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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcacttaccacgtgatagtgttcaagtttaccgttttctttcttcgcagTGGTTTGGTGAGGCGGAGAAATATGTCAAGGCAGTATTTACTTTGGCCAGCAAAATCTCGCCAAGCGTGGTGTTCATTGACGAG

Basic information

species Selaginella moellendorffii
transcript EFJ34631
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ34631 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: GLYMA02G17410.1 (Glycine max), 3'ss of exon 17
----------------------------gtaagcacttacc-acgtgatagtgtt-caagtttaccgt--tttctttcttcgcagTGGTTTGGTGAGGCGGAGAAATATGTCAAGGCAGTATTTACTTTGGCCAGCAAAATCTCGCCAAGCGTGGTGTTCATTGACGAG
                             |  | | || |     || |   ||| ||||   | | |  |||  ||  | ||||||||||||||| |  |||||||||||||| ||||| ||| || |||||||||||||  | ||||| ||  | ||  ||||||||
gtatcaatattgtaaattactttttttgttgtgtatttccttgtatgcttcagttacaagaaaaacatggttttgtttgttgcagTGGTTTGGTGAAGGAGAGAAATATGTCAAAGCAGTCTTTTCTCTGGCCAGCAAAATTGCTCCAAGTGTTATTTTTGTTGACGAG

upper sequence: EFJ34631 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: GLYMA02G17400.1 (Glycine max), 3'ss of exon 18
-------------------------------------gtaagcacttaccacgtgatagtgttcaagtttaccgttttctttcttcgcagTGGTTTGGTGAGGCGGAGAAATATGTCAAGGCAGTATTTACTTTGGCCAGCAAAATCTCGCCAAGCGTGGTGTTCATTGACGAG
                                     |||    | |  ||     ||  ||   ||  ||  ||||| ||  |  ||||||||||||||| |  || ||||||||||| ||||| ||| || |||||||||||||  | ||||| ||  | ||  |||| |||
gtattagttgcaaatttaaactgttttgctctactctgtattttcctttcattcattaa-gtgacaggatattgtttttttgtt--gcagTGGTTTGGTGAAGGAGAAAAATATGTCAAAGCAGTCTTTTCTCTGGCCAGCAAAATTGCTCCAAGTGTTATTTTTGTTGATGAG

upper sequence: EFJ34631 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: GLYMA10G02410.1 (Glycine max), 3'ss of exon 18
-------------------------------------gtaagcacttaccacgtgatagtgttcaagtttaccgttttctttcttcgcagTGGTTTGGTGAGGCGGAGAAATATGTCAAGGCAGTATTTACTTTGGCCAGCAAAATCTCGCCAAGCGTGGTGTTCATTGACGAG
                                     |||    |||  ||      ||||      |  |   | || |||  | ||||||||||||||| |  || ||||||||||| ||||| ||| || |||||||||||||  | ||||| ||  | ||  |||| |||
gtattagttgcaaatttaaacagttttgctctactttgtatttcctt-tcattcataagtgacaggatagatattgtttttttgttgcagTGGTTTGGTGAAGGAGAAAAATATGTCAAAGCAGTCTTTTCTCTGGCCAGCAAAATTGCTCCAAGTGTTATTTTTGTTGATGAG

upper sequence: EFJ34631 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: AT4G24860.1 (Arabidopsis thaliana), 3'ss of exon 21
-------------------------gtaagcacttac-cacgtgatagtgt--tcaagtttaccgttttctttcttc-gcagTGGTTTGGTGAGGCGGAGAAATATGTCAAGGCAGTATTTACTTTGGCCAGCAAAATCTCGCCAAGCGTGGTGTTCATTGACGAG
                          ||   | |||| |||| |||  | |  ||||  ||    | |||||  | | |||||||||||||||||  ||||| |||||||| || || ||| |||||||||| ||||| || || |||||  | ||  | ||||||
gtaactgaatactctatgaaaagttctaccgatttacacacgggatctttttttcaaacttgtgttcttcttaatactgcagTGGTTTGGTGAGGGTGAGAAGTATGTCAAAGCTGTCTTTTCTTTGGCCAGTAAAATGTCCCCTAGCGTTATCTTTGTGGACGAG

