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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGCTGGTTGCACACTGGTGACGTGGCTCTCATCGACGATGACGACGAGGTGTTCATTGTGGACCGGGTCAAGGAGATTATCAAGTACAAGGGCTTCCAGgtaatcttgggtcgctttccctctcacgcgcattattttaccttcag

Basic information

species Selaginella moellendorffii
transcript EFJ13708
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ13708 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: LOC_Os02g46970.1 (Oryza sativa), 5'ss of exon 3
CGGCTGGTTGCACACTGGTGACGTGGCTCTCATCGACGATGACGACGAGGTGTTCATTGTGGACCGGGTCAAGGAGATTATCAAGTACAAGGGCTTCCAGgtaatct----tgggtcgctttccctctcacgcgcattattttac-cttcag-------------------
 || ||| ||||||| || ||| | |    | ||||||| ||||||||||| ||||| || ||||| ||||||||| | ||||| | |||||| |||||||||||        || | |||  | ||          || ||  | ||  |                    
GGGGTGGCTGCACACCGGCGACATCGGCTACGTCGACGACGACGACGAGGTCTTCATCGTCGACCGTGTCAAGGAGCTCATCAAATTCAAGGGGTTCCAGgtaattaacagcaggacacttagcatcagttttctgataattcgcactgtaactattgtctattcatgcag

upper sequence: EFJ13708 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: LOC_Os08g34790.1 (Oryza sativa), 5'ss of exon 3
-----CGGCTGGTT--GCACACTGGTGACGTGGCTCTCATCGACGATGACGACGAGGTGTTCATTGTGGA--CCGG-GTCAAGGAGATTATCAA-GTACAAGGGCTTCCAGgtaatcttgggtcgctttccctctcacgcgcattattttaccttcag-------------------------------------------------------------
       |||  |   | |||  ||   |  ||    |  || |||   ||| |   || |||| |   |  |||  |||   ||      |   || |      |  | || | ||  |  |      ||    |||||||   ||||  | |||                                                               
TCAAGGAGCTCATCAAGTACAAGGGCTTCCAGGTCGCCCCCGCCGAGCTCGAGGCCATGCTCATCGCCCACGCCGCCGTCGCCGACGCCGCCGTCGTCCCgtaagtatccgg-actccggcatgatcaacctcgccacgcgcgc-atttggcattcgcaatttcaggctctgaacatcggcttgacgactgaatggctgaatttttctcaacgatgcag

upper sequence: EFJ13708 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: LOC_Os02g08100.1 (Oryza sativa), 5'ss of exon 4
------------------------------------------------CGGCTG-GTTGCACACTGGTGACGTGGCTCTCATCGACGATGACGACG----AGGTGTTCATTGTGGACCGGGTCAAGGAGATTATCAAGTACAAGGGCTTCCAGgtaatcttgggtcgctttccctctcacgcgcattattttaccttcag
                                                 ||  | | ||| ||    | ||  ||   |||  ||||  | || ||      | || |||    ||     |     |  | || ||   | || |  |  ||  ||      ||| ||    |  |  |  |    | ||    |||||
TCAAGGAGATCATCAAGTACAAGGGGTTCCAGGTGCCACCGGCCGAGCTGGAGGCGCTGCTCATCACTCACCCGGAGATCAAGGACGCCGCCGTCGTCTCgtgagtccatctctgatgaaattcgccat-tgattaatcgcgagagaatgtagtgaact----gtcactgattcagttgctggtgaaactt-gttttcag

upper sequence: EFJ13708 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GRMZM2G054013_T03 (Zea mays), 5'ss of exon 3
CGGCTGGTTGCACACTGGTGACGTGGCTCTCATCGACGATGACGACGAGGTGTTCATTGTGGACCGGGTCAAGGAGATTATCAAGTACAAGGGCTTCCAGgtaat-cttgggtcgctttc-----cctctcacgcgcat-tatt--ttaccttcag-----------------------------------------------------------
||||||| | ||||| || ||| | |    | ||||||| ||||||||||| ||||| || ||||| ||||||||| | ||||||| |||||||||||||||||  |  | |  |   |      |||||   |    | |||   ||   |||||                                                           
CGGCTGGCTCCACACCGGCGACATCGGCTACGTCGACGACGACGACGAGGTCTTCATCGTCGACCGCGTCAAGGAGCTCATCAAGTTCAAGGGCTTCCAGgtaacgcccgcgctggcctgaagaacctctactgtatctgtatcagttggtttcagcgtttcgcctccggttttctgagagctgtatctgcctgccgatcctttcgcccgtgcag

