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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtcgaattctcgtgaaagattttttcactttggatgacgaacttctacagGATGCTGGTATATGAGTACGTAGACAATGGTAATCTGGAGCAGTGGCTTCACGGCCCAGCCTCCATTCTCAACTCTCCAACATGGGAAGTTCGGATGAAA

Basic information

species Selaginella moellendorffii
transcript EFJ36811
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ36811 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: LOC_Os05g36050.1 (Oryza sativa), 3'ss of exon 2
--------------------------------------------------------------------------------gtacgtcgaattctcgtgaaagattttttcactttggatgacgaacttctacagGATGCTGGTATATGAGTACGTAGACAATGGTAATCTGGAGCAGTGGCTTCACGGCCCAGCCTCCATTCTCAACTCTCCAACATGGGAAGTTCGGATGAAA
                                                                                  |   | |  |  |      |||  |  || ||    || |     ||| |||||| || || ||||||||||| |||||||| ||  |||||||||||||||| |||   |         | | | |||   | |||||  |  ||||||| 
gtacactacacacaccacgcaattgccaaatcgccgccttcttttttttctttcctttttttggctgttctcttaccagatcattcctacctacctactccgatcctaccatttct--tgcctgtgatct-cagGATACTTGTGTATGAGTACGTGGACAATGGCAACTTGGAGCAGTGGCTTCATGGCGACGTTGGACCGGTTAGCCCTCTGTCTTGGGACATCAGGATGAAC

upper sequence: EFJ36811 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM2G317938_T01 (Zea mays), 3'ss of exon 2
------------------------------------------------------------------------------gtacgtcgaattctcgtgaaag-attttttcactttggatgacgaacttctacagGATGCTGGTATATGAGTACGTAGACAATGGTAATCTGGAGCAGTGGCTTCACGGCCCAGCCTCCATTCTCAACTCTCCAACATGGGAAGTTCGGATGAAA
                                                                                | |  | |  || |     | || |    ||| |||   | |  |||  |||||||||| || |||||||| || |||||||||||||| || ||||||||||| ||    |    |    | | | | |  ||||||||  |  ||||||| 
gtatgtgtgttggcaggcacattgcaatctcttcttcgttcggtggacacctagttgcttctctcaatttagggttctcaatgatggaagcttgcttctgtatatcactactatggtctatg--cttgaacagGATGCTCGTGTATGAGTATGTGGACAATGGTAATCTTGACCAGTGGCTTCATGGTGATGTTGGCGAAGTGAGCCCACTGACATGGGACATCAGGATGAAC

upper sequence: EFJ36811 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM2G014366_T03 (Zea mays), 3'ss of exon 2
----------------------------------------------------gtacgtcgaattctc----gtgaaag----attttt-tcactttggatgacgaacttctacagGATGCTGGTATATGAGTACGTAGACAATGGTAATCTGGAGCAGTGGCTTCACGGCCCAGCCTCCATTCTCAACTCTCCAACATGGGAAGTTCGGATGAAA
                                                      |  | | ||||||     || |||    |||  | ||||| | |   | |  |||  |||||||||| || || ||||| || |||||||||||||| || ||||||||||| ||    |         | | | | | ||||||||| ||  ||||||| 
gtatgatggcatattgctatctcttcttcattcggtccggtgacacctactctcagtttggattctcaataatggaagcctgattcctgtcactgtcgtctatg--cttgaacagGATGCTTGTGTACGAGTATGTGGACAATGGTAATCTTGACCAGTGGCTTCATGGTGATGTTGGAGAAGTAAGCCCACTAACATGGGACGTCAGGATGAAC

upper sequence: EFJ36811 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA09G39160.1 (Glycine max), 3'ss of exon 2
-----------------------------------------------------gtacgtcgaattctcgtgaaagattttttcactttggatgacgaact---tctacagGATGCTGGTATATGAGTACGTAGACAATGGTAATCTGGAGCAGTGGCTTCACGGCCCAGCCTCCATTCTCAACTCTCCAACATGGGAAGTTCGGATGAAA
                                                       |  |    ||    ||| |   | |   |  |    ||  | |||   |  |||||||||| || |||||||| ||||||||||| ||||| ||||| ||||| || ||    |       | | | | ||   |||||| |  | |||||||| 
gtattgatatcttcttctcttaaaaactaaatagaaaaaaaaaattgatgctatcaattttgtttggtttgacatgatgtgagatctgaagtgtggtactgttttcacagGATGCTTGTGTATGAGTATGTAGACAATGGCAATCTAGAGCAATGGCTGCATGGGGACGTTGGAGCTGTAAGCCCTTTGACATGGAACATACGGATGAAC

upper sequence: EFJ36811 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA11G05830.1 (Glycine max), 3'ss of exon 2
------------------------------------------------------------------gtacgtcgaattctcgtgaaagattttttcactttggatgacgaacttctacagGATGCTGGTATATGAGTACGTAGACAATGGTAATCTGGAGCAGTGGCTTCACGGCCCAGCCTCCATTCTCAACTCTCCAACATGGGAAGTTCGGATGAAA
                                                                  | || |   |  ||  |||    |||||| | ||   || |   ||  || ||| ||||| || ||||||||||| |||||||||||| | ||||||||||| || ||    |       |  ||   ||| ||| |||||| |||| ||||| 
gtattcttactttcttctttaattatccaaaattgcttcttttttttttttttgtagtatagatatgaacttttgaa-ctgatgaggtttttttttaattattattattcacg-ctgcagAATGCTTGTTTATGAGTACGTGGACAATGGTAATTTAGAGCAGTGGCTGCATGGGGATGTTGGGCCTTGCAGTCCTCTAACTTGGGAAATTCGAATGAAC

upper sequence: EFJ36811 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA01G39420.1 (Glycine max), 3'ss of exon 3
-----------------------------gtacgtcgaattctcgtgaaagattttttcactttggatgacgaacttctacagGATGCTGGTATATGAGTACGTAGACAATGGTAATCTGGAGCAGTGGCTTCACGGCCCAGCCTCCATTCTCAACTCTCCAACATGGGAAGTTCGGATGAAA
                              |    | || |  | |      |||||||  |    || |     | || ||| ||||| || ||||||||||| |||||||||||| | ||||||||||| || ||    |       |  ||   ||| ||| |||||| |||| ||||| 
gtactcttcatttcttactttcctctttaattaaccaaaattgcttccttttttttttctttgattattattgg-tcctgcagAATGCTTGTTTATGAGTACGTTGACAATGGTAATTTAGAGCAGTGGCTGCATGGGGATGTTGGGCCTTGCAGTCCTCTAACTTGGGAAATTCGAATGAAC

upper sequence: EFJ36811 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: Vv15s0046g02030.t01 (Vitis vinifera), 3'ss of exon 2
--------------------------------------gtacgtcgaattctcgtgaa----agattttttcactttggat--gacgaacttctac--agGATGCTGGTATATGAGTACGTAGACAATGGTAATCTGGAGCAGTGGCTTCACGGCCCAGCCTCCATTCTCAACTCTCCAACATGGGAAGTTCGGATGAAA
                                       |   | ||     |   ||    | |||||||||  ||  ||  |      || |    |||||||| || |||||||| || |||||||||||| |||| ||||||||||| ||    |         ||| | |||  ||||||||  ||||||| || 
gtattgctacccatcttctgctaaatcctgacactgggttttcttgaggatccaaaaaactaacattttttcatctttcatttgttttttttttgtctagGATGCTTGTGTATGAGTATGTGGACAATGGTAATTTGGACCAGTGGCTTCATGGGGATGTAGGGGAAGTCAGCCCTCTGACATGGGATATTCGGATTAAC

upper sequence: EFJ36811 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: Vv07s0031g00480.t01 (Vitis vinifera), 3'ss of exon 2
-----------------------------------------------------------------------------------------------------------------------------gtacgtcgaattctcgtgaaagatttt-------ttcactttggatgacgaacttctacagGATGCTGGTATATGAGTACGTAGACAATGGTAATCTGGAGCAGTGGCTTCACGGCCCAGCCTCCATTCTCAACTCTCCAACATGGGAAGTTCGGATGAAA
                                                                                                                              ||| |   ||  ||   | | ||  |       | |  |     |  | | ||  |  |||||||| || |||||||| ||| | ||||| ||| |||||||||||||||| ||    |       ||  |   |||  || |||||  |||| ||||| 
gtactttgttattgtctattgcttaatcctgcttgattgtatttgaactgcaaacaagaatatcttattaattccccattgaaaatgattttgtgttgtttaatttttttttcctggctggccttatacatgatatcttcaacagatatgctgatgatgtcctatccttgtttcaatctgttgtagGATGCTTGTGTATGAGTATGTAAATAATGGGAATTTGGAGCAGTGGCTTCATGGTGATGTAGGGCCTCGAAGTCCTCTTACTTGGGAGATTCGAATGAAT

upper sequence: EFJ36811 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S568_2V6.1 (Physcomitrella patens), 3'ss of exon 3
---------------------------------gtacgtcg----aattctcgtgaaagatt--ttttcactttggatgacg-aacttctacagGATGCTGGTATATGAGTACGTAGACAATGGTAATCTGGAGCAGTGGCTTCACGGCCCAGCCTCCATTCTCAACTCTCCAACATGGGAAGTTCGGATGAAA
                                 ||  | |     ||||||| |  | |     |  | |||| |  |  ||   ||| |  |||||||| || || |||||||| |||||||| ||||||||||||||||| || || ||    ||       ||| | |   ||||||||| ||| |||   
gtgaagcatttattcttcccacctggagtttttgtgtgccagcacaattctcttacacgtgcaatgctaacttcgtctctcgtggcttttgtagGATGCTTGTGTACGAGTACGTGGACAATGGGAATCTGGAGCAGTGGCTACATGGACCTCTGTCACAAACAAACACACTTCCATGGGAAGCTCGCATGCGG

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: 34 (upstream exon), 30 (downstream exon)
Score: 12

AAGCCGAGAAGGAATTCCGAGTAGAAGTAGAGGCCATCGGTCGGGTGAGGCACAAAAACCTGGTGCGTTTGCTCGGCTACTGCGTGGAGATAAATTACAGgtacgtcgaa ... acttctacagGATGCTGGTATATGAGTACGTAGACAATGGTAATCTGGAGCAGTGGCTTCACGGCCCAGCCTCCATTCTCAACTCTCCAACATGGGAAGTTCGGATGAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtacgtcgaattctcgtgaaagattttttcactttggatgacgaacttctacagGATGCTGGTATATGAGTACGTAGACAATGGTAATCTGGAGCAGTGGCTTCACGGCCCAGCCTCCATTCTCAACTCTCCAACATGGGAAGTTCGGATGAAA
                                              cttctac  CT-rich tract
                   aaagatttttt  TA-rich tract