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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGTTTGACCTTTTTCGCACCCAGCGAGGAGAGACTTGAGTCAGGTTTATACAGCCGAAGCTACTTGGAGAACCAGATGGCGGTGGCTCTTGGTGGAAGgtacgtgatctaaacttcccattttctttgctttaagcgtgcgattccag

Basic information

species Selaginella moellendorffii
transcript EFJ31931
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ31931 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: LOC_Os06g51029.1 (Oryza sativa), 5'ss of exon 3
GAGGTTTGACCTTTTTCGCACCCAGCGAGGAGAGACTTGAGTCAGGTTTATACAGCCGAAGCTACTTGGAGAACCAGATGGCGGTGGCTCTTGGTGGAAGgtacg---tgatctaaacttcccattttctt---tgctttaagcgtgcgattccag---------------------------------
| ||  | || || || || || ||||||||||| |||||||| || || |||||| | |||||| | |||||||| ||||| || ||||||||||||||||  |   |  |  ||  |||  || | | |   ||   ||    ||   | | |                                  
GTGGACTCACATTCTTTGCTCCAAGCGAGGAGAGGCTTGAGTCTGGATTGTACAGCAGGAGCTACCTAGAGAACCAAATGGCCGTAGCTCTTGGTGGAAGgtgggttttagtgaaatgttcatatctgcgtacatgtgctattgttgttgtgcaaagtcttgaactgtgtgagcttacatggtttgcag

upper sequence: EFJ31931 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: AT5G42270.1 (Arabidopsis thaliana), 5'ss of exon 3
GAGGTTTGACCTTTTTCGCACCCAGCGAGGAGAGACTTGAGTCAGGTTTATACAGCCGAAGCTACTTGGAGAACCAGATGGCGGTGGCTCTTGGTGGAAGgta---cgtgatctaaacttcccattttctttgctttaagcgtgcgattccag------------------------------------
| ||  | ||||||||||| || ||||| ||||| || ||||| || || || ||| |||||||| | |||||||| ||||| || || ||||||||||||||       |   |||||   |   || |    |  ||| ||    ||| ||                                    
GTGGGCTCACCTTTTTCGCTCCTAGCGAAGAGAGGCTAGAGTCCGGATTGTATAGCAGAAGCTACCTTGAGAACCAAATGGCTGTTGCACTTGGTGGAAGgtagtttacaactgaaactgtactggttttgatttacaagagtagtcttcgagtgttaaacaatgtttattgtgtttcacctatggtag
















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|169071577|gb|FE479138.1|FE479138
EST:     TACAGCCGAAGCTACTTGGAGAACCAGATGGCGGTGGCTCTTGGTGGAAG                         GATCGCGGAGGAGGTGATCTTCGGCCCCGAGAACGTCACCACCGGAGCTTC
genomic: TACAGCCGAAGCTACTTGGAGAACCAGATGGCGGTGGCTCTTGGTGGAAGgtacgtgatc ... gcgattccagGATCGCGGAGGAGGTGATCTTCGGCCCCGAGAACGTCACCACCGGAGCTTC
EST: gi|169040866|gb|FE447917.1|FE447917
EST:     TACAGCCGAAGCTACTTGGAGAACCAGATGGCGGTGGCTCTTGGTGGAAG                         GATCGCGGAGGAGGTGATCTTCGGCCCCGAGAACGTCACCACCGGAGCTTC
genomic: TACAGCCGAAGCTACTTGGAGAACCAGATGGCGGTGGCTCTTGGTGGAAGgtacgtgatc ... gcgattccagGATCGCGGAGGAGGTGATCTTCGGCCCCGAGAACGTCACCACCGGAGCTTC
EST: gi|169050495|gb|FE459602.1|FE459602
EST:     TACAGCCGAAGCTACTTGGAGAACCAGATGGCGGTGGCTCTTGGTGGAAG                         GATCGCGGAGGAGGTGATCTTCGGCCCCGAGAACGTCACCACCGGAGCTTC
genomic: TACAGCCGAAGCTACTTGGAGAACCAGATGGCGGTGGCTCTTGGTGGAAGgtacgtgatc ... gcgattccagGATCGCGGAGGAGGTGATCTTCGGCCCCGAGAACGTCACCACCGGAGCTTC
EST: gi|169029308|gb|FE439436.1|FE439436
EST:     TACAGCCGAAGCTACTTGGAGAACCAGATGGCGGTGGCTCTTGGTGGAAG                         GATCGCGGAGGAGGTGATCTTCGGCCCCGAGAACGTCACCACCGGAGCTTC
genomic: TACAGCCGAAGCTACTTGGAGAACCAGATGGCGGTGGCTCTTGGTGGAAGgtacgtgatc ... gcgattccagGATCGCGGAGGAGGTGATCTTCGGCCCCGAGAACGTCACCACCGGAGCTTC
EST: gi|169067885|gb|FE474756.1|FE474756
EST:     TACAGCCGAAGCTACTTGGAGAACCAGATGGCGGTGGCTCTTGGTGGAAG                         GATCGCGGAGGAGGTGATCTTCGGCCCCGAGAACGTCACCACCGGAGCTTC
genomic: TACAGCCGAAGCTACTTGGAGAACCAGATGGCGGTGGCTCTTGGTGGAAGgtacgtgatc ... gcgattccagGATCGCGGAGGAGGTGATCTTCGGCCCCGAGAACGTCACCACCGGAGCTTC
EST: gi|169082831|gb|FE486260.1|FE486260
EST:     TACAGCCGAAGCTACTTGGAGAACCAGATGGCGGTGGCTCTTGGTGGAAG                         GATCGCGGAGGAGGTGATCTTCGGCCCCGAGAACGTCACCACCGGAGCTTC
genomic: TACAGCCGAAGCTACTTGGAGAACCAGATGGCGGTGGCTCTTGGTGGAAGgtacgtgatc ... gcgattccagGATCGCGGAGGAGGTGATCTTCGGCCCCGAGAACGTCACCACCGGAGCTTC
EST: gi|169044422|gb|FE451059.1|FE451059
EST:     TACAGCCGAAGCTACTTGGAGAACCAGATGGCGGTGGCTCTTGGTGGAAG                         GATCGCGGAGGAGGTGATCTTCGGCCCCGAGAACGTCACCACCGGAGCTTC
genomic: TACAGCCGAAGCTACTTGGAGAACCAGATGGCGGTGGCTCTTGGTGGAAGgtacgtgatc ... gcgattccagGATCGCGGAGGAGGTGATCTTCGGCCCCGAGAACGTCACCACCGGAGCTTC
EST: gi|169049265|gb|FE459541.1|FE459541
EST:     TACAGCCGAAGCTACTTGGAGAACCAGATGGCGGTGGCTCTTGGTGGAAG                         GATCGCGGAGGAGGTGATCTTCGGCCCCGAGAACGTCACCACCGGAGCTTC
genomic: TACAGCCGAAGCTACTTGGAGAACCAGATGGCGGTGGCTCTTGGTGGAAGgtacgtgatc ... gcgattccagGATCGCGGAGGAGGTGATCTTCGGCCCCGAGAACGTCACCACCGGAGCTTC
EST: gi|169078967|gb|FE489687.1|FE489687
EST:     TACAGCCGAAGCTACTTGGAGAACCAGATGGCGGTGGCTCTTGGGGGAAG                         AATCGCGGAGGAGGTGATCTTCGGCCCCGAGAACGTCACCACCGGAGCTTC
genomic: TACAGCCGAAGCTACTTGGAGAACCAGATGGCGGTGGCTCTTGGTGGAAGgtacgtgatc ... gcgattccagGATCGCGGAGGAGGTGATCTTCGGCCCCGAGAACGTCACCACCGGAGCTTC

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: 33 (upstream exon), 35 (downstream exon)
Score: 54

GAGGTTTGACCTTTTTCGCACCCAGCGAGGAGAGACTTGAGTCAGGTTTATACAGCCGAAGCTACTTGGAGAACCAGATGGCGGTGGCTCTTGGTGGAAGgtacgtgatc ... gcgattccagGATCGCGGAGGAGGTGATCTTCGGCCCCGAGAACGTCACCACCGGAGCTTCAAACGATTTCCAGCAAGTGTCGCGAGTTGCACGCCAGATGGTGGAGCGA




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGGTTTGACCTTTTTCGCACCCAGCGAGGAGAGACTTGAGTCAGGTTTATACAGCCGAAGCTACTTGGAGAACCAGATGGCGGTGGCTCTTGGTGGAAGgtacgtgatctaaacttcccattttctttgctttaagcgtgcgattccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG