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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtcaccccatacttgtatcatttgttcgtgtctcaagtgctgttttccagGTTTTTAACAACAGTCCAGACGAGACTGCGCACTTCAGAATCCTTTTAGACAGAGAAACAGTGACGAATTCCCTGTTGATGATTCAACCGTCCCTCGTGT

Basic information

species Selaginella moellendorffii
transcript EFJ32207
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ32207 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: GLYMA18G00670.1 (Glycine max), 3'ss of exon 9
--------------------------gttagtcaccccatacttgtatca--tttgttcgtgtctcaagtgctgttttccagGTTTTTAACAACAGTCCAGACGAGACTGCGCACTTCAGAATCCTTTTAGACAGAGAAACAGTGACGAATTCCCTGTTGATGATTCAACCGTCCCTCGTGT
                          ||    |    || ||||   | |  |||||  |||| | || ||    ||  ||||||||||||||||||||||||||||||||  | ||| | ||  | |||||||| ||||   | |  ||| |     | |||||||| |||||  |  | |
gtaccttttgttgtaatttacttcctgtcctgcttttcaaacttcatttaactttgtcagtgt-tgaaatgtg--ttggcagGTTTTTAACAACAGTCCAGACGAGACTGCATATTTCCGCATGTTGTTAGACAGGGAAAATATTAGTAATGCTGCCGTTATGATTCAGCCGTCATTGATAT

upper sequence: EFJ32207 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: GLYMA11G36760.1 (Glycine max), 3'ss of exon 9
--------------------------gttagtcaccccatacttgtatcatttgttcgtgtctcaagtgctgttttccagGTTTTTAACAACAGTCCAGACGAGACTGCGCACTTCAGAATCCTTTTAGACAGAGAAACAGTGACGAATTCCCTGTTGATGATTCAACCGTCCCTCGTGT
                          |||   |    || ||||   | |  |||  |||| | || ||    ||  ||||||||||||||||||||||||||||||||  | ||| | ||  | ||| |||| ||||   | |  ||| |     | |||||||| |||||  |  | |
gtaccttttgttgtaattctcttcctgttctgcttttcaaactttatttaactgtgagtgt-tgaaatgtg--ttgacagGTTTTTAACAACAGTCCAGACGAGACTGCATATTTCCGTATGTTGTTAAACAGGGAAAATATTAGTAATGCTGCTGTTATGATTCAGCCGTCATTGATAT
















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|169041327|gb|FE446857.1|FE446857
EST:     CGCTCTTTCCCCAGTTTATGTTTAATCTTCGGCGATCTCAATTTGTTCAG                         GTTTTTAACAATAGTCCAGACGAGACTGCGCACTTCAGAATCCTTTTAGAC
genomic: CGCTCTTTCCCCAGTTTATGTTTAATCTTCGGCGATCTCAATTTGTTCAGgttagtcacc ... tgttttccagGTTTTTAACAACAGTCCAGACGAGACTGCGCACTTCAGAATCCTTTTAGAC
EST: gi|169108739|gb|FE513008.1|FE513008
EST:     CGCTCTTTCCCCAGTTTATGTTTAATCTTCGGCGATCTCAATTTGTTCAG                         GTTTTTAACAATAGTCCAGACGAGACTGCGCACTTCAGAATCCTTTTAGAC
genomic: CGCTCTTTCCCCAGTTTATGTTTAATCTTCGGCGATCTCAATTTGTTCAGgttagtcacc ... tgttttccagGTTTTTAACAACAGTCCAGACGAGACTGCGCACTTCAGAATCCTTTTAGAC
EST: gi|169051945|gb|FE459049.1|FE459049
EST:     GCTCTTTCCCCAGTTTATGTTTAATCTTCGGCGATCTNCA-TTTGTTCAG                         GTTTTTAACAACAGTC
genomic: GCTCTTTCCCCAGTTTATGTTTAATCTTCGGCGATCT-CAATTTGTTCAGgttagtcacc ... tgttttccagGTTTTTAACAACAGTC
EST: gi|70669204|gb|DN837781.1|DN837781
EST:     CGCTCTTTCCCCAGTTTATGTTTAATCTTCGGCGATCTCAATTTGTTCAG                         GTTTTTAACAACAGTCCAGACGAGACTGCGCACTTCAGAATCCTTTTAGAC
genomic: CGCTCTTTCCCCAGTTTATGTTTAATCTTCGGCGATCTCAATTTGTTCAGgttagtcacc ... tgttttccagGTTTTTAACAACAGTCCAGACGAGACTGCGCACTTCAGAATCCTTTTAGAC
EST: gi|169041328|gb|FE446858.1|FE446858
EST:     CGCTCTTTCCCCAGTTTATGTTTAATCTTCGGCGATCTCAATTTGTTCAG                         GTTTTTAACAATAGTCCAGACGAGACTGCGCACTTCAGAATCCTTTTAGAC
genomic: CGCTCTTTCCCCAGTTTATGTTTAATCTTCGGCGATCTCAATTTGTTCAGgttagtcacc ... tgttttccagGTTTTTAACAACAGTCCAGACGAGACTGCGCACTTCAGAATCCTTTTAGAC
EST: gi|169064389|gb|FE472056.1|FE472056
EST:     CGCTCTTTCCCCAGTTTATGTTTAATCTTCGGCGATCTCAATTTGTTCAG                         GTTTTTAACAATAGTCCAGACGAGACTGCGCACTTCAGAATCCTTTTAGAC
genomic: CGCTCTTTCCCCAGTTTATGTTTAATCTTCGGCGATCTCAATTTGTTCAGgttagtcacc ... tgttttccagGTTTTTAACAACAGTCCAGACGAGACTGCGCACTTCAGAATCCTTTTAGAC
EST: gi|169039834|gb|FE447520.1|FE447520
EST:     CGCTCTTTCCCCAGTTTATGTTTAATCTTCGGCGATCTCAATTTGTTCAG                         GTTTTTAACAATAGTCCAGACGAGACTGCGCACTTCAGAATCCTTTTAGAC
genomic: CGCTCTTTCCCCAGTTTATGTTTAATCTTCGGCGATCTCAATTTGTTCAGgttagtcacc ... tgttttccagGTTTTTAACAACAGTCCAGACGAGACTGCGCACTTCAGAATCCTTTTAGAC

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: 21 (upstream exon), 29 (downstream exon)
Score: 2

TGACTATCGGAAAGATGATGCGAGCTCTTTCCGTCTGAGCTCTAAACTCTCGCTCTTTCCCCAGTTTATGTTTAATCTTCGGCGATCTCAATTTGTTCAGgttagtcacc ... tgttttccagGTTTTTAACAACAGTCCAGACGAGACTGCGCACTTCAGAATCCTTTTAGACAGAGAAACAGTGACGAATTCCCTGTTGATGATTCAACCGTCCCTCGTGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttagtcaccccatacttgtatcatttgttcgtgtctcaagtgctgttttccagGTTTTTAACAACAGTCCAGACGAGACTGCGCACTTCAGAATCCTTTTAGACAGAGAAACAGTGACGAATTCCCTGTTGATGATTCAACCGTCCCTCGTGT
                                            ctgttttcc  CT-rich tract
                    tatcattt  TA-rich tract