

upper sequence: EFJ20478 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: PP1S165_119V6.1 (Physcomitrella patens), 3'ss of exon 6
-----------------------------------------------------------------------------gtgagtctttt-gtctgatcattcgtacttgctaacgccccaagcttcacagATATTTCGCAAAGAACCATTCTTTTATGGCCATGACAATCACGATCAGCTGGTGAAGATTGCCAAG
                                                                              | ||| |||  |  ||||  |   ||              |    |  ||||||||||| || || |||||||||||||| ||||||||| | ||||| || ||||||||||| |||
gtaaatttaattccaagttcaatatttcgatggtccttgattatcacagtttgtcgctacgttgatttgctttttggtttagtttttgagcttgattctcgttaaacaggtgaattgaagtgattgcagATATTTCGGAAGGAGCCATTCTTTTATGGGCATGACAATTATGATCAACTTGTGAAGATTGCTAAG

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|169099873|gb|FE500878.1|FE500878
EST:     ACGATTACTCTCTCGACATGTGGAGCCTAGGCTGCATGTTCGCTGGAATG                         ATATTTCGCAAAGAACCATTCTTTTATGGCCATGACAATCACGATCAGCTG
genomic: ACGATTACTCTCTCGACATGTGGAGCCTAGGCTGCATGTTCGCTGGAATGgtgagtcttt ... agcttcacagATATTTCGCAAAGAACCATTCTTTTATGGCCATGACAATCACGATCAGCTG
EST: gi|169057441|gb|FE465745.1|FE465745
EST:     ACGATTACTCTCTCGACATGTGGAGCCTAGGCTGCATGTTCGCTGGAATG                         ATATTTCGCAAAGAACCATTCTTTTATGGCCATGACAATCACGATCAGCTG
genomic: ACGATTACTCTCTCGACATGTGGAGCCTAGGCTGCATGTTCGCTGGAATGgtgagtcttt ... agcttcacagATATTTCGCAAAGAACCATTCTTTTATGGCCATGACAATCACGATCAGCTG
EST: gi|169099874|gb|FE500879.1|FE500879
EST:     ACGATTACTCTCTCGACATGTGGAGCCTAGGCTGCATGTTCGCTGGAATG                         ATATTTCGCAAAGAACCATTCTTTTATGGCCATGACAATCACGATCAGCTG
genomic: ACGATTACTCTCTCGACATGTGGAGCCTAGGCTGCATGTTCGCTGGAATGgtgagtcttt ... agcttcacagATATTTCGCAAAGAACCATTCTTTTATGGCCATGACAATCACGATCAGCTG
EST: gi|169054797|gb|FE460593.1|FE460593
EST:     ACGATTACTCTCTCGACATGTGGAGCCTAGGCTGCATGTTCGCTGGAATG                         ATATTTCGCAAAGAACCATTCTTTTATGGCCATGACAATCACGATCAGCTG
genomic: ACGATTACTCTCTCGACATGTGGAGCCTAGGCTGCATGTTCGCTGGAATGgtgagtcttt ... agcttcacagATATTTCGCAAAGAACCATTCTTTTATGGCCATGACAATCACGATCAGCTG
EST: gi|169062160|gb|FE469700.1|FE469700
EST:     ACGATTACTCTCTCGACATGTGGAGCCTAGGCTGCATGTTCGCTGGAATG                         ATATTTCGCAAAGAACCATTCTTTTATGGCCATGACAATCACGATCAGCTG
genomic: ACGATTACTCTCTCGACATGTGGAGCCTAGGCTGCATGTTCGCTGGAATGgtgagtcttt ... agcttcacagATATTTCGCAAAGAACCATTCTTTTATGGCCATGACAATCACGATCAGCTG
EST: gi|169099662|gb|FE502643.1|FE502643
EST:     ACGATTACTCTCTCGACATGTGGAGCCTAGGCTGCATGTTCGCTGGAATG                         ATATTTCGCAAAGAACCATTCTTTTATGGCCATGACAATCACGATCAGCTG
genomic: ACGATTACTCTCTCGACATGTGGAGCCTAGGCTGCATGTTCGCTGGAATGgtgagtcttt ... agcttcacagATATTTCGCAAAGAACCATTCTTTTATGGCCATGACAATCACGATCAGCTG
EST: gi|169040608|gb|FE449739.1|FE449739
EST:     ACGATTACTCTCTCGACATGTGGAGCCTAGGCTGCATGTTCGCTGGAATG                         ATATTTCGCAAAGAACCATTCTTTTATGGCCATGACAATCACGATCAGCTG
genomic: ACGATTACTCTCTCGACATGTGGAGCCTAGGCTGCATGTTCGCTGGAATGgtgagtcttt ... agcttcacagATATTTCGCAAAGAACCATTCTTTTATGGCCATGACAATCACGATCAGCTG
EST: gi|169057442|gb|FE465746.1|FE465746
EST:     ACGATTACTCTCTCGACATGTGGAGCCTAGGCTGCATGTTCGCTGGAATG                         ATATTTCGCANAGAACCATTCTTTTATGGCCATGACAATCACGATCAGCTG
genomic: ACGATTACTCTCTCGACATGTGGAGCCTAGGCTGCATGTTCGCTGGAATGgtgagtcttt ... agcttcacagATATTTCGCAAAGAACCATTCTTTTATGGCCATGACAATCACGATCAGCTG
EST: gi|169050669|gb|FE457839.1|FE457839
EST:     ACGATTACTCTCTCGACATGTGGAGCCTAGGCTGCATGTTCGCTGGAATG                         ATATTTCGCAAAGAACCATTCTTTTATGGCCATGACAATCACGATCAGCTG
genomic: ACGATTACTCTCTCGACATGTGGAGCCTAGGCTGCATGTTCGCTGGAATGgtgagtcttt ... agcttcacagATATTTCGCAAAGAACCATTCTTTTATGGCCATGACAATCACGATCAGCTG

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), 29 (downstream exon)
Score: 28

ATACTTCAAAGGTCCGGAGCTGCTTGTGGACCTGCAGGACTACGATTACTCTCTCGACATGTGGAGCCTAGGCTGCATGTTCGCTGGAATGgtgagtcttt ... agcttcacagATATTTCGCAAAGAACCATTCTTTTATGGCCATGACAATCACGATCAGCTGGTGAAGATTGCCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgagtcttttgtctgatcattcgtacttgctaacgccccaagcttcacagATATTTCGCAAAGAACCATTCTTTTATGGCCATGACAATCACGATCAGCTGGTGAAGATTGCCAAG
                                tgctaac  putative branch site (score: 28)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtcttttgtctgatcattcgtacttgctaacgccccaagcttcacagATATTTCGCAAAGAACCATTCTTTTATGGCCATGACAATCACGATCAGCTGGTGAAGATTGCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA