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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAGTTTGGTCTTTCTAGTGTAGCAGCACTTCGTACTGGTCTTTTACTTGCTCCTGGCGGGGAGTTTGCCTTTGTTGCCTTCGGCGAAGCAGTGAACCAGgtacgcagcttcaagcaatcagctttaacttggctttgcaaatgtcgtgcag

Basic information

species Selaginella moellendorffii
transcript EFJ10973
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ10973 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: LOC_Os04g58620.1 (Oryza sativa), 5'ss of exon 13
TCAGTTTGGTCTTTCTAGTGTAGCAGCACTTCGTACTGGTCTTTTACTTGCTCCTGGCGGGGAGTTTGCCTTTGTTGCCTTCGGCGAAGCAGTGAACCAGgtacgcagcttcaagcaatcagctttaacttggctttgcaaatgtcgtgcag-----------------------------------------------------
    |||||  |||| |   |||| ||  ||||   |||||| || ||||| ||||| ||||||||||| |||||||||||||| ||||| || || |||||  |   | |    |  || | |||    |    ||  |  ||    |  |                                                     
AGTATTTGGAATTTCCACCATAGCTGCTGTTCGGGTTGGTCTGTTGCTTGCACCTGGTGGGGAGTTTGCTTTTGTTGCCTTCGGAGAAGCTGTCAATCAGgtttg-gccctggttctttctgtttttttgtattgttttaggtgataagatgtatatgtcacacacatctgagttaagacaaactcatggacaatatttttgcag

upper sequence: EFJ10973 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: GRMZM2G093643_T01 (Zea mays), 5'ss of exon 13
TCAGTTTGGTCTTTCTAGTGTAGCAGCACTTCGTACTGGTCTTTTACTTGCTCCTGGCGGGGAGTTTGCCTTTGTTGCCTTCGGCGAAGCAGTGAACCAGgta-cgcagcttcaagcaatcagctttaacttggctttgcaaatgtcgtgcag-----------------------------------------------
   ||||||  |||||  | |||| ||  |||||  ||| || || ||||| ||||| || |||||||| ||||||||||| || ||||| || ||||||||| |  |  ||       |    |||           |||   |   |||                                                 
GGTGTTTGGGGTTTCTGCTATAGCTGCCATTCGTGTTGGCCTCTTGCTTGCACCTGGTGGTGAGTTTGCTTTTGTTGCCTTTGGAGAAGCTGTCAACCAGgtaacatacgttgttttcttttcttttcgtcgaatgacgcaggagagctgcgtgtcatttcattaagaagggaataaaacaacgtaggagcagcaaagct
















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|169045259|gb|FE453572.1|FE453572
EST:     CTCCTGGCGGGGAGTTTGCTTTTGTTGCCTTCGGCGAAGCAGTGAACCAG                         GGAATCATGAGCCAACAGCTATCTTCCCTCATGTTCCTGATTGTTGGCTTG
genomic: CTCCTGGCGGGGAGTTTGCCTTTGTTGCCTTCGGCGAAGCAGTGAACCAGgtacgcagct ... tgtcgtgcagGGAATCATGAGCCAACAGCTATCTTCCCTCATGTTCCTGATTGTTGGCTTG
EST: gi|169059436|gb|FE467539.1|FE467539
EST:     AAGCAGTGAACCAG                         GGAATCATGAGCCAACAGCTATCTTCCNTCATGTTCCTGATTGTTGGCTTG
genomic: AAGCAGTGAACCAGgtacgcagct ... tgtcgtgcagGGAATCATGAGCCAACAGCTATCTTCCCTCATGTTCCTGATTGTTGGCTTG
EST: gi|169022442|gb|FE430795.1|FE430795
EST:     CTCCTGGCGGGGAGTTTGCCTTTGTTGCCTTCGGCGAAGCAGTGAACCAG                         GGAATCATGAG
genomic: CTCCTGGCGGGGAGTTTGCCTTTGTTGCCTTCGGCGAAGCAGTGAACCAGgtacgcagct ... tgtcgtgcagGGAATCATGAG

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), 35 (downstream exon)
Score: 26

TCAGTTTGGTCTTTCTAGTGTAGCAGCACTTCGTACTGGTCTTTTACTTGCTCCTGGCGGGGAGTTTGCCTTTGTTGCCTTCGGCGAAGCAGTGAACCAGgtacgcagct ... tgtcgtgcagGGAATCATGAGCCAACAGCTATCTTCCCTCATGTTCCTGATTGTTGGCTTGTCCATGGCATTAACTCCTTGGCTTGCTGCGGCCGGACAAATAATCTCAA




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