upper sequence: EFJ13708 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GRMZM2G075333_T02 (Zea mays), 5'ss of exon 1
-----CGGCTGGTTGCACACTGGTGACGT-GGCTCTCATCGACGATGACGACGAGG-TGTTCATTGTGGACCGGG---TCAAGGAGATTATCA----AGTACAAGG-GCTTCCAGgtaat---cttgggtcgctttccctctcacgcgcattattttaccttcag---------------------------------------------------------------------------------------------
       | |  |     ||  | |      | |  |  || ||  |  |  |  | |  ||||   | ||| ||   |||||||      |     |    |||  |||  | | ||||    ||  |  | |||   |  ||     |  |  | || |||||                                                                                             
TCAAGGAGATCATCAAGTACAAGGGCTTCCAGGTGCCGCCGGCGGAGCTGGAGGCGCTCCTCATCACGCACCCGGAGATCAAGGACGCCGCCGTCGTATCgtaagctgctcaccgataatacctttcagatggtttaagttccaaaaaaaaaaaataac-ttcagaattcagatggagccacaacgcaacctgctgcgctgccagcttcttttaagtaaactctgaactaatctcgttcgtctctctctcccccacag

upper sequence: EFJ13708 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GRMZM2G174732_T01 (Zea mays), 5'ss of exon 3
------------------------------------------------CGGCTG-GTTGCACACTGGTGACGTGGCTCTCATCGACGATGACGACGAGGTGTTCATTGTGGACCGGGTCAAGGAGATTATCAAGTACAAGGGCTTCCAGgtaatcttgggtcgc---tttccctctcacgcgcattattt--taccttcag---------------------------------------------------------------------------
                                                 ||  | | ||| ||      ||   |   ||  |||||  | || ||  | || | |  |         | |    || ||||  ||   ||   || || ||  | ||| ||||    | |     ||    || || ||  ||     ||                                                                           
TCAAGGAGATCATCAAGTACAAGGGCCTCCAGGTGGCCCCCGCCGAGCTGGAGGCGCTGCTCATCACCCACCCAGGCATCGCCGACGCCGCCGTCGTCGGgtacgtactacgtaataaccaaccaatcatcacctagctggctatctagctaggcgtggttcgcgcaatgcaacgacagatacagtacttggtagtagtagtagtgtttcagtcgtcgtttgggaagtgagcgagatcacgcaaggtgtctctacctgtcatcgtcatcgttgcag

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|169108888|gb|FE512299.1|FE512299
EST:     TGTTCATTGTGGACCGGGTCAAGGAGATTATCAAGTACAAGGGCTTCCAG                         GTGGCTCCCGCGGAACTGGAAGCGCTTTTCATCTCCAACCCATCCATTGCC
genomic: TGTTCATTGTGGACCGGGTCAAGGAGATTATCAAGTACAAGGGCTTCCAGgtaatcttgg ... ttaccttcagGTGGCTCCCGCGGAACTGGAAGCGCTTCTCATCTCCAACCCATCCATTGCC
EST: gi|169043104|gb|FE454018.1|FE454018
EST:     TGTTCATTGTGGACCGGGTCAAGGAGATTATCAAGTACAAGGGCTTCCAG                         GTGGCTCCCGCGGAACTGGAAGCGCTTCTCATCTCCAACCCATCCATTGCC
genomic: TGTTCATTGTGGACCGGGTCAAGGAGATTATCAAGTACAAGGGCTTCCAGgtaatcttgg ... ttaccttcagGTGGCTCCCGCGGAACTGGAAGCGCTTCTCATCTCCAACCCATCCATTGCC
EST: gi|169082027|gb|FE487484.1|FE487484
EST:     TGTTCATTGTGGACCGGGTCAAGGAGATTATCAAGTACAAGGGCTTCCAG                         GTGGCTCCCGCGGAACTGGAAGCGCTTTTCATCTCCAACCCATCCATTGCC
genomic: TGTTCATTGTGGACCGGGTCAAGGAGATTATCAAGTACAAGGGCTTCCAGgtaatcttgg ... ttaccttcagGTGGCTCCCGCGGAACTGGAAGCGCTTCTCATCTCCAACCCATCCATTGCC
EST: gi|169043103|gb|FE454017.1|FE454017
EST:     TGTTCATTGTGGACCGGGTCAAGGAGATTATCAAGTACAAGGGCTTCCAG                         GTGGCTCCCGCGGAACTGGAAGCGCTTCTCATCTCCAACCCATCCATTGCC
genomic: TGTTCATTGTGGACCGGGTCAAGGAGATTATCAAGTACAAGGGCTTCCAGgtaatcttgg ... ttaccttcagGTGGCTCCCGCGGAACTGGAAGCGCTTCTCATCTCCAACCCATCCATTGCC
EST: gi|169069209|gb|FE480007.1|FE480007
EST:     TGTTCATTGTGGACCGGGTCAAGGAGATTATCAAGTACAAGGGCTTCCAG                         GTGGCTCCCGCGGAACTGGAAGCGCTTCTCATCTCCAACCCATCCATTGCC
genomic: TGTTCATTGTGGACCGGGTCAAGGAGATTATCAAGTACAAGGGCTTCCAGgtaatcttgg ... ttaccttcagGTGGCTCCCGCGGAACTGGAAGCGCTTCTCATCTCCAACCCATCCATTGCC
EST: gi|169096944|gb|FE497074.1|FE497074
EST:     TGTTCATTGTGGACCGGGTCAAGGAGATTATCAAGTACAAGGGCTTCCAG                         GTGGCTCCCGCGGAACTGGAAGCGCTTCTCATCTCCAACCCATCCATTGCC
genomic: TGTTCATTGTGGACCGGGTCAAGGAGATTATCAAGTACAAGGGCTTCCAGgtaatcttgg ... ttaccttcagGTGGCTCCCGCGGAACTGGAAGCGCTTCTCATCTCCAACCCATCCATTGCC
EST: gi|169082028|gb|FE487485.1|FE487485
EST:     TGTTCATTGTGGACCGGGTCAAGGAGATTATCAAGTACAAGGGCTTCCAG                         GTGGCTCCCGCGGAACTGGAAGCGCTTCTCATCTCCAACCCATCCATTGCC
genomic: TGTTCATTGTGGACCGGGTCAAGGAGATTATCAAGTACAAGGGCTTCCAGgtaatcttgg ... ttaccttcagGTGGCTCCCGCGGAACTGGAAGCGCTTCTCATCTCCAACCCATCCATTGCC
EST: gi|169075419|gb|FE483053.1|FE483053
EST:     TGTTCATTGTGGACCGGGTCAAGGAGATTATCAAGTACAAGGGCTTCCAG                         GTGGCTCCCGCGGAACTGGAAGCGCTTCTCATCTCCAACCCATCCATTGCC
genomic: TGTTCATTGTGGACCGGGTCAAGGAGATTATCAAGTACAAGGGCTTCCAGgtaatcttgg ... ttaccttcagGTGGCTCCCGCGGAACTGGAAGCGCTTCTCATCTCCAACCCATCCATTGCC

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: 35 (upstream exon), 35 (downstream exon)
Score: 24

CGGCTGGTTGCACACTGGTGACGTGGCTCTCATCGACGATGACGACGAGGTGTTCATTGTGGACCGGGTCAAGGAGATTATCAAGTACAAGGGCTTCCAGgtaatcttgg ... ttaccttcagGTGGCTCCCGCGGAACTGGAAGCGCTTCTCATCTCCAACCCATCCATTGCCGACGCTGCAGTCGTTGC




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGCTGGTTGCACACTGGTGACGTGGCTCTCATCGACGATGACGACGAGGTGTTCATTGTGGACCGGGTCAAGGAGATTATCAAGTACAAGGGCTTCCAGgtaatcttgggtcgctttccctctcacgcgcattattttaccttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT