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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcacggagtgctaaaatatttgttgcttaatgctcctcgtctgcagGCAATCAAGGCCAAGGAAGAAGGTCGTTCCATCCCGGAGTATGACTACCTCCCCTTCTTTTACTCCCGTGCTTTCGATCTGTCGTGGCAATTCTATGGTG

Basic information

species Selaginella moellendorffii
transcript EFJ06061
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ06061 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: GRMZM2G084881_T02 (Zea mays), 3'ss of exon 1
------------------------------------------gtaagtcacggagtg-ctaaaatatttgttgct-taatgct----cctcgt-ctgcagGCAATCAAGGCCAAGGAAGAAGGTCGTTCCATCCCGGAGTATGACTACCTCCCCTTCTTTTACTCCCGTGCTTTCGATCTGTCGTGGCAATTCTATGGTG
                                          || |  |     ||  | ||| |  |||      ||||| |    |||| |  | ||||| ||||||| ||| ||    |||    |  | ||||||||||||||||| || | ||| ||||||||  | ||||| ||| ||||||||||||| || |
cccccccccccaaaaaaaaaagtagtgtaattcatttatattgtcatccgtttggtatccaaattggttgcgatggtaatgttatggcctcttatttcagGCGATCAAGGGCAAAGAGTCCGGTGAACCAGTTCCGGAGTATGACTACCTGCCATACTTCTACTCCCGATCATTCGACCTGGCGTGGCAATTCTACGGCG

upper sequence: EFJ06061 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: GLYMA10G07820.1 (Glycine max), 3'ss of exon 9
-------------------------------------------------------------------------------------------------------------------------------------------gtaagtcacggagtgctaaaatatttgttgcttaatg----ctcctcgtctgcagGCAATCAAGGCCAAGGAAGAAGGTCGTTCCATCCCGGAGTATGACTACCTCCCCTTCTTTTACTCCCGTGCTTTCGATCTGTCGTGGCAATTCTATGGTG
                                                                                                                                              || ||  |  |||     | ||| |   |   ||    ||  |  | || |||| ||||||||    || |||||     |  |   ||||||||| ||||| || | ||| || |||||| | ||||||||||| |||||||||||||| |
gtaagtagcttacctaaatttgtcagctcatgcacaatatacatatttatcattgccccggcatgctctctctagctattcagtagatatctgcttaaacgttttttttttctggtcctccaaatcgaagtttcaagtaaagagccaatgcttgcagtgctgtttctcattctgtgattacttgttttatgtagGCCATCAAGGCAGCTGAGGAAGGAAAAACAGTTGAGGAGTATGATTACCTTCCATACTTCTATTCCCGTTCATTCGATCTGTCTTGGCAATTCTATGGCG

upper sequence: EFJ06061 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: Vv08s0007g03610.t01 (Vitis vinifera), 3'ss of exon 9
-------------------------------------------gtaagtcacggagtgctaaaat---atttgttgcttaatgctc-ctcgtct--gcagGCAATCAAGGCCAAGGAAGAAGGTCGTTCCATCCCGGAGTATGACTACCTCCCCTTCTTTTACTCCCGTGCTTTCGATCTGTCGTGGCAATTCTATGGTG
                                            | ||  | | | |  ||  |    ||  ||   ||| | ||  || || |  ||||||||||||||| |  || |||||    ||  |   ||||||||||||||| || | ||| ||||| ||||| || |||||||| ||||| ||||||||||
ctttttttctgccatgatcattccttaggtgctcaaaatatacattagatatgcatttttaggagtgaatcagtgaattacttctggcttgtttatgcagGCAATCAAGGCAAGTGAGGAAGGGAAATCAGTTGAGGAGTATGACTACCTTCCATACTTCTACTCTCGTGCCTTTGATCTGTCCTGGCAGTTCTATGGTG

upper sequence: EFJ06061 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: PP1S237_59V6.1 (Physcomitrella patens), 3'ss of exon 10
--------------------------------------------------------------------------------gtaagtcacggagtgctaaaatatttgttgcttaatgctcctcgtctgcagGCAATCAAGGCCAAGGAAGAAGGTCGTTCCATCCCGGAGTATGACTACCTCCCCTTCTTTTACTCCCGTGCTTTCGATCTGTCGTGGCAATTCTATGGTG
                                                                                |||| |||||      | | || |    || | ||       ||  | ||||| ||||| |||   ||  ||||     |  |    || || |||||||| |||||||||||||| ||  ||||||| || || |||||||||||||| |
gtttgtaatataacccaagttttcgtccaatcggtattctaccccgtgtattctggtaatttaactcttacattttcgttgtaaatcacg---cctttatat-tgaaatgttcaaattgttgcgaatccagGCCATCAAAGCCGCTGAGAAAGGCGAAACTGTGGACGACTACGACTACCTGCCCTTCTTTTACTCACGATCTTTCGACCTCTCATGGCAATTCTATGGAG

