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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgattttgagagacgaatcgatggcttggtgcaaagaagtaacgattttctcttcgatctctggctcagTTTGGTTACATTGTGCTGACAACATCGTCCGGTATCATGGATCACGACGAAGCGAGGAGGAAGAATGTTGGTGGCAAGGTCCTCGGCTTCTTCTATTGAT

Basic information

species Selaginella moellendorffii
transcript EFJ14550
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ14550 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G059624_T01 (Zea mays), 3'ss of exon 2
-------------------------------------------gtttgattttgag-agacgaatcgatggcttggtgcaaagaagtaa--cgattttctcttcg-atctctggctcagTTTGGTTACATTGTGCTGACAACATCGTCCGGTATCATGGATCACGACGAAGCGAGGAGGAAGAATGTTGGTGGCAAGGTCCTCGGCTTCTTCTATTGAT
                                            | |    ||||| |   | |      | ||| | | |     |||    | |  || | |   ||  | |  || |||||||  |||||  |||| || ||| | || |||||||||||| | ||||| | |||||||||||||||||| || || || || || |||||     
gtacgtccgttccttcgctacacattcttgtttctaactatagatctagcattgagtatttgtacatgcagtttgattctatattataatttaactagctttccctgtccattgtGCAATTTGGTTTTATTGTCTTGACCACCTCGGCTGGCATCATGGATCACAAAGAAGCCACGAGGAAGAATGTTGGTGGAAATGTGCTAGGTTTTTTCTAC----

upper sequence: EFJ14550 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA07G38520.1 (Glycine max), 3'ss of exon 3
------------gtttgattttgagagacgaatcgatg--gcttggtgcaaaga--------agtaacgattttctcttcgatct---ctggct---cagTTTGGTTACATTGTGCTGACAACATCGTCCGGTATCATGGATCACGACGAAGCGAGGAGGAAGAATGTTGGTGGCAAGGTCCTCGGCTTCTTCTATTGAT
            |    ||  |||  |   | ||  |   | |   | ||||          | | |    || |  || ||| |   ||   |   |||||||| || |||||  |||| || ||  |||| |||||||||||||| ||||| ||||| || ||||||||||| ||||| || || |||||||| |   
agattaaccattgaactatactgattggttactctgttatgttgaatacaaatggttcctccacttatcccttaccttttgatttatactaattttgcagTTTGGGTATATTGTATTGACTACCTCTGCCGGCATCATGGATCACGAAGAAGCTAGGAGAAAAAATGTTGGTGGTAAGGTACTGGGTTTCTTCTACTAGA

upper sequence: EFJ14550 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA01G45060.1 (Glycine max), 3'ss of exon 3
--------------gtttgattttgagagacgaatcgatggcttg-gtgcaaa-gaagtaacgattttctcttcgatctctggct------------cagTTTGGTTACATTGTGCTGACAACATCGTCCGGTATCATGGATCACGACGAAGCGAGGAGGAAGAATGTTGGTGGCAAGGTCCTCGGCTTCTTCTATTGAT
               ||  | |||  |       |   |  |||| | ||| | |   |  |   |||  |    | || ||  |            ||||||||||| |||||  ||||||| ||  | |||||||||||||| || || || ||||| |||||||||||||| || ||  | || |||||||| |   
ctaacctatctgtgattaaactttatgttgtccgttattctcttgtgcgcatatggtttctcctgtttgcccctaaactttgattgctcaaaatgcgcagTTTGGTTATATTGTCTTGACAACCTCTGCTGGTATCATGGATCATGAAGAGGCTAGGAGAAAGAATGTTGGTGGTAAAGTGTTGGGTTTCTTCTACTAGG

upper sequence: EFJ14550 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA17G02200.1 (Glycine max), 3'ss of exon 3
------------gtttgattttgagagacgaatcgatg--gcttggtgcaaagaagt-----aacgat---tttctcttcgatctctggct------cagTTTGGTTACATTGTGCTGACAACATCGTCCGGTATCATGGATCACGACGAAGCGAGGAGGAAGAATGTTGGTGGCAAGGTCCTCGGCTTCTTCTATTGAT
            |    || |||| ||   | ||  |   | |   | ||||    |     | | ||   || |  || ||| | |||        |||||||| || |||||  |||| || ||  | || ||||||||||| || || || |||||||| ||||||||||| |||||  | ||||||||||| |  |
agattaaccattgaactatattgatagtttactctgttatgttgaatacaaatggttcctccacctatcccttacattttgatttatggtaattatgcagTTTGGGTATATTGTATTGACTACCTCTGCTGGCATCATGGATCATGAAGAGGCTAGGAGGAAAAATGTTGGTGGTAAGGTATTGGGCTTCTTCTACTAGT

upper sequence: EFJ14550 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA11G00590.1 (Glycine max), 3'ss of exon 2
-------------gtttgattttgagagacgaatcgatggcttg-gtgca-aagaagtaacgattttctcttcgatctctggct-------------cagTTTGGTTACATTGTGCTGACAACATCGTCCGGTATCATGGATCACGACGAAGCGAGGAGGAAGAATGTTGGTGGCAAGGTCCTCGGCTTCTTCTATTGAT
              ||  | |||  |       |   |  ||||  |||| | |   |  |   |||  |    | || ||| |             |||||||| || |||||  ||||||| ||  | |||||||||||||| || || || ||||| |||||||||||||| || ||  | || |||||||| |   
taacctatctgtgattaaactttatgttgtccgttattctcttgtatgcatatggtttctcctgtttgcccctaaactttggttgctcaaaatgatgcagTTTGGGTATATTGTCTTGACAACCTCTGCTGGTATCATGGATCATGAAGAGGCTAGGAGAAAGAATGTTGGTGGTAAAGTGTTGGGTTTCTTCTACTAGG

upper sequence: EFJ14550 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA11G00600.2 (Glycine max), 3'ss of exon 3
--------------gtttgattttgagagacgaatcgatggcttg-gtgca-aagaagtaacgattttctcttcgatctctggct-------------cagTTTGGTTACATTGTGCTGACAACATCGTCCGGTATCATGGATCACGACGAAGCGAGGAGGAAGAATGTTGGTGGCAAGGTCCTCGGCTTCTTCTATTGAT
               ||  | |||  |   |   |   |  ||||  |||| | |   |  |   |||  |    | || ||| |             |||||||| || |||||  ||||||| ||  | |||||||||||||| || || || ||||| |||||||||||||| || ||  | || |||||||| |   
ctaacctatctgtgattaaactttatgttgccg-ttattctcttgtatgcatatggtttctcctgtttgcccctaaactttggttgctcaaaatgatgcagTTTGGGTATATTGTCTTGACAACCTCTGCTGGTATCATGGATCATGAAGAGGCTAGGAGAAAGAATGTTGGTGGTAAAGTGTTGGGTTTCTTCTACTAGG

upper sequence: EFJ14550 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: AT1G07770.1 (Arabidopsis thaliana), 3'ss of exon 3
-------------------------------------------------------------------------------------gtttgattttgagagacgaatcg--atggcttggtgcaaaga--agtaacgattttctc---ttcgatctctg-----gctcagTTTGGTTACATTGTGCTGACAACATCGTCCGGTATCATGGATCACGACGAAGCGAGGAGGAAGAATGTTGGTGGCAAGGTCCTCGGCTTCTTCTATTGAT
                                                                                      |    |   || | |  ||| |   | |||| ||  || |     ||| | | ||      ||  | || |      |  |||||||||||||| |||||||| |||||  | || || ||||| || || ||||| || |||||||||||||| |||||||| |||||||||||||||||| 
gttcgctcttcttataaactttctagttacagtggccttatgaattataagatcaagatttggaaatgtttttgaatcactttgcatactgtcccgaaacatcaatagtagtagctttgtttaatgctcgctaatggtattaatggattgaagctattaaattgtgcagTTTGGTTACATCGTGCTGACTACATCTGCTGGCATTATGGACCATGAAGAAGCTAGAAGGAAGAATGTTGGAGGCAAGGTTCTCGGCTTCTTCTATTGAA

upper sequence: EFJ14550 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: AT5G59850.1 (Arabidopsis thaliana), 3'ss of exon 3
-------gtttgattttgagagacgaatcgat---ggcttggtgcaaagaagt---------aacgattttctcttcgatctctg----gctcagTTTGGTTACATTGTGCTGACAACATCGTCCGGTATCATGGATCACGACGAAGCGAGGAGGAAGAATGTTGGTGGCAAGGTCCTCGGCTTCTTCTATTGAT
        ||| | | |     |    | | |   || ||  |  | || | |         |  ||| ||   ||   |   |     |  |||||||| |||||||| || || || ||| | ||||| ||||| ||||| ||||| ||||| |||||||||||||||||||| || |||||||| || ||| 
gtctgtcttttaagtcttgttcatattttggttctggttttttaaagagcaatcttatattcagtgatcttacattgagttcttaaattgtgcagTTTGGGTACATTGTTCTTACGACCTCGGCTGGTATTATGGACCACGAAGAAGCCAGGAGAAAGAATGTTGGTGGCAAGGTTCTTGGCTTCTTTTACTGAA

upper sequence: EFJ14550 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: AT3G46040.1 (Arabidopsis thaliana), 3'ss of exon 3
----------------------------------------------------------------------------------------gtttgattttgagagacgaatcgatggcttggtgca----aagaagtaacgattttctcttcgatctctg---gctcagTTTGGTTACATTGTGCTGACAACATCGTCCGGTATCATGGATCACGACGAAGCGAGGAGGAAGAATGTTGGTGGCAAGGTCCTCGGCTTCTTCTATTGAT
                                                                                         || ||| || || | |    |  || |||  |  |       | || || | ||  |     |  |||    |  |||||||||| |||||| ||||| || ||  | || ||||||||||| || ||||| ||||| ||||| ||||||||||| || || || ||||| || ||| 
gttagtctagagactatatagtagtggtaccaatcaatgttttagctattgatctgctgccttactttgctgttcctattatggtttaattggatgtttagtgtcattactttgccttactttatctttcaatgttacaacttcattgaacacttctctatgtgcagTTTGGTTTCATTGTTCTGACGACCTCAGCGGGAATCATGGATCATGAAGAAGCTAGGAGAAAGAACGTTGGTGGCAAAGTTCTTGGGTTCTTTTACTGAA

upper sequence: EFJ14550 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: Vv13s0019g00530.t01 (Vitis vinifera), 3'ss of exon 4
-----------------------------gtttgattttgagagacgaatcgatggcttggtgcaaagaagtaacgattttctcttcgatctctggct-cagTTTGGTTACATTGTGCTGACAACATCGTCCGGTATCATGGATCACGACGAAGCGAGGAGGAAGAATGTTGGTGGCAAGGTCCTCGGCTTCTTCTATTGAT
                             | | |||||     | | |    ||    ||||   |     | ||  |||  |  | |  |      | |||||||| |||||||||||||| || ||| | || ||||||||||| || || || ||||| ||||||||||||||||| || || || |||||||| |   
tattttagctgcatactagtgtattacaggctagatttcctttgccaacaatata-tgtggtttcatttgatgacc-tttgatgatggtccaaaaattgcagTTTGGATACATTGTGCTGACTACTTCGGCTGGCATCATGGATCATGAGGAGGCTAGGAGAAAGAATGTTGGTGGCAAAGTGCTTGGTTTCTTCTACTAGG

upper sequence: EFJ14550 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S45_88V6.1 (Physcomitrella patens), 3'ss of exon 2
----------------gtttgattttgagagacgaatcgatggcttggtgcaaagaa----------gtaacgatt--ttctcttcgatctctggctcagTTTGGTTACATTGTGCTGACAACATCGTCCGGTATCATGGATCACGACGAAGCGAGGAGGAAGAATGTTGGTGGCAAGGTCCTCGGCTTCTTCTATTGAT
                |  |   ||| | |    |     |   |      ||  ||          ||| ||| |  || | || | | | |||  |||||||||||||||||| ||||||| ||  | || || ||||||||||| || || ||| | ||||| || || ||||||||||| |||||||| || ||| 
gtttctctactcttccgcatcgctttcaaaatatagcttctatttcaagaaaataaacccgtaagccgtatcgacttgttgttttggttttgtggtgcagTTTGGTTACATTGTGATGACAACGTCAGCTGGCATTATGGATCACGATGAGGCCAGGCGAAAGAACGTAGGAGGCAAGGTCCTTGGCTTCTTTTACTGAG

