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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgacaccgttgttttcttcgtgcgcattctcattctcgatcttacagACCTTCAATGGAAAGAAGTGGGAGAAGTTCAACAGCGAGAAGGTTGCTTCTCTGGCTTACGCTCGAATACAAGGCAAGGTTGCCCTCGTCGCACATTTCC

Basic information

species Selaginella moellendorffii
transcript EFJ28199
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ28199 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: LOC_Os02g31290.1 (Oryza sativa), 3'ss of exon 13
------------------------------------------gtttgacaccgttgttttcttcgtg---------cgcattctcattctcgatcttacagACCTTCAATGGAAAGAAGTGGGAGAAGTTCAACAGCGAGAAGGTTGCTTCTCTGGCTTACGCTCGAATACAAGGCAAGGTTGCCCTCGTCGCACATTTCC
                                           ||  |||   |    ||     |           |    ||||| |    | || ||||| |||||||| ||||||||||| ||||| ||||| ||||| || || || || ||||| ||| |||| ||||| ||    || ||  | || || ||||
ggcaatagcttacgttctgcatgcggcttgtcaactttggacattgtacattatccaatttgaaataaatcaatattgtgccctcatccctt-ttttgcagACGTTCAATGGCAAGAAGTGGGAAAAGTTTAACAGTGAGAAAGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAATCAGCTCTTATTGCTCACTTCC

upper sequence: EFJ28199 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: GRMZM2G004455_T01 (Zea mays), 3'ss of exon 11
-------------------------------------------------gtttgacaccgttgttttcttcgtgcgcattctcat-tctcgatcttacagACCTTCAATGGAAAGAAGTGGGAGAAGTTCAACAGCGAGAAGGTTGCTTCTCTGGCTTACGCTCGAATACAAGGCAAGGTTGCCCTCGTCGCACATTTCC
                                                  | |||     |||     ||  |   ||     |   ||  | | | ||| | || ||||| ||||| ||||||||||||||||| |||||||| || ||| ||||||| ||| |||| |||||   |  ||| ||  |  ||||||| |
taataccgggagggcggtctttccctccccggccgagttttttttgtttctgtgaagaacttgaaagatttatttacagatgtacacctataacctgcagGCTTTTAATGGTAAGAAATGGGAGAAGTTCAACAGTGAGAAGGTAGCATCTTTGGCTTATGCTAGAATTCAAGGACGGTCTGCACTGATATCACATTTTC

upper sequence: EFJ28199 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: GRMZM2G154229_T01 (Zea mays), 3'ss of exon 11
-------------------------------------------------------------------------------------------------------------------gtttgacaccgttgttttcttcgtgcgc-attctcattctcgatcttacagACCTTCAATGGAAAGAAGTGGGAGAAGTTCAACAGCGAGAAGGTTGCTTCTCTGGCTTACGCTCGAATACAAGGCAAGGTTGCCCTCGTCGCACATTTCC
                                                                                                                    | |||     ||||  | ||  ||  |   | |   |||  | | | ||| | || ||||| ||||| ||||| |||||||||||||||||||| || ||  ||||||| ||| |||| |||||   |  ||| ||  |  ||||||| |
gtgctttcctttcttggcctttgtcctgtgtttgcaatagttacctgcagagttaagaacttgttccctgtccagctgagttaatcagcaatacggattagcaatagtataattactctgaacagcttgtaatatttatgtactgatgtacatctataacctgcagGCTTTTAATGGTAAGAAATGGGAAAAGTTCAACAGCGAGAAGGTAGCCTCGTTGGCTTATGCTAGAATTCAAGGACGGTCTGCACTGATATCACATTTTC

upper sequence: EFJ28199 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: GRMZM2G459746_T01 (Zea mays), 3'ss of exon 13
---------------------------------------------------------------------------------------------------------------gtttga-caccgttgttttcttcgtgcgcattctcattctcgatcttacagACCTTCAATGGAAAGAAGTGGGAGAAGTTCAACAGCGAGAAGGTTGCTTCTCTGGCTTACGCTCGAATACAAGGCAAGGTTGCCCTCGTCGCACATTTCC
                                                                                                               | |||| || ||  ||  | | | || ||  | |  |  ||  | || ||||| || ||||| || |||||||||||||| ||||| |||||||| || || || ||||| ||| |||| ||||| ||    || ||  | || |||||||
gtcagaaaattattccaattgacgaagtgctactgcattgatgtaaagttgtaaactagcctttggtcaacttatatgccttgccaaatttgtactttgataaaatatccggcttgaacatcgacgtgctatcc-tgagccattttgtcatc--tttttcagACTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAAACAGCTCTGATTGCTCATTTCC

