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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATGTCATGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTCGCGATGgtatgagctttacgagttcttctccgaatgaaatcgttattgttctctcctgtttttcccag

Basic information

species Selaginella moellendorffii
transcript EFJ26022
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ26022 (Selaginella moellendorffii), 5'ss of exon 19
lower sequence: AT2G20580.1 (Arabidopsis thaliana), 5'ss of exon 18
---AATGTCATGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTCGCGATGgt-----atga----gctttacgagttcttct-----------ccgaatgaaatcg-----ttattgttctctcctgtttttcccag--
   | ||| |||||||| |||||| |||| |||||||||||||| |||||||| || |||||     || |    |||| |     | | |            | ||||   || |       | || ||| || | |   ||  |   
GTGACTGTAATGGACACCTTGAGCCGGCTTAGCCATGACACAGATTCGGAAGTTGCCATGgttagcaatcatttcgcttcatagcctgtcccatattatttagctgaatagtattgagagaggactgatctttcttttgactcgtacag

upper sequence: EFJ26022 (Selaginella moellendorffii), 5'ss of exon 19
lower sequence: AT4G28470.1 (Arabidopsis thaliana), 5'ss of exon 18
---AATGTCATGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTCGCGATGgtatg--agctttacg--agttcttctccgaatgaaatcgttattgttctctcctgtttttcccag------------------------------
   | ||| |||||||| |||||||| || |||||||||||||| || ||||| || |||||  |  | |||| ||  | |  |  |     |  | | ||||||  | |  | || | | |   |                              
GTGACTGTTATGGACACTTTGAGCAGACTAAGCCATGACACAGATTCAGAAGTTGCAATGgtgagttatcttttcgccactcatggttgaggtagagtagttatttctttgacttgctatgcagcgttggactgatgtttcatctgattcctacag

upper sequence: EFJ26022 (Selaginella moellendorffii), 5'ss of exon 19
lower sequence: Vv12s0028g03130.t01 (Vitis vinifera), 5'ss of exon 20
---AATGTCATGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTCGCGATGgtatg-------agctttacgagttcttctccgaatgaaatcgttattgttctctcctgtttttcccag-------------------
   ||||| ||||||||||| ||||| || ||||||||||||||  | ||||| || ||||||||       ||||   |   || ||||| || |       | | | |  |  |||         |                    
GTCAATGTTATGGACACATTAAGCAGACTTAGCCATGACACAGATACAGAAGTAGCAATGgtatggtgatagagctagcctttttgttctctgagtagttctatcaatatattggcctaaacgcagaaatatttgtgggattctacag

