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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaaaaagaaaaaaaaaaaaaaaaaaggttcttttcttttgtggggaatctaaaaacaaattgcactttgcagCCCCAAGATGCCTATGGACTGGAGAAGCTGTGCACTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGGATCGAGTGCCGCATTGGACGATTCCACA

Basic information

species Selaginella moellendorffii
transcript EFJ18599
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ18599 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os10g28200.1 (Oryza sativa), 3'ss of exon 3
gtatgaaaaagaaaaaaaaaaaaaaaaaaggttcttttcttttgtgg----ggaatctaaaaacaaattgc-------actttgcagCCCCAAGATGCCTATGGACTGGAGAAGCTGTGCACTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGGATCGAGTGCCGCATTGGACGATTCCACA
|| ||   |  |||| ||    |       ||  | |  ||| ||       |||  | |   |  | ||        ||| | ||||| ||||||||||||||  ||||||||||    ||||| ||||| |||||||||||||||||||| ||||| || ||||||||  |||| || |||||||
gtttgtccatcaaaataattttaggctttagtgttatgttttagtaaaaccagaagttgatttcctactgttttaactactgtccagCCTCAAGATGCCTATGGTTTGGAGAAGCTTGCAACTGAGGAGCTCTGCAAGCACTACACCAAGGACTTTGGCATTGAGTGCCGTGTTGGCCGCTTCCACA

upper sequence: EFJ18599 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G124434_T01 (Zea mays), 3'ss of exon 3
gtatgaaaaagaaaaaaaaaaaaaaaaaaggttctttt--cttttgtgggg---aatctaaaaaca---aattgcactttgcagCCCCAAGATGCCTATGGACTGGAGAAGCTGTGCACTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGGATCGAGTGCCGCATTGGACGATTCCACA
|| ||   |   ||| | ||  |       |||  ||   | | | |   |   ||||||||  |      |   || || ||||| ||||||||||||||  ||||||||||    || || |||||||||||||||||||||||||| ||||| |||||||||||| | || || |||||||
gtgtgttcatcgaaatacaatgacgttcctgtttgttagacatatatacagtcaaatctaaatcccctcggtgttacgtttcagCCTCAAGATGCCTATGGCTTGGAGAAGCTTGCAACCGAGGAGCTGTGCAAGCACTACACCAAGGACTTTGGCATCGAGTGCCGCGTCGGCCGCTTCCACA

upper sequence: EFJ18599 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G138907_T01 (Zea mays), 3'ss of exon 3
---------------------------------gtatgaaaaagaaaaaaaaaaaaaaaaaaggttcttttcttttgtggggaatctaaaaacaaattgcactttgcagCCCCAAGATGCCTATGGACTGGAGAAGCTGTGCACTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGGATCGAGTGCCGCATTGGACGATTCCACA
                                 || | |      |   |    |      |  | |  |       |||    |    ||   |     | |||  |||| |||||||||||||| ||||| || ||    ||||| ||||||||||||||||| || ||||||||||| ||||||||||| ||||| || || ||||
gtttctaataaacttctgcatttctttacgctcgtgttagctgtcacctacttgagctgtgacttgcgatggcaaaatggtttttactgaactgatgcctaatttttagCCTCAAGATGCCTATGGCCTGGAAAAACTCGCGACTGAGGAGCTGTGCAAGCACTATACAAAGGATTTTGGCATCGAGTGCCGGATTGGTCGCTTTCACA

upper sequence: EFJ18599 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA03G40720.1 (Glycine max), 3'ss of exon 3
---------------------------gtatgaaaaagaaaaaaaaaaaaaaaaaaggttcttttcttttgtggggaatctaaaaacaaattgcactttgcagCCCCAAGATGCCTATGGACTGGAGAAGCTGTGCACTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGGATCGAGTGCCGCATTGGACGATTCCACA
                           ||   |   |        |   |   |||  | |||    |    |||  || |  ||     |||   |||  |||| |||||||| ||||| |||||||||||    || |||||| | |||||||| || | |||||||||||| || ||||||||||||||  ||||||| |
gtatgttgctgattctttgaattacttgttcaagttattctggttattcacttaaaaatacttaggctagcagggatatatttaattt--ttgacttttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGCATTGGGAGATTCCATA

upper sequence: EFJ18599 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA19G43400.1 (Glycine max), 3'ss of exon 3
---------------------------gtatgaaaaagaaaaaaaaaaaaaaaaaaggttcttttcttttgtggggaatctaaaaacaaattgcactttgcagCCCCAAGATGCCTATGGACTGGAGAAGCTGTGCACTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGGATCGAGTGCCGCATTGGACGATTCCACA
                           ||   |   |        |   |    ||  | |||   ||    |||  || |  ||  |  |  |  |||  |||| |||||||| ||||| |||||||||||    || |||||| | |||||||| || | |||||||||||| || |||||||| |||||  ||||||| |
gtttgttgctgattcttttaattagttgttcaacttattctggttattcacttgaaaatacttaggttagcagggatatatttaa-tatttgactttttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGGATTGGGAGATTCCATA

upper sequence: EFJ18599 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA20G36740.2 (Glycine max), 3'ss of exon 3
--------gtatgaaaaagaaaaaaaaaaaaaaaaaaggttcttttcttttgtggggaatctaaaaacaa---attgcactttgc----------agCCCCAAGATGCCTATGGACTGGAGAAGCTGTGCACTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGGATCGAGTGCCGCATTGGACGATTCCACA
        ||         ||      ||   |    |||||||   |||      |    |   |  ||    ||  | ||||           |||| |||||||| ||||| || ||||||||    || || ||  | ||||||||||| | |||||||||||| || ||||||||||||||  | |||||||
gtttgttggtgatcttttcaattgttcaatttatgttggttcttgattttcacattgggattgggattaatgtgtttaattttgtgactgtttttagCCACAAGATGCATATGGGCTAGAGAAGCTTGCAACAGAGGAATTATGCAAGCACTATAACAAGGATTTTGGAATTGAGTGCCGCATTGGGAGGTTCCACA

upper sequence: EFJ18599 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA10G30400.1 (Glycine max), 3'ss of exon 2
--------gtatgaaaaagaaaaaaaaaaaaaaaaaaggttcttttcttttgtggggaatctaaaaacaaattg-------------cactttgcagCCCCAAGATGCCTATGGACTGGAGAAGCTGTGCACTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGGATCGAGTGCCGCATTGGACGATTCCACA
        ||        |||      ||   |    |||||||   |||      |    |   |  || |||             |  |||  |||| |||||||| ||||| || ||||| ||    || || ||  | ||||||||||| | |||||||||||| || ||||||||||||||  | |||||||
gttagttggtgatcttttgaattgttcaatttatgttggttcttgattttcacattgggattgggattaatttgtttaattttgtgactttttttagCCTCAAGATGCATATGGGCTAGAGAAACTTGCAACAGAGGAATTATGCAAGCACTATAACAAGGATTTTGGAATTGAGTGCCGCATTGGGAGGTTCCACA

upper sequence: EFJ18599 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: Vv05s0020g04510.t01 (Vitis vinifera), 3'ss of exon 3
---------------gtatgaaaaagaaaaaaaaaaaaaaaaaaggttcttttcttttgtggggaatctaaaaacaaattgcactt-tgcagCCCCAAGATGCCTATGGACTGGAGAAGCTGTGCACTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGGATCGAGTGCCGCATTGGACGATTCCACA
                ||| ||||| |  |     ||| | |    ||      || |  |   ||   |  | |   ||||  || |  |||| ||||||||||||||  | ||||||||    ||||| ||| | |||||||||||||| ||||| ||||| || ||||| ||||||||||| ||||| |
gtttttcctctaatcttataaaaaatatcagttctaaatatattcatttgaggattattggcataactgatgagctttttgcttttgtttagCCTCAAGATGCCTATGGCTTAGAGAAGCTCGCAACTGAGGAGTTATGCAAGCACTACACTAAGGACTTTGGAATTGAGTGTCGCATTGGACGGTTCCATA

upper sequence: EFJ18599 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: EDP09235 (Chlamydomonas reinhardtii), 3'ss of exon 5
--------------------gtatgaaaaagaaaaaaaaa-aaaaaaaaaggttcttttcttttgtggggaatctaaaaacaaattgcactt---tgcagCCCCAAGATGCCTATGGACTGGAGAAGCTGTGCACTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGGATCGAGTGCCGCATTGGACGATTCCACA
                    |  ||     |            |     | |    | ||  |  ||     |  |    | ||  |   |     ||||||||||||||| || || ||||||||||||  ||| || ||||||||||||||||||| |||||| || || || ||||||||||| |  || |||||||
gtcctctcggccgtgtgtctgcgtgtcgccggctgcttgctgcaccgcgacgccgctgtcactgctgattcttacacctcccaaacgtcttcgcccgcagCCCCAAGATGCGTACGGCCTGGAGAAGCTGGCCACCGAGGAGCTGTGCAAGCACTACAACAAGGACTTCGGCATTGAGTGCCGCATCGCGCGCTTCCACA

upper sequence: EFJ18599 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S237_14V6.1 (Physcomitrella patens), 3'ss of exon 2
--------------------gtatgaaaaagaaaaaaaaaaaaaaaaaaggtt--cttttcttttgtggggaatctaaaaacaaattgcacttt--gcagCCCCAAGATGCCTATGGACTGGAGAAGCTGTGCACTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGGATCGAGTGCCGCATTGGACGATTCCACA
                    ||    |  ||        || |   |  | ||  | |   |||| |||       |   | || || |  ||   ||||||||||||||| || || || || ||| ||  ||| || ||| ||||||| || ||||| ||||| ||||| || |||||||||||||| || || ||||
cagtcgccacgcagttctctgtggtgaccagtgtccgcgaacatccattgctttacataatttttttggattgggcattgataagttacttttctggcagCCCCAAGATGCTTACGGTCTTGAAAAGTTGGCCACCGAGGAGTTGTGCAAACATTACACGAAGGACTTTGGCATGGAGTGCCGCATTGGTCGCTTTCACA

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|169041899|gb|FE449379.1|FE449379
EST:     AGTCAGATGCATGGCCGGCAGAG                         CCCCAAGATGCCTATGGACTGGAGAAGCTGTGCACTGAAGAGCTGTGCAAG
genomic: AGTCAGATGCATGGCCGGCAGAGgtatgaaaaa ... cactttgcagCCCCAAGATGCCTATGGACTGGAGAAGCTGTGCACTGAAGAGCTGTGCAAG
EST: gi|169064800|gb|FE476120.1|FE476120
EST:     AGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCGGCAGAG                         CCCCAAGATGCCTATGGACTGGAGAAGCTGTGCACTGAAGAGCTGTGCAAG
genomic: AGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCGGCAGAGgtatgaaaaa ... cactttgcagCCCCAAGATGCCTATGGACTGGAGAAGCTGTGCACTGAAGAGCTGTGCAAG
EST: gi|169064799|gb|FE476119.1|FE476119
EST:     AGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCGGCAGAG                         CCCCAAGATGCCTATGGACTGGAGAAGCTGTGCACTGAAGAGCTGTGCAAG
genomic: AGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCGGCAGAGgtatgaaaaa ... cactttgcagCCCCAAGATGCCTATGGACTGGAGAAGCTGTGCACTGAAGAGCTGTGCAAG

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: 31 (upstream exon), 29 (downstream exon)
Score: 9

ATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCGGCAGAGgtatgaaaaa ... cactttgcagCCCCAAGATGCCTATGGACTGGAGAAGCTGTGCACTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGGATCGAGTGCCGCATTGGACGATTCCACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaaaaaggttcttttcttttgtggggaatctaaaaacaaattgcactttgcagCCCCAAGATGCCTATGGACTGGAGAAGCTGTGCACTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGGATCGAGTGCCGCATTGGACGATTCCACA
                             atctaaa  putative branch site (score: 9)
                            aatctaaaaacaaatt  TA-rich tract