upper sequence: EFJ28199 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: GLYMA18G12730.1 (Glycine max), 3'ss of exon 10
---------------------------------------------------------------------------------------------gtttgacaccgttgttttcttcgtgcgcattctcattctcgatcttacagACCTTCAATGGAAAGAAGTGGGAGAAGTTCAACAGCGAGAAGGTTGCTTCTCTGGCTTACGCTCGAATACAAGGCAAGGTTGCCCTCGTCGCACATTTCC
                                                                                             | |    |    | |  | ||     |   | ||||      |  |  || |||| ||||| || |||||||||||||||||||| || ||||||||||| ||||| || || || |||||||| |||| ||| || ||    |||||||
gtttgaattctatatcttttcacgtctgaggtcttctgttactactacatttattgatagtttctggtaatttgcaagtattaaacttgtcctgatctggagaagtatgatgttaagaagt-ctatcatggaaatttctgtagGCCTTTAATGGGAAAAAGTGGGAGAAGTTCAACAGTGAAAAGGTTGCTTCACTGGCATATGCACGGATACAAGGAAAGGCTGCGCTTGTGATGCATTTCC

upper sequence: EFJ28199 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: GLYMA08G42230.1 (Glycine max), 3'ss of exon 9
---------------------------------------------------gtttgacaccgttgttttcttcgtgcgcattctcattctcgatcttacagACCTTCAATGGAAAGAAGTGGGAGAAGTTCAACAGCGAGAAGGTTGCTTCTCTGGCTTACGCTCGAATACAAGGCAAGGTTGCCCTCGTCGCACATTTCC
                                                   | |    |    | |  | ||     |   | ||||      |     || |||| ||||| || |||||||||||||||||||| || ||||||||||| ||||| || || || |||||||| |||| ||| || ||    |||||||
aaagtattttattgatagtttctgttaatttgcaagtattaaacttgtcctgatctggagaagtataatgttgagaagt-ctatcatggaaatttacgtagGCCTTTAATGGGAAAAAGTGGGAGAAGTTCAACAGTGAAAAGGTTGCTTCACTGGCATATGCACGGATACAAGGAAAGGCTGCGCTTGTGATGCATTTCC

upper sequence: EFJ28199 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: AT5G07290.1 (Arabidopsis thaliana), 3'ss of exon 12
-------------------------------------------------------gtttgacaccgttgttttcttcgtgcgcattctcattctcgatctta-cagACCTTCAATGGAAAGAAGTGGGAGAAGTTCAACAGCGAGAAGGTTGCTTCTCTGGCTTACGCTCGAATACAAGGCAAGGTTGCCCTCGTCGCACATTTCC
                                                        || || |     |       |||  |  | |   ||    | |||| ||| | ||||| || ||||| ||||| |||||||||||||||||||| || || || || || | ||| || || || ||    || ||  | || |||||||
gtataagctttgtacctttttatgatcaatttgtgtagatgatgtatcattgttctttagaaaaaaaggaaaaaagcgtttggttacaagtttaaaaccttaacagGCATTCAACGGTAAGAAATGGGAAAAGTTCAACAGCGAGAAGGTGGCATCGCTTGCATATGGTCGGATTCAGGGGAAATCAGCTCTTATTGCCCATTTCC

upper sequence: EFJ28199 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: Vv12s0142g00100.t01 (Vitis vinifera), 3'ss of exon 11
-------------------------------------------------gtttgacaccgttgttttcttcgtgcgcattctcattctcgatct-tacagACCTTCAATGGAAAGAAGTGGGAGAAGTTCAACAGCGAGAAGGTTGCTTCTCTGGCTTACGCTCGAATACAAGGCAAGGTTGCCCTCGTCGCACATTTCC
                                                  |  ||   |  |  | | || |   |  || | || |   || | | ||| | || ||||||||||||||||| ||||||||||| || || ||||||||  |||| || || ||||||||||||||||  ||||| ||  |||| ||||
gacttgccaatgtgttggatattaccttaatacttgttaaggaagaataatgggagttctatcatattttggaaagacttataatgcggaatttgtgcagGCATTTAATGGAAAGAAGTGGGAAAAGTTCAACAGTGAAAAAGTTGCTTCATTGGCATATGCGCGAATACAAGGCAAGGCAGCCCTTGTTACACACTTCC

upper sequence: EFJ28199 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: Vv17s0000g00240.t01 (Vitis vinifera), 3'ss of exon 13
---------------------------------------------------------------------------------------gtttgacaccgttgttttcttcg---tgcgcatt----ctcattctcgatcttacagACCTTCAATGGAAAGAAGTGGGAGAAGTTCAACAGCGAGAAGGTTGCTTCTCTGGCTTACGCTCGAATACAAGGCAAGGTTGCCCTCGTCGCACATTTCC
                                                                                       || ||  || | | |   ||  |   |||  ||        ||  |  || | |||| | |||||||| || |||||||||||||||||||| |||||||| || ||||| || || |||||||| ||||| ||   ||| ||  | || |||||||
gttagaatccatgcattgtaatataattatacttaatacttttttcggctttcaaaggaaagcttcttgtctacagaatttcataaggtctgcaactgatatggactgagaactgctaatcagaatgtatcatatatttcacagGCATTCAATGGTAAAAAGTGGGAGAAGTTCAACAGTGAGAAGGTGGCATCTCTTGCATATGCTCGAATTCAAGGAAAAACTGCTCTTATTGCTCATTTCC

upper sequence: EFJ28199 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: Vv00s0239g00110.t01 (Vitis vinifera), 3'ss of exon 3
---------------------------------------------------------------------------------------gtttgacaccgttgttttcttcg---tgcgcatt----ctcattctcgatcttacagACCTTCAATGGAAAGAAGTGGGAGAAGTTCAACAGCGAGAAGGTTGCTTCTCTGGCTTACGCTCGAATACAAGGCAAGGTTGCCCTCGTCGCACATTTCC
                                                                                       || |   || | | |   ||  |   |||  ||        ||  |  || | |||| | ||||||||||| ||||||||||||||||| || |||||||| || ||||| || || |||| |||  |||| ||   ||| ||    || |||||||
gtttgaatccatggattgtaatataattatacttaatatttttttcgactttcaaaggaaagcttcttgtctacagaatttcataaggtctacaactgatatggactgagaactgctaatcagaatgtatcatatatttcacagGCATTCAATGGAAAAAAGTGGGAGAAGTTCAATAGTGAGAAGGTGGCATCTCTTGCATATGCTCAAATTTAAGGAAAAACTGCTCTTACTGCTCATTTCC

upper sequence: EFJ28199 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: Vv10s0003g02670.t01 (Vitis vinifera), 3'ss of exon 11
---------------------------------------------------gtttgacaccgttgttttcttcgtgcgcattctcattctcgatcttacagACCTTCAATGGAAAGAAGTGGGAGAAGTTCAACAGCGAGAAGGTTGCTTCTCTGGCTTACGCTCGAATACAAGGCAAGGTTGCCCTCGTCGCACATTTCC
                                                     ||||       | | | ||  |   | || |  ||||   |  | ||| | || ||||| |||||||||||||| ||||| || ||||| ||||||||  |||| || ||| |||| || || |||| |||||| ||| |||||||||
ttctagcatcattcctcatgaacagaaaagaaagacacttcactaatgaatacttgaagataaagctgtatt-atctactttttgtttctaatttatgcagGCTTTTAATGGTAAGAAGTGGGAGAAATTCAATAGTGAGAAAGTTGCTTCCTTGGCATATGCTAGAATCCAGGGAAAGGCTGCCCTAGTCACACATTTCC

upper sequence: EFJ28199 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: Vv01s0150g00090.t01 (Vitis vinifera), 3'ss of exon 14
------------------------------------------------gtttgacaccgttgtt--ttcttcgtgcgcattctcattctcgatcttacagACCTTCAATGGAAAGAAGTGGGAGAAGTTCAACAGCGAGAAGGTTGCTTCTCTGGCTTACGCTCGAATACAAGGCAAGGTTGCCCTCGTCGCACATTTCC
                                                |||    |   |  ||  ||  | |     | | | |  |    | |  ||| | |||||||||||||| |||||||||||||| ||||| ||||| || || || || || || || ||||| || |||| ||| ||| | || |||||||
aaataccacctaaaagagtttgtatgttaccattagagcttctctcgagttacctattatgattcattacttgaaaaaaatttaaacccaattttggcagGCATTCAATGGAAAGAAATGGGAGAAGTTCAATAGCGAAAAGGTGGCATCACTTGCATATGCCCGCATACAGGGAAAGGCTGCTCTCATTGCCCATTTCC

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), 17 (downstream exon)
Score: 3

AATAAGTGTAACGTGGGGTATGCTTTCATCAACATGATTGCACCTGTGCATATCGTCCCTTTCTTCAAGgtttgacacc ... gatcttacagACCTTCAATGGAAAGAAGTGGGAGAAGTTCAACAGCGAGAAGGTTGCTTCTCTGGCTTACGCTCGAATACAAGGCAAGGTTGCCCTCGTCGCACATTTCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttgacaccgttgttttcttcgtgcgcattctcattctcgatcttacagACCTTCAATGGAAAGAAGTGGGAGAAGTTCAACAGCGAGAAGGTTGCTTCTCTGGCTTACGCTCGAATACAAGGCAAGGTTGCCCTCGTCGCACATTTCC
                         ttgtttt  TA-rich tract