upper sequence: EFJ14550 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S41_94V6.2 (Physcomitrella patens), 3'ss of exon 3
--------------------------------------------------------------------------------------------------gtttgattttgagagacgaatcgatggcttggtgcaaagaagtaacgattttc------------tcttcgatctctggct---cagTTTGGTTACATTGTGCTGACAACATCGTCCGGTATCATGGATCACGACGAAGCGAGGAGGAAGAATGTTGGTGGCAAGGTCCTCGGCTTCTTCTATTGAT
                                                                                                  |  | ||  |   |      |   |  ||| ||  | ||  |     || |||            | ||  || | || ||   ||||| || ||||||||  |||| || ||| | || |||||||||||||||||||| |||||||| ||||| || ||||||||  | || ||||| || |  |
gttattatttaccacctgtcatcgtggtctactcaatattattcaaaatcggtggtacaatgtggtgctgtggagatagcttaacgcatgtgacggttgcgtcatcctagtacttctctttttttcttcgtttagagtcggtggaatcttcattccttatatgtattttatttttgcctgtgcagTTCGGATACATTGTTTTGACCACTTCGGCTGGAATCATGGATCACGACGAAGCTAGGAGGAAAAATGTCGGAGGCAAGGTTTTGGGATTCTTTTACTAGT

upper sequence: EFJ14550 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S1_304V6.1 (Physcomitrella patens), 3'ss of exon 2
------------------------------gtttgattttgagagacgaatcgatggcttggtgcaaagaagtaacgattttctcttcgatctctggctcagTTTGGTTACATTGTGCTGACAACATCGTCCGGTATCATGGATCACGACGAAGCGAGGAGGAAGAATGTTGGTGGCAAGGTCCTCGGCTTCTTCTATTGAT
                               ||| || || |  |  |  |  | ||  ||   |  | |  | |   ||   | ||  |||| |    |||||||| ||||||||  |||| || ||  | || |||||||| |||||||| || || |||||||||||||| || |||||||| || ||||| || ||| 
aacgatcaagcgttaatcctcctcaagaggatttcatgtt-accgctgctttta-ggtatgaacctgaaatctgattgttgagtttttcatcttttttgcagTTTGGATACATTGTTTTGACCACCTCAGCTGGCATCATGGACCACGACGAGGCTAGAAGGAAGAATGTTGGAGGAAAGGTCCTTGGTTTCTTTTACTGAG

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|169025515|gb|FE434985.1|FE434985
EST:     GCGTCAAGGAGCTCGAGGCCTGGACTGCTCGGCTTCTTCCATCTCGCCAG                         TTTGGCTACATTGTGCTGACAACATCGTCTGGTATCATGGATCACGACGAA
genomic: GCGTCAAGGAGCTCGAGGCCTGGACTGCTCGGCTTCTTCCATCTCGCCAGgtttgatttt ... tctggctcagTTTGGTTACATTGTGCTGACAACATCGTCCGGTATCATGGATCACGACGAA
EST: gi|169025248|gb|FE434146.1|FE434146
EST:     GCGTCAAGGAGCTCGAGGCCTGGACTGCTCGGCTTCTTCCATCTCGCCAG                         TTTGGTTACATTGTGCTGACAACATCGTCCGGTATCATGGATCACGACGAA
genomic: GCGTCAAGGAGCTCGAGGCCTGGACTGCTCGGCTTCTTCCATCTCGCCAGgtttgatttt ... tctggctcagTTTGGTTACATTGTGCTGACAACATCGTCCGGTATCATGGATCACGACGAA
EST: gi|169062172|gb|FE471038.1|FE471038
EST:     GCGTCAAGGAGCTCGAGGCCTGGACTGCTCGGCTTCTTCCATCTCGCCAG                         TTTGGCTACATTGTGCTGACAACATCGTCTGGTATCATGGATCACGACGAA
genomic: GCGTCAAGGAGCTCGAGGCCTGGACTGCTCGGCTTCTTCCATCTCGCCAGgtttgatttt ... tctggctcagTTTGGTTACATTGTGCTGACAACATCGTCCGGTATCATGGATCACGACGAA
EST: gi|169044242|gb|FE452972.1|FE452972
EST:     GCGTCAAGGAGCTCGAGGCCTGGACTGCTCGGCTTCTTCCATCTCGCCAG                         TTTGGCTACATTGTGCTGACAACATCGTCTGGTATCATGGATCACGACGAA
genomic: GCGTCAAGGAGCTCGAGGCCTGGACTGCTCGGCTTCTTCCATCTCGCCAGgtttgatttt ... tctggctcagTTTGGTTACATTGTGCTGACAACATCGTCCGGTATCATGGATCACGACGAA
EST: gi|169025516|gb|FE434986.1|FE434986
EST:     GCGTCAAGGAGCTCGAGGCCTGGACTGCTCGGCTTCTTCCATCTCGCCAG                         TTTGGCTACATTGTGCTGACAACATCGTCTGGTATCATGGATCACGACGAA
genomic: GCGTCAAGGAGCTCGAGGCCTGGACTGCTCGGCTTCTTCCATCTCGCCAGgtttgatttt ... tctggctcagTTTGGTTACATTGTGCTGACAACATCGTCCGGTATCATGGATCACGACGAA
EST: gi|169106922|gb|FE508818.1|FE508818
EST:     GCGTCAAGGAGCTCGAGGCCTGGACTGCTCGGCTTCTTCCATCTCGCCAG                         TTTGGTTACATTGTGCTGACAACATCGTCCGGTATCATGGATCACGACGAA
genomic: GCGTCAAGGAGCTCGAGGCCTGGACTGCTCGGCTTCTTCCATCTCGCCAGgtttgatttt ... tctggctcagTTTGGTTACATTGTGCTGACAACATCGTCCGGTATCATGGATCACGACGAA
EST: gi|169106923|gb|FE508819.1|FE508819
EST:     GCGTCAAGGAGCTCGAGGCCTGGACTGCTCGGCTTCTTCCATCTCGCCAG                         TTTGGTTACATTGTGCTGACAACATCGTCCGGTATCATGGATCACGACGAA
genomic: GCGTCAAGGAGCTCGAGGCCTGGACTGCTCGGCTTCTTCCATCTCGCCAGgtttgatttt ... tctggctcagTTTGGTTACATTGTGCTGACAACATCGTCCGGTATCATGGATCACGACGAA
EST: gi|169025247|gb|FE434145.1|FE434145
EST:     GCGTCAAGGAGCTCGAGGCCTGGACTGCTCGGCTTCTTCCATCTCGCCAG                         TTTGGTTACATTGTGCTGACAACATCGTCCGGTATCATGGATCACGACGAA
genomic: GCGTCAAGGAGCTCGAGGCCTGGACTGCTCGGCTTCTTCCATCTCGCCAGgtttgatttt ... tctggctcagTTTGGTTACATTGTGCTGACAACATCGTCCGGTATCATGGATCACGACGAA

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), 35 (downstream exon)
Score: 64

AAACGGCAGGCTCAACAAGTGTGGAGTCATCAGCCCGCGCTACGATATCAGCGTCAAGGAGCTCGAGGCCTGGACTGCTCGGCTTCTTCCATCTCGCCAGgtttgatttt ... tctggctcagTTTGGTTACATTGTGCTGACAACATCGTCCGGTATCATGGATCACGACGAAGCGAGGAGGAAGAATGTTGGTGGCAAGGTCCTCGGCTTCTTCTATTGAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatcgatggcttggtgcaaagaagtaacgattttctcttcgatctctggctcagTTTGGTTACATTGTGCTGACAACATCGTCCGGTATCATGGATCACGACGAAGCGAGGAGGAAGAATGTTGGTGGCAAGGTCCTCGGCTTCTTCTATTGAT
                      aagtaac  putative branch site (score: 64)
                               ttttctcttcgatctc  putative PPT
                              attttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgattttgagagacgaatcgatggcttggtgcaaagaagtaacgattttctcttcgatctctggctcagTTTGGTTACATTGTGCTGACAACATCGTCCGGTATCATGGATCACGACGAAGCGAGGAGGAAGAATGTTGGTGGCAAGGTCCTCGGCTTCTTCTATTGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG