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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCATCGGGGAAGCTCGTCCAGATCGAGCATGCTCTCACAGCCGTGGCCGCCGGGCAGACCTCGCTCGGGATCAGAGgtaatttctctctttcctggttctatgatctcttcccttgttgtggcattcgcag

Basic information

species Selaginella moellendorffii
transcript EFJ19637
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ19637 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GRMZM5G824831_T04 (Zea mays), 5'ss of exon 3
TCCATCGGGGAAGCTCGTCCAGATCGAGCATGCTCTCACAGCCGTGGCCGCCGGGCAGACCTCGCTCGGGATCAGAGgtaatttctc--------tctttcctggttctatgatctcttcccttgttgtggcattcgcag---------------------------------------
||| |||||||||||||| ||||| ||||| || ||||| || || |   |||||||||||||||||||||||| ||||    |||         ||    ||    || |||| | ||    | || || | ||   ||                                       
TCCGTCGGGGAAGCTCGTGCAGATTGAGCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCGCTCGGGATCAAAGgttcgatctgcgcagtaatcccctctcaccctttgatgtattag--tattttgccgttgctaggacacggagatttgaaacggcattatgacgtcttgtcac
















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|169115599|gb|FE517809.1|FE517809
EST:     GCATGCTCTCACAGCCGTGGCCGCCGGGCAGACCTCGCTCGGGATCAGAG                         TCCGGAATGGAGTTGTCATTGCGACCGAGAAAAAACTTCCATCGATTCTTG
genomic: GCATGCTCTCACAGCCGTGGCCGCCGGGCAGACCTCGCTCGGGATCAGAGgtaatttctc ... gcattcgcagTCCGGAATGGAGTTGTCATTGCGACCGAGAAAAAACTTCCATCGATTCTTG
EST: gi|169109748|gb|FE511819.1|FE511819
EST:     GCATGCTCTCACAGCTGTGGCCGCCGGGCAGACCTCGCTCGGGATCAGAG                         TCCGGAATGGAGTTGTCATTGCGACCGAGAAAAAACTTCCATCGATTCTTG
genomic: GCATGCTCTCACAGCCGTGGCCGCCGGGCAGACCTCGCTCGGGATCAGAGgtaatttctc ... gcattcgcagTCCGGAATGGAGTTGTCATTGCGACCGAGAAAAAACTTCCATCGATTCTTG
EST: gi|169115598|gb|FE517808.1|FE517808
EST:     GCATGCTCTCACAGCCGTGGCCGCCGGGCAGACCTCGCTCGGGATCAGAG                         TCCGGAATGGAGTTGTCATTGCGACCGAGAAAAAACTTCCATCGATTCTTG
genomic: GCATGCTCTCACAGCCGTGGCCGCCGGGCAGACCTCGCTCGGGATCAGAGgtaatttctc ... gcattcgcagTCCGGAATGGAGTTGTCATTGCGACCGAGAAAAAACTTCCATCGATTCTTG

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), 34 (downstream exon)
Score: 62

TCCATCGGGGAAGCTCGTCCAGATCGAGCATGCTCTCACAGCCGTGGCCGCCGGGCAGACCTCGCTCGGGATCAGAGgtaatttctc ... gcattcgcagTCCGGAATGGAGTTGTCATTGCGACCGAGAAAAAACTTCCATCGATTCTTGTCGATGAAACATCT




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