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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgttaatccattcgggcttcgcacacttgtttgacagcgctatgcatgacacagGTAGTGGAGCTGGATTTCCTCTATCCCAGCGAAGGCATCCACCGGCGGTGGGATTGTGGATATCGCATCACCGCCACTGCGGCAACTTGGGATCAAGCAG

Basic information

species Selaginella moellendorffii
transcript EFJ31718
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: GRMZM2G480263_T01 (Zea mays), 3'ss of exon 11
--------------------------------------------------------------------------------gtctgttaatccattcgggcttcgcacacttgtttgacagcgctatgcatgacac----agGTAGTGGAGCTGGATTTCCTCTATCCCAGCGAAGGCATCCACCGGCGGTGGGATTGTGGATATCGCATCACCGCCACTGCGGCAACTTGGGATCAAGCAG
                                                                                |||   | ||   |      ||  || |    |||  |  | || | |     ||    |||| || ||| |||||||||| || |||||||||||||||||||| || |||||  | || ||  | || ||  |||| ||||| ||     | ||||| |
gttaggatgattgctttgaccgcgtagcagtatctgtgttgtgggctcgccttgccagcgctcacactcctctgaattatgtcaactgatgtctgaacatttaaca-aggcatttagcccccctttcccaactactgtcagGTTGTAGAGTTGGATTTCCTGTACCCCAGCGAAGGCATCCACCGACGCTGGGAGAGCGGCTACAGGATAACTTCCACGGCGGCCACCAACAACCAAGCCG

upper sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: GRMZM2G037923_T02 (Zea mays), 3'ss of exon 15
------------------------------------------------------gtctg--ttaatccattcgggcttcgcacacttgtttgacag-----------cgctatgcatgacac----agGTAGTGGAGCTGGATTTCCTCTATCCCAGCGAAGGCATCCACCGGCGGTGGGATTGTGGATATCGCATCACCGCCACTGCGGCAACTTGGGATCAAGCAG
                                                       ||||  ||    ||   |      | ||| || ||| |||            | || | |     ||    |||| || ||| |||||||||| || |||||||| |||||||||||||| |||||  | || ||  | || ||  |||| || || ||    || ||||| |
gttaggatgattgctttgaccgcgcagcagtatctgtgctgtgggctcacactcctctgaattgtgtcaactgatgcctgaacatttatttaacaagccatttacccctctttcccaactactgtcagGTTGTAGAGTTGGATTTCCTGTACCCCAGCGAGGGCATCCACCGGCGCTGGGAGAGCGGCTACAGGATAACTTCCACGGCAGCCACCAACGACCAAGCCG

upper sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: GRMZM2G110085_T01 (Zea mays), 3'ss of exon 10
--------------------------------------------------------------------------------gtctgttaatccattcgggcttcgcacacttgtttgacagcgctatgcatgacac----agGTAGTGGAGCTGGATTTCCTCTATCCCAGCGAAGGCATCCACCGGCGGTGGGATTGTGGATATCGCATCACCGCCACTGCGGCAACTTGGGATCAAGCAG
                                                                                |||   | || | |      ||  || |    |||  |  | || | |     ||    |||| || ||| |||||||||| || ||||||||||||||| ||||||| |||||  | || ||  | || ||  |||  ||||| ||    || ||||  |
gttaggatgattgctttgaccgcgcagcagtatctgtgttgtgggctcgccttgccagcgctcacactcctctgaattgtgtcaactgatgcctgaacatttaaca-aggcatttagcccccctttcccaactactgtcagGTTGTAGAGTTGGATTTCCTGTACCCCAGCGAAGGCATCTACCGGCGCTGGGAGAGCGGCTACAGGATAACTTCCATGGCGGCCACCAACGACCAAGTCG

upper sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 14
-------------------------gtctgttaatccattcgggcttcgcacacttgtttgac---------agcgctatgcatgacac-agGTAGTGGAGCTGGATTTCCTCTATCCCAGCGAAGGCATCCACCGGCGGTGGGATTGTGGATATCGCATCACCGCCACTGCGGCAACTTGGGATCAAGCAG
                         |  |  | |||| |  ||   |   | |    | |||            | | |  | | |  | |||| ||||| || |||||| | |||||||| |||||||| || ||  |||||||| |||| |||||||||||| | ||||| ||||| ||||| ||||| |
gtcttgtatttcaaaaattaattgtgattaattatccttgtggcactgaaaaatccatctgatttatgtattctctccaaacttaatgccagGTTGTGGAACTTGATTTCTTGTATCCCAGTGAAGGCATTCATCGAAGGTGGGATAGTGGTTATCGCATCACCTCAACTGCTGCAACATGGGACCAAGCTG

upper sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: GLYMA06G09190.1 (Glycine max), 3'ss of exon 14
-----------------------------------gtctgttaatccattcgggcttcgcacacttgtttgacagcgctatgcatgacac-agGTAGTGGAGCTGGATTTCCTCTATCCCAGCGAAGGCATCCACCGGCGGTGGGATTGTGGATATCGCATCACCGCCACTGCGGCAACTTGGGATCAAGCAG
                                      |||    |        |    |  | || | |     | | |  | | |  | |||| ||||| || |||||| | |||||||| ||||| || || ||  ||||||||  ||| |||||||||||| | ||||| ||||| ||||||||||| |
gtcttgtatttaaaaaattaattgtgattaaatatccttgtggcactgaaaaatcccatctgatttatgtattctctccaaacttaatgccagGTTGTGGAACTTGATTTCTTGTATCCCAGTGAAGGTATTCATCGAAGGTGGGATAATGGTTATCGCATCACCTCAACTGCTGCAACATGGGATCAAGCTG

upper sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: GLYMA04G09070.2 (Glycine max), 3'ss of exon 14
----------------------------------gtctgttaatccattcgggcttcg-cacacttgtttgacagcgctatgcatgacac-agGTAGTGGAGCTGGATTTCCTCTATCCCAGCGAAGGCATCCACCGGCGGTGGGATTGTGGATATCGCATCACCGCCACTGCGGCAACTTGGGATCAAGCAG
                                   ||  |    |  |      | |  |  | || | |     | | |  | | |  | |||| ||||| || |||||| | |||||||| ||||| || || ||  |||||||| |||| |||||||||||| | ||||| ||||| ||||| ||||| |
gtcttgtattttaaaaaattaattgtgattaaatatccttgtggcactgaaaaatccatctgatttatgtattctctccaaacttaatgccagGTTGTGGAACTTGATTTCTTGTATCCCAGTGAAGGTATTCATCGAAGGTGGGATAGTGGTTATCGCATCACCTCAACTGCTGCAACATGGGACCAAGCTG

upper sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: GLYMA06G09190.2 (Glycine max), 3'ss of exon 14
-----------------------------------gtctgttaatccattcgggcttcgcacacttgtttgacagcgctatgcatgacac-agGTAGTGGAGCTGGATTTCCTCTATCCCAGCGAAGGCATCCACCGGCGGTGGGATTGTGGATATCGCATCACCGCCACTGCGGCAACTTGGGATCAAGCAG-----------------------------
                                      |||    |        |    |  | || | |     | | |  | | |  | |||| ||||| || |||||| | |||||||| ||||| || || ||  ||||||||  ||| |||||||||||| | ||||| ||||| ||||||||||| |                             
gtcttgtatttaaaaaattaattgtgattaaatatccttgtggcactgaaaaatcccatctgatttatgtattctctccaaacttaatgccaggttgtggaacttgatttcttgtatcccagTGAAGGTATTCATCGAAGGTGGGATAATGGTTATCGCATCACCTCAACTGCTGCAACATGGGATCAAGCTGCTTTTGTTCTTAGTGTCCCAAGAAGAAAA

upper sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: AT3G13670.1 (Arabidopsis thaliana), 3'ss of exon 14
------------------------------------------gtctgttaatccatt---cgggcttcgcacacttgtttgacagcgc-tatgcatgacacagGTAGTGGAGCTGGATTTCCTCTATCCCAGCGAAGGCATCCACCGGCGGTGGGATTGTGGATATCGCATCACCGCCACTGCGGCAACTTGGGATCAAGCAG
                                             | |  |||  |      |  |||  |  ||  | |    ||   |||       |||||| ||||| || ||||| || ||||| || |||||||||||| |||| |||||| ||||||   | |||||  | || || || ||    |||||||| |
gttagacttcaccgatatagatgaatttcttccgtttccttcagttttggatctgtcgcgttgatttctaattctcctgttttcgcttatatctcctctacagGTTGTGGAACTTGATTTTCTGTATCCAAGTGAAGGCATCCACAGGCGTTGGGATGGTGGATTCAGAATCACATCAACAGCAGCCACAACCGATCAAGCTG

upper sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 14
----------------------------------------------------------------------------------------------------------------------------------------------gtctgttaatccattcgggcttcgcacacttgtttgacagcgctatgcatgacacagGTAGTGGAGCTGGATTTCCTCTATCCCAGCGAAGGCATCCACCGGCGGTGGGATTGTGGATATCGCATCACCGCCACTGCGGCAACTTGGGATCAAGCAG
                                                                                                                                               |   |||  | ||| |    || ||    || ||        | ||| |    ||||| || ||||| || ||| | ||||| |||||||| || ||| |||| |||||  ||||||||||||||||  | ||||| || || |||||||||||||
gtgattaaaaccgtcgatcggtttttttattaaactttcatttatttttatcagctttatgattttagcatgatccaaagtgtacatcaattgagagacatatcgaggactttgtgacctaacaccttagaagtgacgtgtttttgattatgctatttgtttctcacaatgctgctt-----tcttttgcctc-tgcagGTGGTTGAGCTTGACTTCTTGTATCCTAGCGAAGGTATTCACAGGCGATGGGACAGTGGATATCGCATCACATCTACTGCTGCCACATGGGATCAAGCAG

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|169079095|gb|FE488619.1|FE488619
EST:     GAACCCGCTGGGGAGTGGTCATGTCGAGAAACGCTGGTTTCACGGACCAG                         GTAGTGGAGCTGGATTTCCTCTATCCCAGCGAAGGCATCCACCGGCGGTGG
genomic: GAACCCGCTGGGGAGTGGTCATGTCGAGAAACGCTGGTTTCACGGACCAGgtctgttaat ... catgacacagGTAGTGGAGCTGGATTTCCTCTATCCCAGCGAAGGCATCCACCGGCGGTGG
EST: gi|169077785|gb|FE485463.1|FE485463
EST:     GAACCCGCTGGGGAGTGGTCATGTCGAGAAACGCTGGTTTCACGGACCAG                         GTAGTGGAGCTGGATTTCCTCTATCCCAGCGAAGGCATCCACCGGCGGTGG
genomic: GAACCCGCTGGGGAGTGGTCATGTCGAGAAACGCTGGTTTCACGGACCAGgtctgttaat ... catgacacagGTAGTGGAGCTGGATTTCCTCTATCCCAGCGAAGGCATCCACCGGCGGTGG
EST: gi|169051034|gb|FE458204.1|FE458204
EST:     GAACCCGCTGGGGAGTGGTCATGTCGAGAAACGCTGGTTTCACGGACCAG                         GTAGTGGAGCTGGATTTCCTCTATCCCAGCGAAGGCATCCACCGGCGGTGG
genomic: GAACCCGCTGGGGAGTGGTCATGTCGAGAAACGCTGGTTTCACGGACCAGgtctgttaat ... catgacacagGTAGTGGAGCTGGATTTCCTCTATCCCAGCGAAGGCATCCACCGGCGGTGG

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: 72

CAACAAAAAGTGGAGGGAAGGGTTTTACGTGACTTCCATGGCGACCGCTGGAACCCGCTGGGGAGTGGTCATGTCGAGAAACGCTGGTTTCACGGACCAGgtctgttaat ... catgacacagGTAGTGGAGCTGGATTTCCTCTATCCCAGCGAAGGCATCCACCGGCGGTGGGATTGTGGATATCGCATCACCGCCACTGCGGCAACTTGGGATCAAGCAG




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