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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttggcgttccaaaatcttgtctcggtctcgagccaacttttcgggcgtttcttttgcagACTTTAACCTTTGCGTGGGTGAACTTCTTCTTCTCCGGATTTGTCACCG

Basic information

species Selaginella moellendorffii
transcript EFJ16068
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ16068 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: AT4G12590.1 (Arabidopsis thaliana), 3'ss of exon 3
---------gtttggcgt------tccaaaatcttgtctc---ggtc-tcgagccaacttttcgggcgtttc-ttttgcagACTTTAACCTTTGCGTGGGTGAACTTCTTCTTCTCCGGATTTGTCACCG
          ||||   |      || |   | |||  |    |||| |  |   ||||  |    | |  | ||||||||||  | || ||||| ||||| |||||||||||||| ||||||||  | |
gtgagttgtatttgaaatgtttcatctatgtttttgcgttactggtcatttaagaaactgatatcacttaccattttgcagACACTCACTTTTGCATGGGTCAACTTCTTCTTCTCTGGATTTGTTGCAG
















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|169103763|gb|FE506128.1|FE506128
EST:     ACATGGCAATGGACATGATGAAGAAGAACTTGTCCATGATCATTCCTCAG                         ACTTTAACCTTTGCGTGGGTGAACTTCTTCTTCTCCGGATTTGTCACCG
genomic: ACATGGCAATGGACATGATGAAGAAGAACTTGTCCATGATCATTCCTCAGgtttggcgtt ... tcttttgcagACTTTAACCTTTGCGTGGGTGAACTTCTTCTTCTCCGGATTTGTCACCG
EST: gi|169054694|gb|FE461634.1|FE461634
EST:     ACATGGCAATGGACATGATGAAGAAGAACTTGTCCATGATCATTCCTCAG                         ACTTTAACCTTTGCGTGGGTGAACTTCTTCTTCTCCGGATTTGTCACCG
genomic: ACATGGCAATGGACATGATGAAGAAGAACTTGTCCATGATCATTCCTCAGgtttggcgtt ... tcttttgcagACTTTAACCTTTGCGTGGGTGAACTTCTTCTTCTCCGGATTTGTCACCG
EST: gi|169102913|gb|FE505278.1|FE505278
EST:     ACATGGCAATGGACATGATGAAGAAGAACTTGTCCATGATCATTCCTCAG                         ACTTTAACCTTTGCGTGGGTGAACTTCTTCTTCTCCGGATTTGTCACCG
genomic: ACATGGCAATGGACATGATGAAGAAGAACTTGTCCATGATCATTCCTCAGgtttggcgtt ... tcttttgcagACTTTAACCTTTGCGTGGGTGAACTTCTTCTTCTCCGGATTTGTCACCG
EST: gi|169078345|gb|FE490378.1|FE490378
EST:     ACATGGCAATGGACATGATGAAGAAGAACTTGTCCATGATCATTCCTCAG                         ACTTTAACCTTTGCGTGGGTGAACTTCTTCTTCTCCGGATTTGTCACCG
genomic: ACATGGCAATGGACATGATGAAGAAGAACTTGTCCATGATCATTCCTCAGgtttggcgtt ... tcttttgcagACTTTAACCTTTGCGTGGGTGAACTTCTTCTTCTCCGGATTTGTCACCG
EST: gi|169076017|gb|FE480999.1|FE480999
EST:     ACATGGCAATGGACATGATGAAGAAGAACTTGTCCATGATCATTCCTCAG                         ACTTTAACCTTTGCGTGGGTGAACTTCTTCTTCTCCGGATTTGTCACCG
genomic: ACATGGCAATGGACATGATGAAGAAGAACTTGTCCATGATCATTCCTCAGgtttggcgtt ... tcttttgcagACTTTAACCTTTGCGTGGGTGAACTTCTTCTTCTCCGGATTTGTCACCG
EST: gi|169070878|gb|FE480662.1|FE480662
EST:     ACATGGCAATGGACATGATGAAGAAGAACTTGTCCATGATCATTCCTCAG                         ACTTTAACCTTTGCGTGGGTGAACTTCTTCTTCTCCGGATTTGTCACCG
genomic: ACATGGCAATGGACATGATGAAGAAGAACTTGTCCATGATCATTCCTCAGgtttggcgtt ... tcttttgcagACTTTAACCTTTGCGTGGGTGAACTTCTTCTTCTCCGGATTTGTCACCG

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), 33 (downstream exon)
Score: 16

TCCAAAGGGCCAGGGCCAGAACGTCCAGGCTCAAATGCTTTCGGACCCAAACATGGCAATGGACATGATGAAGAAGAACTTGTCCATGATCATTCCTCAGgtttggcgtt ... tcttttgcagACTTTAACCTTTGCGTGGGTGAACTTCTTCTTCTCCGGATTTGTCACCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgttccaaaatcttgtctcggtctcgagccaacttttcgggcgtttcttttgcagACTTTAACCTTTGCGTGGGTGAACTTCTTCTTCTCCGGATTTGTCACCG
                                         cgtttctttt  CT-rich tract
      aaaatctt  TA-rich tract