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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACGgtatgttacaagccaaaagcagccatctaacagttgttgttttgacag

Basic information

species Selaginella moellendorffii
transcript EFJ34434
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ34434 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: LOC_Os01g47410.1 (Oryza sativa), 5'ss of exon 8
GGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACGgtatgttacaagc-caaaagcagccatctaacagttgttgttttgacag---------------------------------------------------
| ||||||||    || ||||| ||||| |||||||||||||||||||||||| ||||||| |||||||| |   | | |          ||  || |  |||   |  |  ||                                                   
GATTCTGTGCAGCTGGGTGTGCAGCAATAGCAGATTCTGGAACTTCACTGCTTACTGGTCCCACGgtatggtgtgaactcttctttttttataaaaaaaatgtccataagcaaggaaaagtggtctggattgcatctgatactggggttcctaacattggtttat

upper sequence: EFJ34434 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: LOC_Os05g04630.5 (Oryza sativa), 5'ss of exon 6
-----------------------------------GGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACGgtatgttacaagccaaaagcagccatctaacagtt---gttgttttgacag---------------------------------------------------
                                   | |||||||| ||||| |||||||| ||||  || || ||||||||  ||||||||||||| || ||||||   |    || | |  | |  |||   |     | |  || | |                                                    
CATGGGGGATCTCCTTATTGATGGCCACTCAACTGGCTTCTGTGCAAAAGGCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACAgtatgtatta--ttaatatcttcaaattaaggatccagatcgcctttatatttgtttgttcatggttactgagctcaaagtttccatgctaagataaagtag

upper sequence: EFJ34434 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: GRMZM2G153977_T01 (Zea mays), 5'ss of exon 2
GGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACGgtatgttacaagccaaaagc-----agccatctaacagttgttgttttgacag-----------------------------------------------
|||| ||||||   || ||||| ||||| |||||||||||||||||  |||||||||| || || ||| |||   |||     |      | |     |||| |  | | ||     |                                               
GGTTTTGTGCTGGTGGTTGTGCAGCAATAGCAGATTCTGGAACTTCCTTGCTTGCTGGCCCCACAgtaagttttgagctttgtgttctttatctgcagaacaatgatgggttattgggattcaccattttgcgattgaagcagcttcgtagtttttttttctgtt

upper sequence: EFJ34434 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: Vv10s0116g01210.t01 (Vitis vinifera), 5'ss of exon 8
GGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACGgtatgttaca--agccaaaagcagccatctaacagttgttgttttgacag--------------------------------------------------
||| ||||||   ||| ||||| |||||||||||||||||||||||  || | || ||||| |||||||||  ||  |  |  |||        |||  ||| || |||| ||                                                    
GGTACTGTGCCGGAGGTTGTGCAGCAATTGCAGATTCTGGAACTTCTTTGTTGGCAGGTCCAACGgtatgtatcagtactcttaagagtttggttaattgtttttattttaacttctgtcccatcaaatattcttctaggatttattgtactagttgatacactt

upper sequence: EFJ34434 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: PP1S99_158V6.1 (Physcomitrella patens), 5'ss of exon 7
GGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACGgtatgttacaagccaaaagcagc-catctaacagttgttgttttgacag----------------------------------------------------------------------------------------------------------------
| |||||||||  |||||||||||||||||||||||| |||||||| ||| | ||||||||||||||  ||| |   ||| |  ||    |  |     |  | ||   ||||                                                                                                                 
GATTCTGTGCTGGAGGATGTGCTGCAATTGCAGATTCCGGAACTTCTCTGTTAGCTGGTCCTACGgttagttcctgcccagagccaaagtaaatgtatttcatggtcgcgacaactggtgctctcccgattgaatgcagatatggatgttgcctactattctaagtgatgccacttgaaaatttgtctctaataagtgcttatgtactgggattgttgtctgatag

