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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctcgcaaatctctttgcgtgatcgttgttttggtttctataagttttgggtgtgcgttgtttcagGCCGCCACTGATACTGCTTCGACCGATCTGCCTCCTACGCATCCAATTCGGCTTGGGCTGGCACTGAACTTCTCAGTTTTCTACTACGAGATACTCAACT

Basic information

species Selaginella moellendorffii
transcript EFJ35972
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ35972 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA07G35240.1 (Glycine max), 3'ss of exon 3
-----------------------------------------gtaagctcgcaaatctctttgcgtg---atcgttgttttggtttctataagttttgggtgtgcgttgtt-tcagGCCGCCACTGATACTGCTTCGACCGATCTGCCTCCTACGCATCCAATTCGGCTTGGGCTGGCACTGAACTTCTCAGTTTTCTACTACGAGATACTCAACT
                                          ||       || |   | ||  |    ||  ||| | | |||  |  | |||     | |  ||| |  | |||| ||    | ||||||    || ||||| ||  | || |||||||| || ||||| || ||||| ||||||||||| ||||| || |||||||| ||||
gttggtgtatgatatctctcatttcagcaaagaactgcttcatacatatataatttcttgtgtttatctatatttggtgttgttgtttgatgttcaaactat-tgttatcattagGCTGCTTTAGCTACTGCAAGCACAGATCTTCCATCAACACATCCAATCCGTCTTGGACTTGCACTCAACTTCTCAGTCTTCTATTATGAGATACTGAACT

upper sequence: EFJ35972 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S67_176V6.1 (Physcomitrella patens), 3'ss of exon 3
---------------------------------------------------------------------------------------------------------------------gtaagctcgcaaatctctttgcgtgatcgttgtttt---ggtttctataagttttgggtgtgcgttgtttcagGCCGCCACTGATACTGCTTCGACCGATCTGCCTCCTACGCATCCAATTCGGCTTGGGCTGGCACTGAACTTCTCAGTTTTCTACTACGAGATACTCAACT
                                                                                                                       |    ||    ||   |  || |   |     ||   ||   || |||  |     || | ||     ||||| ||  |  |||| ||  |||| ||  |  | || || || || || || |||||||| ||||| ||||||||||| |||||||| |||||  | ||||
gtgtgtgtcgctggattatgttgtcttcgattggacattgagtgtcgtggatttaaatgtttctagtagtatcacattctagaaaggccaatgctggcgttagacagttgcagtttctcacatgcgtgcgtcctgtgacgcggctgcctccttatgggggcctgtaacat---aatgcgtgtgtgcgcagGCTGCATCCAATACAGCCACGACGGACTTAGCGCCCACCCACCCTATCCGACTTGGGCTCGCACTTAACTTCTCAGTGTTCTACTATGAGATTTTGAACT
















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|169037539|gb|FE446280.1|FE446280
EST:     CCGGTAACGAAAGAAAGGAGGCGGCCGATCAATCATTCAAGGCTTACCAG                         GCCGCCACTGATACTGCTTCGACCGATCTGCCTCCTACGCATCCAATTCGG
genomic: CCGGTAACGAAAGAAAGGAGGCGGCCGATCAATCATTCAAGGCTTACCAGgtaagctcgc ... gttgtttcagGCCGCCACTGATACTGCTTCGACCGATCTGCCTCCTACGCATCCAATTCGG
EST: gi|169043569|gb|FE452663.1|FE452663
EST:     CCGGTAACGAAAGAAAGGAGGCGGCCGATCAATCATTCAAGGCTTACCAG                         GCCGCCACTGATACTGCTTCGACCGATCTGCCTCCTACGCATCCAATTCGG
genomic: CCGGTAACGAAAGAAAGGAGGCGGCCGATCAATCATTCAAGGCTTACCAGgtaagctcgc ... gttgtttcagGCCGCCACTGATACTGCTTCGACCGATCTGCCTCCTACGCATCCAATTCGG
EST: gi|169096262|gb|FE497848.1|FE497848
EST:     CCGGTAACGAAAGAAAGGAGGCGGCCGATCAATCATTCAAGGCTTACCAG                         GCCGCCACTGATACTGCTTCGACCGATCTGCCTCCTACGCATCCAATTCGG
genomic: CCGGTAACGAAAGAAAGGAGGCGGCCGATCAATCATTCAAGGCTTACCAGgtaagctcgc ... gttgtttcagGCCGCCACTGATACTGCTTCGACCGATCTGCCTCCTACGCATCCAATTCGG
EST: gi|169034332|gb|FE443105.1|FE443105
EST:     CCGGTAACGAAAGAAAGGAGGCGGCCGATCAATCATTCAAGGCTTACCAG                         GCCGCCACTGATACTGCTTCGACCGATCTGCCTCCTACGCATCCAATTCGG
genomic: CCGGTAACGAAAGAAAGGAGGCGGCCGATCAATCATTCAAGGCTTACCAGgtaagctcgc ... gttgtttcagGCCGCCACTGATACTGCTTCGACCGATCTGCCTCCTACGCATCCAATTCGG
EST: gi|169034593|gb|FE446473.1|FE446473
EST:     CCGGTAACGAAAGAAAGGAGGCGGCCGATCAATCATTCAAGGCTTACCAG                         GCCGCCACTGATACTGCTTCGACCGATCTGCCTCCTACGCATCCAATTCGG
genomic: CCGGTAACGAAAGAAAGGAGGCGGCCGATCAATCATTCAAGGCTTACCAGgtaagctcgc ... gttgtttcagGCCGCCACTGATACTGCTTCGACCGATCTGCCTCCTACGCATCCAATTCGG
EST: gi|169051570|gb|FE458453.1|FE458453
EST:     CCGGTAACGAAAGAAAGGAGGCGGCCGATCAATCATTCAAGGCTTACCAG                         GCCGCCACTGATACTGCTTCGACCGATCTGCCTCCTACGCATCCAATTCGG
genomic: CCGGTAACGAAAGAAAGGAGGCGGCCGATCAATCATTCAAGGCTTACCAGgtaagctcgc ... gttgtttcagGCCGCCACTGATACTGCTTCGACCGATCTGCCTCCTACGCATCCAATTCGG
EST: gi|169111479|gb|FE510339.1|FE510339
EST:     CCGGTAACGAAAGAAAGGAGGCGGCCGATCAATCATTCAAGGCTTACCAG                         GCCGCCACTGATACTGCTTCGACCGATCTGCCTCCTACGCATCCAATTCGG
genomic: CCGGTAACGAAAGAAAGGAGGCGGCCGATCAATCATTCAAGGCTTACCAGgtaagctcgc ... gttgtttcagGCCGCCACTGATACTGCTTCGACCGATCTGCCTCCTACGCATCCAATTCGG

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: 34 (upstream exon), 35 (downstream exon)
Score: 56

GAAAGGAGACTACTTCCGTTATCTCGCGGAGTTCAAGACCGGTAACGAAAGAAAGGAGGCGGCCGATCAATCATTCAAGGCTTACCAGgtaagctcgc ... gttgtttcagGCCGCCACTGATACTGCTTCGACCGATCTGCCTCCTACGCATCCAATTCGGCTTGGGCTGGCACTGAACTTCTCAGTTTTCTACTACGAGATACTCAACT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttgcgtgatcgttgttttggtttctataagttttgggtgtgcgttgtttcagGCCGCCACTGATACTGCTTCGACCGATCTGCCTCCTACGCATCCAATTCGGCTTGGGCTGGCACTGAACTTCTCAGTTTTCTACTACGAGATACTCAACT
                                              ttgtttc  CT-rich tract
                       tttctataagtttt  TA-rich tract