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|169101972|gb|FE507782.1|FE507782
EST:     GAGTTGAGCACGTCGATCACTCCAGAAAATCAGCTATTCAAGCTGTGCAG                         GCAATCAAGGCCAAGGAAGAAGGTCGTTCCATCCCGGAGTATGACTACCTC
genomic: GAGTTGAGCACGTCGATCACTCCAGAAAATCAGCTATTCAAGCTGTGCAGgtaagtcacg ... tcgtctgcagGCAATCAAGGCCAAGGAAGAAGGTCGTTCCATCCCGGAGTATGACTACCTC
EST: gi|169066869|gb|FE473649.1|FE473649
EST:     GAGTTGAGCACGTCGATCACTCCAGAAAATCAGCTATTCAAGCTGTGCAG                         GCAATCAAGGCCAAGGAAGAAGGTCGTTCCATCCCGGAGTATGACTACCTC
genomic: GAGTTGAGCACGTCGATCACTCCAGAAAATCAGCTATTCAAGCTGTGCAGgtaagtcacg ... tcgtctgcagGCAATCAAGGCCAAGGAAGAAGGTCGTTCCATCCCGGAGTATGACTACCTC
EST: gi|169054711|gb|FE460507.1|FE460507
EST:     GAGTTGAGCACGTCGATCACTCCAGAAAATCAGCTATTCAAGCTGTGCAG                         GCAATCAAGGCCAAGGAAGAAGGTCGTTCCATCCCGGAGTATGACTACCTC
genomic: GAGTTGAGCACGTCGATCACTCCAGAAAATCAGCTATTCAAGCTGTGCAGgtaagtcacg ... tcgtctgcagGCAATCAAGGCCAAGGAAGAAGGTCGTTCCATCCCGGAGTATGACTACCTC
EST: gi|169050020|gb|FE458112.1|FE458112
EST:     GAGTTGAGCACGTCGATCACTCCAGAAAATCAGCTATTCAAGCTGTGCAG                         GCAATCAAGGCCAAGGAAGAAGGTCGTTCCATCCCGGAGTATGACTACCTC
genomic: GAGTTGAGCACGTCGATCACTCCAGAAAATCAGCTATTCAAGCTGTGCAGgtaagtcacg ... tcgtctgcagGCAATCAAGGCCAAGGAAGAAGGTCGTTCCATCCCGGAGTATGACTACCTC
EST: gi|169055396|gb|FE463766.1|FE463766
EST:     GAGTTGAGCACGTCGATCACTCCAGAAAATCAGCTATTCAAGCTGTGCAG                         GCAATCAAGGCCAAGGAAGAAGGTCGTTCCATCCCGGAGTATGACTACCTC
genomic: GAGTTGAGCACGTCGATCACTCCAGAAAATCAGCTATTCAAGCTGTGCAGgtaagtcacg ... tcgtctgcagGCAATCAAGGCCAAGGAAGAAGGTCGTTCCATCCCGGAGTATGACTACCTC
EST: gi|169098861|gb|FE502258.1|FE502258
EST:     GAGTTGAGCACGTCGATCACTCCAGAAAATCAGCTATTCAAGCTGTGCAG                         GCAATCAAGGCCAAGGAAGAAGGTCGTTCCATCCCGGAGTATGACTACCTC
genomic: GAGTTGAGCACGTCGATCACTCCAGAAAATCAGCTATTCAAGCTGTGCAGgtaagtcacg ... tcgtctgcagGCAATCAAGGCCAAGGAAGAAGGTCGTTCCATCCCGGAGTATGACTACCTC
EST: gi|169041821|gb|FE449340.1|FE449340
EST:     GAGTTGAGCACGTCGATCACTCCAGAAAATCAGCTATTCAAGCTGTGCAG                         GCAATCAAGGCCAAGGAAGAAGGTCGTTCCATCCCGGAGTATGACTACCTC
genomic: GAGTTGAGCACGTCGATCACTCCAGAAAATCAGCTATTCAAGCTGTGCAGgtaagtcacg ... tcgtctgcagGCAATCAAGGCCAAGGAAGAAGGTCGTTCCATCCCGGAGTATGACTACCTC
EST: gi|169066650|gb|FE475432.1|FE475432
EST:     GAGTTGAGCACGTCGATCACTCCAGAAAATCAGCTATTCAAGCTGTGCAG                         GCAATCAAGGCCAAGGAAGAAGGTCGTTCCATCCCGGAGTATGACTACCTC
genomic: GAGTTGAGCACGTCGATCACTCCAGAAAATCAGCTATTCAAGCTGTGCAGgtaagtcacg ... tcgtctgcagGCAATCAAGGCCAAGGAAGAAGGTCGTTCCATCCCGGAGTATGACTACCTC

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: 48

AGTTGGAGATATCGCAACGTTTCCGATGAAAATCTATGGAGAGCAGAGGAGAGTTGAGCACGTCGATCACTCCAGAAAATCAGCTATTCAAGCTGTGCAGgtaagtcacg ... tcgtctgcagGCAATCAAGGCCAAGGAAGAAGGTCGTTCCATCCCGGAGTATGACTACCTCCCCTTCTTTTACTCCCGTGCTTTCGATCTGTCGTGGCAATTCTATGGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaagtcacggagtgctaaaatatttgttgcttaatgctcctcgtctgcagGCAATCAAGGCCAAGGAAGAAGGTCGTTCCATCCCGGAGTATGACTACCTCCCCTTCTTTTACTCCCGTGCTTTCGATCTGTCGTGGCAATTCTATGGTG
                                            ctcctcgtct  CT-rich tract
                    taaaatatttgtt  TA-rich tract