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|169113000|gb|FE515480.1|FE515480
EST:     GATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACG                         GGTATTGTGGCTCAAATCAACCAAGCTATCGGGGCTACGGGGCTCGTCAGC
genomic: GATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACGgtatgttaca ... gttttgacagGGTATTGTGGCTCAAATCAACCAAGCTATCGGGGCTACAGGGCTCGTCAGC
EST: gi|169031797|gb|FE438482.1|FE438482
EST:     GATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACG                         GGTATTGTGGCTCAAATCAACCAAGCTATCGGGGCTACAGGGCTCGTCAGC
genomic: GATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACGgtatgttaca ... gttttgacagGGTATTGTGGCTCAAATCAACCAAGCTATCGGGGCTACAGGGCTCGTCAGC
EST: gi|169055215|gb|FE461076.1|FE461076
EST:     GATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACG                         GGTATTGTGGCTCAAATCAACCAAGCTATCGGGGCTACAGGGCTCGTCAGC
genomic: GATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACGgtatgttaca ... gttttgacagGGTATTGTGGCTCAAATCAACCAAGCTATCGGGGCTACAGGGCTCGTCAGC
EST: gi|169031872|gb|FE438505.1|FE438505
EST:     GATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACG                         GGTATTGTGGCTCAAATCAACCAAGCTATCGGGGCTACAGGGCTCGTCAGC
genomic: GATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACGgtatgttaca ... gttttgacagGGTATTGTGGCTCAAATCAACCAAGCTATCGGGGCTACAGGGCTCGTCAGC
EST: gi|169112151|gb|FE513494.1|FE513494
EST:     GATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACG                         GGTATTGTGGCTCAAATCAACCAAGCTATCGGGGCTACAGGGCTCGTCAGC
genomic: GATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACGgtatgttaca ... gttttgacagGGTATTGTGGCTCAAATCAACCAAGCTATCGGGGCTACAGGGCTCGTCAGC
EST: gi|169060203|gb|FE467565.1|FE467565
EST:     GATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACG                         GGTATTGTGGCTCAAATCAACCAAGCTATCGGGGCTACAGGGCTCGTCAGC
genomic: GATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACGgtatgttaca ... gttttgacagGGTATTGTGGCTCAAATCAACCAAGCTATCGGGGCTACAGGGCTCGTCAGC
EST: gi|169110929|gb|FE509334.1|FE509334
EST:     GATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACG                         GGTATTGTGGCTCAAATCAACCAAGCTATCGGGGCTACAGGGCTCGTCAGC
genomic: GATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACGgtatgttaca ... gttttgacagGGTATTGTGGCTCAAATCAACCAAGCTATCGGGGCTACAGGGCTCGTCAGC
EST: gi|169048945|gb|FE456062.1|FE456062
EST:     GATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACG                         GGTATTGTGGCTCANATCAACCAAGCTATCGGGGCTACGGGGCTCGTCAGC
genomic: GATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACGgtatgttaca ... gttttgacagGGTATTGTGGCTCAAATCAACCAAGCTATCGGGGCTACAGGGCTCGTCAGC
EST: gi|169112990|gb|FE515470.1|FE515470
EST:     GATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACG                         GGTATTGTGGCTCAAATCAACCAAGCTATCGGGGCTACGGGGCTCGTCAGC
genomic: GATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACGgtatgttaca ... gttttgacagGGTATTGTGGCTCAAATCAACCAAGCTATCGGGGCTACAGGGCTCGTCAGC
EST: gi|169058238|gb|FE466005.1|FE466005
EST:     GATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACG                         GGTATTGTGGCTCAAATCAACCAAGCTATCGGGGCTACAGGGCTCGTCAGC
genomic: GATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACGgtatgttaca ... gttttgacagGGTATTGTGGCTCAAATCAACCAAGCTATCGGGGCTACAGGGCTCGTCAGC
EST: gi|169114468|gb|FE516538.1|FE516538
EST:     GATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACG                         GGTATTGTGGCTCAAATCAACCAAGCTATCGGGGCTACAGGGCTCGTCAGC
genomic: GATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACGgtatgttaca ... gttttgacagGGTATTGTGGCTCAAATCAACCAAGCTATCGGGGCTACAGGGCTCGTCAGC
EST: gi|169065200|gb|FE474024.1|FE474024
EST:     GATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACG                         GGTATTGTGGCTCAAATCAACCAAGCTATCGGGGCTACAGGGCTCGTCAGC
