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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgattcttgtgttgggtgttgaaataatcctccggcgcctctgttttggcagTCTCTGGTGAGCAATGAGGAGTTCCAGCACATTCTTCGTGTGCTCAACACGAATGTGGACGGGCGGCAGAAGATTATGTTCGCGCTGACTTCCATCAAGG

Basic information

species Selaginella moellendorffii
transcript EFJ22352
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ22352 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os07g07709.1 (Oryza sativa), 3'ss of exon 1
---------------------------------gta-tgattcttgtgt-tgggtgttga---aataatcctccggcgcctctg-ttttggcagTCTCTGGTGAGCAATGAGGAGTTCCAGCACATTCTTCGTGTGCTCAACACGAATGTGGACGGGCGGCAGAAGATTATGTTCGCGCTGACTTCCATCAAGG
                                 | | || |   | ||    |||| | |    |  |  | |  | |  | || |||| |||||| ||| |       ||||| ||||||||||| || ||| |||| |||||||| ||||| |||  ||||||||| ||||||||||| || ||||||||||
gtaagctccgttcctctcccgcatctcccctttgcagtggtctctttgcgcaggtgctaaggggaggaatcgcgtgtgtgtttgatttttgcagTCGCTGATCGCGGGGGAGGATTTCCAGCACATCCTGCGTCTGCTGAACACGAACGTGGATGGGAAGCAGAAGATCATGTTCGCGCTCACCTCCATCAAGG

upper sequence: EFJ22352 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os03g58050.1 (Oryza sativa), 3'ss of exon 1
--------------------------------------------gtatga-ttcttgtgttgggtgttg-aaataatcctc--cggcgcctctgttttggcagTCTCTGGTGAGCAATGAGGAGTTCCAGCACATTCTTCGTGTGCTCAACACGAATGTGGACGGGCGGCAGAAGATTATGTTCGCGCTGACTTCCATCAAGG
                                             |  |  |||| |||  |  |  |   | | |  |||   ||||| |||||    |||||| ||| |   |   ||||| ||||||||||| || ||| |||| ||||| || || || |||  ||||||||| ||||||||||| || ||||||||||
gtaaccttctcgctcgcttctcctctcctccattcccgtctccgattcgccttctcgtgacgcctcctctgactgactctcgttggcgcttctgtccccgcagTCGCTGATCGCCGGGGAGGACTTCCAGCACATCCTGCGTCTGCTGAACACCAACGTCGATGGGAAGCAGAAGATCATGTTCGCGCTCACCTCCATCAAGG

upper sequence: EFJ22352 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA20G30970.1 (Glycine max), 3'ss of exon 1
--------------------------------------------------------------gtatgattcttgtgttgggtgttgaaataatcctcc------ggcgc-ctctgttttg--gcagTCTCTGGTGAGCAATGAGGAGTTCCAGCACATTCTTCGTGTGCTCAACACGAATGTGGACGGGCGGCAGAAGATTATGTTCGCGCTGACTTCCATCAAGG
                                                                | ||  | |   | ||    |||| |  |  |        |  |  || |||| ||  |||||||||||||   || ||||| |||||||||||||| |||||||| ||||| || ||||| |||  ||||||||| ||||||||  |||| ||||||||||
gtacgttcccatttcatcgaacctctccgagcgcgacgttaattgaaaaaaaaggattactttgaggaacccttaatcggtaactgaatttgttttttttgtgtgttgtgctgtgttgtgttgcagTCTCTGGTGGCGAACGAGGATTTCCAGCACATTCTGCGTGTGCTGAACACCAACGTGGATGGGAAGCAGAAGATAATGTTCGCTATGACCTCCATCAAGG

upper sequence: EFJ22352 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA10G36610.2 (Glycine max), 3'ss of exon 1
-------------------------------------------------------gtatgattc--ttgtgttgggtgttgaaataatcctccggcgcctctgttttg--------gcagTCTCTGGTGAGCAATGAGGAGTTCCAGCACATTCTTCGTGTGCTCAACACGAATGTGGACGGGCGGCAGAAGATTATGTTCGCGCTGACTTCCATCAAGG
                                                         | |||||  || ||  |     | ||   ||  || |     | | |||||        |||||||||||||   || ||||| |||||||||||||| |||||||| ||||| || ||||| |||  ||||||||| ||||||||  |||| ||||||||||
gtgcgctctcattatttcatcgcacctctcccttcacaacgttgattgaaaagaaaaaagattcaattttgaggaacccttaatcgata-tctgattttttttttttgtgtgtgttgcagTCTCTGGTGGCGAACGAGGATTTCCAGCACATTCTGCGTGTGCTGAACACCAACGTGGATGGGAAGCAGAAGATAATGTTCGCAATGACCTCCATCAAGG

upper sequence: EFJ22352 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA10G36610.3 (Glycine max), 3'ss of exon 1
-----------------------------------------------------gtatgattc--ttgtgttgggtgttgaaataatcctccggcgcctctgttttg--------gcagTCTCTGGTGAGCAATGAGGAGTTCCAGCACATTCTTCGTGTGCTCAACACGAATGTGGACGGGCGGCAGAAGATTATGTTCGCGCTGACTTCCATCAAGG
                                                       | |||||  || ||  |     | ||   ||  || |     | | |||||        |||||||||||||   || ||||| |||||||||||||| |||||||| ||||| || ||||| |||  ||||||||| ||||||||  |||| ||||||||||
gcgctctcattatttcatcgcacctctcccttcacaacgttgattgaaaagaaaaaagattcaattttgaggaacccttaatcgata-tctgattttttttttttgtgtgtgttgcagTCTCTGGTGGCGAACGAGGATTTCCAGCACATTCTGCGTGTGCTGAACACCAACGTGGATGGGAAGCAGAAGATAATGTTCGCAATGACCTCCATCAAGG

upper sequence: EFJ22352 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA10G36880.3 (Glycine max), 3'ss of exon 1
-------------------------------------------------------gtatgattct--tgtgttgggtgttgaaataatcctccggcgcctctgttttg------gcagTCTCTGGTGAGCAATGAGGAGTTCCAGCACATTCTTCGTGTGCTCAACACGAATGTGGACGGGCGGCAGAAGATTATGTTCGCGCTGACTTCCATCAAGG
                                                         | ||||||  | ||  |     | ||   ||         | | | || ||      |||||||||||||   || ||||| |||||||||||||| |||||||| ||||| || ||||| |||  ||||||||| ||||||||  |||| ||||||||||
gtgcgctcccattattttattgcacctctcccttcacaacgttgattgaacaataaaaggattctattttgaggaacccttaatcgataactgatttctttttttgtgtgtgttgcagTCTCTGGTGGCGAACGAGGATTTCCAGCACATTCTGCGTGTGCTGAACACCAACGTGGATGGGAAGCAGAAGATAATGTTCGCAATGACCTCCATCAAGG

upper sequence: EFJ22352 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA02G08690.1 (Glycine max), 3'ss of exon 1
---------------------------------------------------------------------------------gtatgattcttgtg--ttgggtgttgaaataatc----ctccggcgcctctgttttggcagTCTCTGGTGAGCAATGAGGAGTTCCAGCACATTCTTCGTGTGCTCAACACGAATGTGGACGGGCGGCAGAAGATTATGTTCGCGCTGACTTCCATCAAGG
                                                                                     |||| || ||  |  | | ||| |  | ||     |     |  | || ||   ||||||||||||   || ||||| |||||||||||||| |||||||| ||||| || || || |||  ||||||||| |||||||| || || || ||||| |
gtacgatttcagcgtttccgaattgattttgataaacaaagattcttcaaaagattcgttttatcttttggcaatttcaaaaggcgatttttttggctctgtttttggaggagtcacattttaaatggttttgctt--acagTCTCTGGTGGCGAACGAGGATTTCCAGCACATTCTGCGTGTGCTGAACACCAACGTAGATGGGAAGCAGAAGATAATGTTCGCTCTCACCTCTATCAAAG

upper sequence: EFJ22352 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: AT1G34030.1 (Arabidopsis thaliana), 3'ss of exon 1
--------------------------------------gtat-gattcttg--tgttgggtgttgaaataatcctccggcgcctctgttttggca----gTCTCTGGTGAGCAATGAGGAGTTCCAGCACATTCTTCGTGTGCTCAACACGAATGTGGACGGGCGGCAGAAGATTATGTTCGCGCTGACTTCCATCAAGG
                                      || | ||||   |  | || | ||||    |     |  |     | ||||   |||    |||||||||    ||||||||||| ||||||||| | |||||||||||||| || || || ||   ||| ||||||||||| || || || || ||||| |
atcagagaaccaagtatcgaacagaaagtttaggttatgtgttgattagggaatttttgatgtttggctgtaattgtgtgatttttgttactgcatgtagTCTCTGGTTGCAAATGAGGAGTTTCAGCACATTTTGCGTGTGCTCAACACTAACGTTGATGGTAAGCAAAAGATTATGTTTGCCCTTACCTCTATCAAAG

upper sequence: EFJ22352 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: Vv05s0020g03450.t01 (Vitis vinifera), 3'ss of exon 1
----------------------------gtatgattcttgtgttgggtgttga-----aataatcctccggcgcctctgttttggcagTCTCTGGTGAGCAATGAGGAGTTCCAGCACATTCTTCGTGTGCTCAACACGAATGTGGACGGGCGGCAGAAGATTATGTTCGCGCTGACTTCCATCAAGG
                                 |||||||||| |  | | |        |  |        |  |  | ||| ||||||||| ||    || ||||| || |||||||||||||||||||||||||| || || || |||  ||||||||| ||||| || || |||||||||||||
gtgagtgggcttgttttcatttctgttaaatcaattcttgtgtcgaatatggttgtttgttgttatgttaatgaattggattttgcagTCTCTTGTTGCAAACGAGGAATTTCAGCACATTCTTCGTGTGCTCAACACCAACGTCGATGGGAAGCAGAAGATCATGTTTGCCCTCACTTCCATCAAGG

upper sequence: EFJ22352 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S72_222V6.1 (Physcomitrella patens), 3'ss of exon 1
-------------------------------------------------------------------------------------------------------gtatgattcttgtgttgggtgttgaaataat----cctccggcgcctctgttttgg---------cagTCTCTGGTGAGCAATGAGGAGTTCCAGCACATTCTTCGTGTGCTCAACACGAATGTGGACGGGCGGCAGAAGATTATGTTCGCGCTGACTTCCATCAAGG
                                                                                                         ||| ||    | || ||  |||||   ||    ||   |  |  |  ||||||          ||||| || ||      |||||||||||| || ||||||||||||||||||||||| || || || || |||||||| ||||| || ||||| ||||| ||||
gtgtgtagtttcccctccctctgctgtgtgcacaagctggatttttttcttttcattttctcggttctttctttctgtcattttcgttatggtttggttgtgcacatgtttgagattttagggtttgaaggtatgtgaccctggttggtttggttttgttgaagcggccagTCGCTCGTTGCGGGTGAGGAGTTCCAACATATTCTTCGTGTGCTCAACACGAACGTCGATGGACGTCAGAAGATCATGTTTGCCCTGACCTCCATTAAGG

upper sequence: EFJ22352 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S215_71V6.1 (Physcomitrella patens), 3'ss of exon 1
---------------------------------------------------------------------------------------gtatgattcttgtgttgggtgttgaaa--taatcctccggcgcctctgttttggcagTCTCTGGTGAGCAATGAGGAGTTCCAGCACATTCTTCGTGTGCTCAACACGAATGTGGACGGGCGGCAGAAGATTATGTTCGCGCTGACTTCCATCAAGG
                                                                                        || | ||   || || |    |||||  |  |  |  |      |  | ||||||||| ||  |       |||||||||||||||||||||||||| || || || || || || ||||| |||||||||||||| || || || ||||||||||
gtgtgtctgatctgcctcgtccttgtcattgtgctgctcttcttggctcttattcagtgctatcttcgtgttcgtgaaattttatgtttagggtttacgtctttgtgactgaaagttggttgtgtgtgtttccgatgttggcagTCGCTCATTGCGGGCGAGGAGTTCCAGCACATTCTTCGTGTTCTGAATACCAACGTCGATGGGCGTCAGAAGATTATGTTTGCCCTAACCTCCATCAAGG

upper sequence: EFJ22352 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S72_222V6.2 (Physcomitrella patens), 3'ss of exon 1
-------------------------------------------------------------------------------------------------------gtatgattcttgtgttgggtgttgaaataat----cctccggcgcctctgttttgg---------cagTCTCTGGTGAGCAATGAGGAGTTCCAGCACATTCTTCGTGTGCTCAACACGAATGTGGACGGGCGGCAGAAGATTATGTTCGCGCTGACTTCCATCAAGG
                                                                                                         ||| ||    | || ||  |||||   ||    ||   |  |  |  ||||||          ||||| || ||      |||||||||||| || ||||||||||||||||||||||| || || || || |||||||| ||||| || ||||| |||       
gtgtgtagtttcccctccctctgctgtgtgcacaagctggatttttttcttttcattttctcggttctttctttctgtcattttcgttatggtttggttgtgcacatgtttgagattttagggtttgaaggtatgtgaccctggttggtttggttttgttgaagCGGCCAGTCGCTCGTTGCGGGTGAGGAGTTCCAACATATTCTTCGTGTGCTCAACACGAACGTCGATGGACGTCAGAAGATCATGTTTGCCCTGACCTCC-------

upper sequence: EFJ22352 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S242_94V6.1 (Physcomitrella patens), 3'ss of exon 1
--------------------------------------------------------------------------------------gtatgattcttgtgttgggtgttgaaataatcctccggcgcctctgttttggcagTCTCTGGTGAGCAATGAGGAGTTCCAGCACATTCTTCGTGTGCTCAACACGAATGTGGACGGGCGGCAGAAGATTATGTTCGCGCTGACTTCCATCAAGG
                                                                                       | |  | |   | | ||||      ||      | |    ||   | |   ||||| ||  |       ||||| || |||||||||||||||||||| ||||| || || || || || |||||||| ||||| || |||||||| || ||||
gtgcgtgttcatcgcttcctccccatgcagctttcgtcgactcgtttctttgcgtacgatgagattgttatttttttttcttccaaatgttgtacacttctagggttcgtgcatctgtgactgaaagctggttgtgaacagTCGCTCATTGCGGGCGAGGAATTTCAGCACATTCTTCGTGTGCTGAACACTAACGTCGATGGACGTCAGAAGATCATGTTTGCCCTGACTTCGATTAAGG

upper sequence: EFJ22352 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S215_81V6.1 (Physcomitrella patens), 3'ss of exon 1
-----------------------------------gtatgattcttgt-gttgggtgttgaaataatcctccg-gcgcctctg--------ttttggcagTCTCTGGTGAGCAATGAGGAGTTCCAGCACATTCTTCGTGTGCTCAACACGAATGTGGACGGGCGGCAGAAGATTATGTTCGCGCTGACTTCCATCAAGG
                                    || | ||  ||  || | |  |   | || |  |  | | |  | ||        ||||  ||||| ||  |      |||||| || ||||||||||||||||| || |||||||| || || || || |||||||| ||||| ||  |||| ||||| ||||
tcctctcgctctctctccgacgacattgttgatgtctagggtttatgccgtcgtgactgatactagttgtgtgtgtgtgtgtggtggtggtttttttcagTCGCTCATCGCGGGTGAGGAATTTCAGCACATTCTTCGTGTCCTTAACACGAACGTCGATGGACGCCAGAAGATCATGTTTGCCTTGACCTCCATTAAGG

upper sequence: EFJ22352 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S14_433V6.1 (Physcomitrella patens), 3'ss of exon 1
-------------------------------------------------------------------------------------------------------------------------gtatgattcttgtgttgggt--gttgaaataatcctccggc--gcctctgttttggc-agTCTCTGGTGAGCAATGAGGAGTTCCAGCACATTCTTCGTGTGCTCAACACGAATGTGGACGGGCGGCAGAAGATTATGTTCGCGCTGACTTCCATCAAGG
                                                                                                                           |||||  ||   | ||||   |||   |    ||  ||   |   | ||| |||| |||| ||| |      ||||||||| |||||||||||||||||| | ||||| || || || || || || ||||||||||| ||  |||| ||||| ||||
gtttgtgctcctctgctgttgcgtatatctgtggtgtcgttttttgtttggtactgagttctgggtgtgtttttttttttttttttttttttttttttttttggtttttcaatttttaggttaatgatcgtttgctagggttaattgggctgtgactgaggttggtggcggttgtggccagTCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACTAACGTCGATGGACGTCAAAAGATTATGTTTGCCTTGACCTCCATTAAGG

upper sequence: EFJ22352 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S14_438V6.1 (Physcomitrella patens), 3'ss of exon 1
---------------------------------------------------------------------------gtatgattct----tgtgttgggtgttgaaataatcc--tccggcgcctctgttttggc-agTCTCTGGTGAGCAATGAGGAGTTCCAGCACATTCTTCGTGTGCTCAACACGAATGTGGACGGGCGGCAGAAGATTATGTTCGCGCTGACTTCCATCAAGG
                                                                           |   || | |    ||||  || |  |||  |||     | | |       | | || | |||| ||  |      ||| ||||| || || |||||||||||||| || || || || || || ||||||||||| |||||||| ||||| ||||| || |
gtgggtagtttctcccacctgtgctacacgtaaaaatttcagtttttcggttccgttctgtttggagtgttttttgctcgactttagggtgtgcaggttcatgatctaaattggttcagaatggtgggtgtgactagTCGCTCATCGCGGGTGAAGAGTTTCAACATATTCTTCGTGTGCTGAATACAAACGTCGATGGACGGCAGAAGATCATGTTCGCCCTGACCTCCATTAAAG

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|169094756|gb|FE492933.1|FE492933
EST:     TAAGAGCAAGGGATCTCGGGTCGGGAGCTGAGGCGCTCGGCGGCAAGATG                         TCTCTGGTGAGCAATGAGGAGTTCCAGCACATTCTTCGTGTGCTCAACACG
genomic: TAAGAGCAAGGGATCTCGGGTCGGGAGCTGAGGCGCTCGGCGGCAAGATGgtatgattct ... gttttggcagTCTCTGGTGAGCAATGAGGAGTTCCAGCACATTCTTCGTGTGCTCAACACG
EST: gi|169023844|gb|FE436395.1|FE436395
EST:     AAAGAGCAAGGGATCTCGGGTCGGGAGCTGAGGCGCTCGGCGGCAAGATG                         TCTCTGGTGAGCAATGAGGAGTTCCAGCACATTCTTCGTGTGCTCAACACG
genomic: -AAGAGCAAGGGATCTCGGGTCGGGAGCTGAGGCGCTCGGCGGCAAGATGgtatgattct ... gttttggcagTCTCTGGTGAGCAATGAGGAGTTCCAGCACATTCTTCGTGTGCTCAACACG
EST: gi|169075906|gb|FE480966.1|FE480966
EST:     GAGCAAGGGATCTCGGGTCGGGAGCTGAGGCGCTCGGCGGCAAGATG                         TCTCTGGTGAGCAATGAGGAGTTCCAGCACATTCTTCGTGTGCTCAACACG
genomic: GAGCAAGGGATCTCGGGTCGGGAGCTGAGGCGCTCGGCGGCAAGATGgtatgattct ... gttttggcagTCTCTGGTGAGCAATGAGGAGTTCCAGCACATTCTTCGTGTGCTCAACACG
EST: gi|70669635|gb|DN838212.1|DN838212
EST:     TAAGAGCAAGGGATCTCGGGTCGGGAGCTGAGGCGCTCGGCGGCAAGATG                         TCTCTGGTGAGCAATGAGGAGTTCCAGCACATTCTTCGTGTGCTCAACACG
genomic: TAAGAGCAAGGGATCTCGGGTCGGGAGCTGAGGCGCTCGGCGGCAAGATGgtatgattct ... gttttggcagTCTCTGGTGAGCAATGAGGAGTTCCAGCACATTCTTCGTGTGCTCAACACG
EST: gi|169024190|gb|FE433036.1|FE433036
EST:     AAAGAGCAAGGGATCTCGGGTCGGGAGCTGAGGCGCTCGGCGGCAAGATG                         TCTCTGGTGAGCAATGAGGAGTTCCAGCACATTCTTCGTGTGCTCAACACG
genomic: -AAGAGCAAGGGATCTCGGGTCGGGAGCTGAGGCGCTCGGCGGCAAGATGgtatgattct ... gttttggcagTCTCTGGTGAGCAATGAGGAGTTCCAGCACATTCTTCGTGTGCTCAACACG

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: 124

GGGTTTTTGGAATTAGGGTTCTTCAGCCGCCAGTAAGAGCAAGGGATCTCGGGTCGGGAGCTGAGGCGCTCGGCGGCAAGATGgtatgattct ... gttttggcagTCTCTGGTGAGCAATGAGGAGTTCCAGCACATTCTTCGTGTGCTCAACACGAATGTGGACGGGCGGCAGAAGATTATGTTCGCGCTGACTTCCATCAAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatgattcttgtgttgggtgttgaaataatcctccggcgcctctgttttggcagTCTCTGGTGAGCAATGAGGAGTTCCAGCACATTCTTCGTGTGCTCAACACGAATGTGGACGGGCGGCAGAAGATTATGTTCGCGCTGACTTCCATCAAGG
                                        cctctgtttt  CT-rich tract
                     ttgaaataat  TA-rich tract