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|169064751|gb|FE476097.1|FE476097
EST:     TGGACACATTGAGCAGGCTGAGCCATGACACTGACTCGGAAGTCGCGATG                         GCTGCAACCATTTCTCTTGGACTTATTGGCGCTGGAACAAACAATGCGCGT
genomic: TGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTCGCGATGgtatgagctt ... tttttcccagGCTGCAACCATTTCTCTTGGACTTATTGGCGCCGGAACAAACAATGCGCGT
EST: gi|169025374|gb|FE435988.1|FE435988
EST:     TGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTCGCGATG                         GCTGCAACCATTTCTCTTGGACTTATTGGCGCCGGAACAAACAATGCGCGT
genomic: TGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTCGCGATGgtatgagctt ... tttttcccagGCTGCAACCATTTCTCTTGGACTTATTGGCGCCGGAACAAACAATGCGCGT
EST: gi|169088930|gb|FE494442.1|FE494442
EST:     TGGACACATTGAGCAGGTTGAGCCATGACACAGACTCGGAAGTCGCGATG                         GCTGCAACCATTTCTCTTGGATTTATTGGCGCGGGAACAAACAATGCGCGT
genomic: TGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTCGCGATGgtatgagctt ... tttttcccagGCTGCAACCATTTCTCTTGGACTTATTGGCGCCGGAACAAACAATGCGCGT
EST: gi|169088931|gb|FE494443.1|FE494443
EST:     TGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTCGCGATG                         GCTGCAACCATTTCTCTTGGACTTATTGGCGCCGGAACAAACAATGCGCGT
genomic: TGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTCGCGATGgtatgagctt ... tttttcccagGCTGCAACCATTTCTCTTGGACTTATTGGCGCCGGAACAAACAATGCGCGT
EST: gi|169019957|gb|FE431022.1|FE431022
EST:     TGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTCGCGATG                         GCTGCAACCATTTCTCTTGGACTTATTGGCGCCGGAACAAACAATGCGCGT
genomic: TGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTCGCGATGgtatgagctt ... tttttcccagGCTGCAACCATTTCTCTTGGACTTATTGGCGCCGGAACAAACAATGCGCGT
EST: gi|169080935|gb|FE486104.1|FE486104
EST:     TGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTCGCGATG                         GCTGCAACCATTTCTCTTGGACTTATTGGCGCCGGAACAAACAATGCGCGT
genomic: TGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTCGCGATGgtatgagctt ... tttttcccagGCTGCAACCATTTCTCTTGGACTTATTGGCGCCGGAACAAACAATGCGCGT
EST: gi|169030421|gb|FE438677.1|FE438677
EST:     TGGACACATTGAGCAGGCTGAGCCATGACACTGACTCGGAAGTCGCGATG                         GCTGCAACCATTTCTCTTGGACTTATTGGCGCTGGAACAAACAATGCGCGT
genomic: TGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTCGCGATGgtatgagctt ... tttttcccagGCTGCAACCATTTCTCTTGGACTTATTGGCGCCGGAACAAACAATGCGCGT
EST: gi|169116305|gb|FE517252.1|FE517252
EST:     TGGACACATTGAGCAGGCTGAGCCATGACACTGACTCGGAAGTCGCGATG                         GCTGCAACCATTTCTCTTGGACTTATTGGCGCTGGAACAAACAATGCGCGT
genomic: TGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTCGCGATGgtatgagctt ... tttttcccagGCTGCAACCATTTCTCTTGGACTTATTGGCGCCGGAACAAACAATGCGCGT
EST: gi|169066440|gb|FE474663.1|FE474663
EST:     TGGACACATTGAGCAGGCTGAGCCATGACACTGACTCGGAAGTCGCGATG                         GCTGCAACCATTTCTCTTGGACTTATTGGCGCTGGAACAAACAATGCGCGT
genomic: TGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTCGCGATGgtatgagctt ... tttttcccagGCTGCAACCATTTCTCTTGGACTTATTGGCGCCGGAACAAACAATGCGCGT
EST: gi|169028508|gb|FE439923.1|FE439923
EST:     TGGACACATTGAGCAGGCTGAGCCATGACACTGACTCGGAAGTCGCGATG                         GCTGCAACCATTTCTCTTGGACTTATTGGCGCTGGAACAAACAATGCGCGT
genomic: TGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTCGCGATGgtatgagctt ... tttttcccagGCTGCAACCATTTCTCTTGGACTTATTGGCGCCGGAACAAACAATGCGCGT
EST: gi|169097980|gb|FE498777.1|FE498777
EST:     TGGACACATTGAGCAGGCTGAGCCATGACACTGACTCGGAAGTCGCGATG                         GCTGCAACCATTTCTCTTGGACTTATTGGCGCTGGAACAAACAATGCGCGT
genomic: TGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTCGCGATGgtatgagctt ... tttttcccagGCTGCAACCATTTCTCTTGGACTTATTGGCGCCGGAACAAACAATGCGCGT
EST: gi|169064752|gb|FE476098.1|FE476098
EST:     TGGACACATTGAGCAGGCTGAGCCATGACACTGACTCGGAAGTCGCGATG                         GCTGCAACCATTTCTCTTGGACTTATTGGCGCTGGAACAAACAATGCGCGT
genomic: TGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTCGCGATGgtatgagctt ... tttttcccagGCTGCAACCATTTCTCTTGGACTTATTGGCGCCGGAACAAACAATGCGCGT
EST: gi|169059060|gb|FE468205.1|FE468205
EST:     TGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTCGCGATG                         GCTGCAACCATTTCTCTTGGACTTATTGGCGCCGGAACAAACAATGCGCGT
genomic: TGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTCGCGATGgtatgagctt ... tttttcccagGCTGCAACCATTTCTCTTGGACTTATTGGCGCCGGAACAAACAATGCGCGT
EST: gi|169116306|gb|FE517253.1|FE517253
EST:     TGGACACATTGAGCAGGCTGAGCCATGACACTGACTCGGAAGTCGCGATG                         GCTGCAACCATTTCTCTTGGACTTATTGGCGCTGGAACAAACAATGCGCGT
genomic: TGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTCGCGATGgtatgagctt ... tttttcccagGCTGCAACCATTTCTCTTGGACTTATTGGCGCCGGAACAAACAATGCGCGT
EST: gi|169097109|gb|FE498955.1|FE498955
EST:     TGGACACATTGAGCAGGCTGAGCCATGACACTGACTCGGAAGTCGCGATG                         GCTGCAACCATTTCTCTTGGACTTATTGGCGCTGGAACAAACAATGCGCGT
genomic: TGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTCGCGATGgtatgagctt ... tttttcccagGCTGCAACCATTTCTCTTGGACTTATTGGCGCCGGAACAAACAATGCGCGT
EST: gi|169064768|gb|FE473735.1|FE473735
EST:     TGGACACATTGAGCAGGCTGAGCCATGACACTGACTCGGAAGTCGCGATG                         GCTGCAACCATTTCTCTTGGACTTATTGGCGCTGGAACAAACAATGCGCGT
genomic: TGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTCGCGATGgtatgagctt ... tttttcccagGCTGCAACCATTTCTCTTGGACTTATTGGCGCCGGAACAAACAATGCGCGT
EST: gi|169025373|gb|FE435987.1|FE435987
EST:     TGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTCGCGATG                         GCTGCAACCATTTCTCTTGGACTTATTGGCGCCGGAACAAACAATGCGCGT
genomic: TGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTCGCGATGgtatgagctt ... tttttcccagGCTGCAACCATTTCTCTTGGACTTATTGGCGCCGGAACAAACAATGCGCGT

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: 18

AATGTCATGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTCGCGATGgtatgagctt ... tttttcccagGCTGCAACCATTTCTCTTGGACTTATTGGCGCCGGAACAAACAATGCGCGTATTGCGGGAATGCTTCGAAGCTTGTCCAGCTATTACTACAAGGATCCCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATGTCATGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTCGCGATGgtatgagctttacgagttcttctccgaatgaaatcgttattgttctctcctgtttttcccag

- - - - - - - -  GAGCAG