genomic: GATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACGgtatgttaca ... gttttgacagGGTATTGTGGCTCAAATCAACCAAGCTATCGGGGCTACAGGGCTCGTCAGC
EST: gi|169039673|gb|FE448607.1|FE448607
EST:     GATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACG                         GGTATTGTGGCTCAAATCAACCAAGCTATCGGGGCTACAGGGCTCGTCAGC
genomic: GATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACGgtatgttaca ... gttttgacagGGTATTGTGGCTCAAATCAACCAAGCTATCGGGGCTACAGGGCTCGTCAGC
EST: gi|169112152|gb|FE513495.1|FE513495
EST:     GATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACG                         GGTATTGTGGCTCAAATCAACCAAGCTATCGGGGCTACAGGGCTCGTCAGC
genomic: GATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACGgtatgttaca ... gttttgacagGGTATTGTGGCTCAAATCAACCAAGCTATCGGGGCTACAGGGCTCGTCAGC
EST: gi|169096046|gb|FE500024.1|FE500024
EST:     GATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACG                         GGTATTGTGGCTCAAATCAACCAAGCTATCGGGGCTACAGGGCTCGTCAGC
genomic: GATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACGgtatgttaca ... gttttgacagGGTATTGTGGCTCAAATCAACCAAGCTATCGGGGCTACAGGGCTCGTCAGC
EST: gi|169021618|gb|FE432137.1|FE432137
EST:     GATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACG                         GGTATTGTGGCTCAAATCAACCAAGCTATCGGGGCTACAGGGCTCGTCAGC
genomic: GATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACGgtatgttaca ... gttttgacagGGTATTGTGGCTCAAATCAACCAAGCTATCGGGGCTACAGGGCTCGTCAGC
EST: gi|169096045|gb|FE500023.1|FE500023
EST:     GATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACG                         GGTATTGTGGCTCAAATCAACCAAGCTATCGGGGCTACAGGGCTCGTCAGC
genomic: GATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACGgtatgttaca ... gttttgacagGGTATTGTGGCTCAAATCAACCAAGCTATCGGGGCTACAGGGCTCGTCAGC
EST: gi|169093446|gb|FE495727.1|FE495727
EST:     GATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACG                         GGTATTGTGGCTCAAATCAACCAAGCTATCGGGGCTACAGGGCTCGTCAGC
genomic: GATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACGgtatgttaca ... gttttgacagGGTATTGTGGCTCAAATCAACCAAGCTATCGGGGCTACAGGGCTCGTCAGC
EST: gi|169031873|gb|FE438506.1|FE438506
EST:     GATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACG                         GGTATTGTGGCTCAAATCAACCAAGCTATCGGGGCTACAGGGCTCGTCAGC
genomic: GATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACGgtatgttaca ... gttttgacagGGTATTGTGGCTCAAATCAACCAAGCTATCGGGGCTACAGGGCTCGTCAGC
EST: gi|169044448|gb|FE451072.1|FE451072
EST:     GATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACG                         GGTATTGTGGCTCAAATCAACCAAGCTATCGGGGCTACAGGGCTCGTCAGC
genomic: GATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACGgtatgttaca ... gttttgacagGGTATTGTGGCTCAAATCAACCAAGCTATCGGGGCTACAGGGCTCGTCAGC
EST: gi|169021619|gb|FE432138.1|FE432138
EST:     GATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACG                         GGTATTGTGGCTCAAATCAACCAAGCTATCGGGGCTACAGGGCTCGTCAGC
genomic: GATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACGgtatgttaca ... gttttgacagGGTATTGTGGCTCAAATCAACCAAGCTATCGGGGCTACAGGGCTCGTCAGC
EST: gi|169021385|gb|FE431176.1|FE431176
EST:     GATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACG                         GGTATTGTGGCTCAAATCAACCAAGCTATCGGGGCTACAGGGCTCGTCAGC
genomic: GATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACGgtatgttaca ... gttttgacagGGTATTGTGGCTCAAATCAACCAAGCTATCGGGGCTACAGGGCTCGTCAGC

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: 193

GGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACGgtatgttaca ... gttttgacagGGTATTGTGGCTCAAATCAACCAAGCTATCGGGGCTACAGGGCTCGTCAGCGAGGAGTGTAAGATGGTCGTTGCTCAGTATGGTGACTTGATTGTGGAAC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACGgtatgttacaagccaaaagcagccatctaacagttgttgttttgacag

- - - - - - - - -  TGCTGC
- - - - - - - - - - - - - -  GCAGAT