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|169043401|gb|FE451338.1|FE451338
EST:     AGGCTGGTGCAAATTTCATCAATATTTCAATGTCCACAATTGCATCTAAA                         TGGTTTGGTGAGGCGGAGAAATATGTCAAGGCAGTATTTACTTTGGCCAGC
genomic: AGGCTGGTGCAAATTTCATCAATATTTCAATGTCCACAATTGCATCTAAAgtaagcactt ... ttcttcgcagTGGTTTGGTGAGGCGGAGAAATATGTCAAGGCAGTATTTACTTTGGCCAGC
EST: gi|169052464|gb|FE462272.1|FE462272
EST:     AGGCTGGTGCAAATTTCATCAATATTTCAATGTCCACAATTGCATCTAAA                         TGGTTTGGTGAGGCGGAGAAATATGTCAAGGCAGTATTTACTTTGGCCAGC
genomic: AGGCTGGTGCAAATTTCATCAATATTTCAATGTCCACAATTGCATCTAAAgtaagcactt ... ttcttcgcagTGGTTTGGTGAGGCGGAGAAATATGTCAAGGCAGTATTTACTTTGGCCAGC
EST: gi|169082585|gb|FE489069.1|FE489069
EST:     AGGCTGGTGCAAATTTCATCAATATTTCAATGTCCACAATTGCATCTAAA                         TGGTTTGGTGAGGCGGAGAAATATGTCAAGGCAGTATTTACTTTGGCCAGC
genomic: AGGCTGGTGCAAATTTCATCAATATTTCAATGTCCACAATTGCATCTAAAgtaagcactt ... ttcttcgcagTGGTTTGGTGAGGCGGAGAAATATGTCAAGGCAGTATTTACTTTGGCCAGC
EST: gi|169115759|gb|FE517345.1|FE517345
EST:     GGCTGGTGCAAA-TTCATCAAATATTTCAATGTCCACAATTGCATCTAAA                         TGGTTTGGTGAGGCGGAGAAATATGTCAAGGCAGTATTTACTTTGGCCAGC
genomic: GGCTGGTGCAAATTTCATC-AATATTTCAATGTCCACAATTGCATCTAAAgtaagcactt ... ttcttcgcagTGGTTTGGTGAGGCGGAGAAATATGTCAAGGCAGTATTTACTTTGGCCAGC
EST: gi|169107241|gb|FE504119.1|FE504119
EST:     AGGCTGGTGCAAATTTCATCAATATTTCAATGTCCACAATTGCATCTAAA                         TGGTTTGGTGAGGCGGAGAAATATGTCAAGGCAGTATTTACTTTGGCCAGC
genomic: AGGCTGGTGCAAATTTCATCAATATTTCAATGTCCACAATTGCATCTAAAgtaagcactt ... ttcttcgcagTGGTTTGGTGAGGCGGAGAAATATGTCAAGGCAGTATTTACTTTGGCCAGC
EST: gi|169076790|gb|FE485833.1|FE485833
EST:     CAATGTCCACAATTGCATCTAAA                         TGGTTTGGGGAGGCGGAGAAATATGTCAAGGCAGTATTTACTTTGGCCAGC
genomic: CAATGTCCACAATTGCATCTAAAgtaagcactt ... ttcttcgcagTGGTTTGGTGAGGCGGAGAAATATGTCAAGGCAGTATTTACTTTGGCCAGC
EST: gi|169081355|gb|FE489293.1|FE489293
EST:     AGGCTGGTGCAAATTTCATCAATATTTCAATGTCCACAATTGCATCTAAA                         TGGTTTGGTGAGGCGGAGAAATATGTCAAGGCAGTATTTACTTTGGCCAGC
genomic: AGGCTGGTGCAAATTTCATCAATATTTCAATGTCCACAATTGCATCTAAAgtaagcactt ... ttcttcgcagTGGTTTGGTGAGGCGGAGAAATATGTCAAGGCAGTATTTACTTTGGCCAGC
EST: gi|169064336|gb|FE471899.1|FE471899
EST:     AGGCTGGTGCAAATTTCATCAATATTTCAATGTCCACAATTGCATCTAAA                         TGGTTTGGTGAGGCGGAGAAATATGTCAAGGCAGTATTTACTTTGGCCAGC
genomic: AGGCTGGTGCAAATTTCATCAATATTTCAATGTCCACAATTGCATCTAAAgtaagcactt ... ttcttcgcagTGGTTTGGTGAGGCGGAGAAATATGTCAAGGCAGTATTTACTTTGGCCAGC
EST: gi|169064335|gb|FE471898.1|FE471898
EST:     GCAAATTTCATCAATATTTCAATGTCCACAATTGCATCTAAA                         TGGTTTGGTGAGGCGGAGAAATATGTCAAGGCAGTATTTACTTTGGCCAGC
genomic: GCAAATTTCATCAATATTTCAATGTCCACAATTGCATCTAAAgtaagcactt ... ttcttcgcagTGGTTTGGTGAGGCGGAGAAATATGTCAAGGCAGTATTTACTTTGGCCAGC

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), 33 (downstream exon)
Score: 15

TGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTTCAATGTCCACAATTGCATCTAAAgtaagcactt ... ttcttcgcagTGGTTTGGTGAGGCGGAGAAATATGTCAAGGCAGTATTTACTTTGGCCAGCAAAATCTCGCCAAGCGTGGTGTTCATTGACGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaagcacttaccacgtgatagtgttcaagtttaccgttttctttcttcgcagTGGTTTGGTGAGGCGGAGAAATATGTCAAGGCAGTATTTACTTTGGCCAGCAAAATCTCGCCAAGCGTGGTGTTCATTGACGAG
       cacttac  putative branch site (score: 15)
                                tttaccgttttctttc  putative PPT
                                       ttttcttt  TA-rich tract