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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgatttttattttcgcggcgtgttttctacgttcttacatttgtcattgtctttgtgaagGTTCTCAAAGCAGGTGTGTTGGATCCAGAGACAACGGTGGTGGCAATCTTCCCCTCGCCAATGCATTACGCCGGGCCAACGGAAGTCCAATGGCACGCCA

Basic information

species Selaginella moellendorffii
transcript EFJ22935
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ22935 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os03g53230.1 (Oryza sativa), 3'ss of exon 2
-----------------------------------------------------------------------------gtttgattt--ttattttcgcggcgtgttttctacgttcttacatttgtcat---tgtctttgtgaagGTTCTCAAAGCAGGTGTGTTGGATCCAGAGACAACGGTGGTGGCAATCTTCCCCTCGCCAATGCATTACGCCGGGCCAACGGAAGTCCAATGGCACGCCA
                                                                              ||||||||  |||   |   |    |     | | | |  |  ||||       | | |||  | |||||||  | | ||||||  |  | |||||  |||| || || |||||||||||||| ||||||||||| || |||||||| ||||| |||||||| || |
gtacgctttaagagtagcaatcgtactgtcaaatctttttagcaaatgcatgttggtgccttgttgttgatgaaaccatttgatttaattacactactgtaaggcccaattcatgcacaattttgatgcgtgtttattttggtagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTCGTTGCAATCTTCCCCTCTCCAATGCATTATGCAGGGCCAACTGAAGTGCAATGGCATGCTA

upper sequence: EFJ22935 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S166_97V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------------------------------------------------------------------------------------gtttgatttt-tattttcgcggcgtgttttctacgttcttacatttgtcattgtctttgtgaagGTTCTCAAAGCAGGTGTGTTGGATCCAGAGACAACGGTGGTGGCAATCTTCCCCTCGCCAATGCATTACGCCGGGCCAACGGAAGTCCAATGGCACGCCA
                                                                                                     || | |  |  ||||  |   ||  | | ||  | ||      |      || |  || |||| ||   ||| || ||| | || || | ||| || |||||||| |||||||| || || ||||| ||||| || |||||||| || |||||||||||||
gtttttaatccatctactaggtcttatgattatcctttagttctacgtgtgttacgataccttactcagcgaaattgagcttgcgaattttaagtcataactgctgtaatgctttcctgagctgggtacaacactgttctgac-gcagcaatcatattgcagGTCCTTGCAGCCGGAGTGCTAGACCCTGCGACCACTGTGGTGGCTATCTTCCCGTCTCCTATGCACTACGCTGGACCAACGGAGGTGCAATGGCACGCCA
















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|169071541|gb|FE480467.1|FE480467
EST:     CAAAGGCCGACGATGTTCCTCTCGAGTGGCGTATGAGGCAGCACGACGAG                         GTTCTCAAAGCAGGTGTGTTGGATCCAGAGACAACGGTGGTGGCAATCTTC
genomic: CAAAGGCCGACGATGTTCCTCTCGAGTGGCGTATGAGGCAGCACGACGAGgtttgatttt ... ctttgtgaagGTTCTCAAAGCAGGTGTGTTGGATCCAGAGACAACGGTGGTGGCAATCTTC
EST: gi|169095221|gb|FE496677.1|FE496677
EST:     CAAAGGCCGACGATGTTCCTCTCGAGTGGCGTATGAGGCAGCACGACGAG                         GTTCTCAAAGCAGGTGTGTTGGATCCAGAGACAACGGTGGTGGCAATCTTC
genomic: CAAAGGCCGACGATGTTCCTCTCGAGTGGCGTATGAGGCAGCACGACGAGgtttgatttt ... ctttgtgaagGTTCTCAAAGCAGGTGTGTTGGATCCAGAGACAACGGTGGTGGCAATCTTC
EST: gi|169095222|gb|FE496678.1|FE496678
EST:     CAAAGGCCGACGATGTTCCTCTCGAGTGGCGTATGAGGCAGCACGACGAG                         GTTCTCAAAGCAGGTGTGTTGGATCCAGAGACAACGGTGGTGGCAATCTTC
genomic: CAAAGGCCGACGATGTTCCTCTCGAGTGGCGTATGAGGCAGCACGACGAGgtttgatttt ... ctttgtgaagGTTCTCAAAGCAGGTGTGTTGGATCCAGAGACAACGGTGGTGGCAATCTTC
EST: gi|169100400|gb|FE501301.1|FE501301
EST:     CGAGTGGCGTATGAGGCAGCACGACGAG                         GTTCTCAAAGCAGGTGTGTTGGATCCAGAGACAACGGTGGTGGCAATCTTC
genomic: CGAGTGGCGTATGAGGCAGCACGACGAGgtttgatttt ... ctttgtgaagGTTCTCAAAGCAGGTGTGTTGGATCCAGAGACAACGGTGGTGGCAATCTTC

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: 29 (upstream exon), 30 (downstream exon)
Score: 11

GATGGGGTATAAGAATCCAATTCTACTGCTCCATCCTCTTGGTGGCTTCACAAAGGCCGACGATGTTCCTCTCGAGTGGCGTATGAGGCAGCACGACGAGgtttgatttt ... ctttgtgaagGTTCTCAAAGCAGGTGTGTTGGATCCAGAGACAACGGTGGTGGCAATCTTCCCCTCGCCAATGCATTACGCCGGGCCAACGGAAGTCCAATGGCACGCCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttattttcgcggcgtgttttctacgttcttacatttgtcattgtctttgtgaagGTTCTCAAAGCAGGTGTGTTGGATCCAGAGACAACGGTGGTGGCAATCTTCCCCTCGCCAATGCATTACGCCGGGCCAACGGAAGTCCAATGGCACGCCA
                          ttcttac  putative branch site (score: 11)
                                         ttgtcttt  putative PPT
                             ttacattt  TA-rich tract