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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTATGATTCACCTGGGCAAATTTTTGTTGCTTTTGAAAAGCCAGAACATGTTCCTGCTACTGGGAAATTTTCAAATGTGCTGAAGTTTATTGTTAAAGAGgtaaatgtttccttctgctgttggatcctgatatgaccgacagtaatatcctttgttatactaattcaagtatgactgttctatatcatatgctttggat...

Basic information

species Oryza sativa
transcript LOC_Os03g12590.1
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g12590.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G012501_T02 (Zea mays), 5'ss of exon 14
TTATGATTCACCTGGGCAAATTTTTGTTGCTTTTGAAAAGCCAGAACATGTTCCTGCTACTGGGAAATTTTCAAATGTGCTGAAGTTTATTGTTAAAGAGgtaaatgtttccttctgctgttggatcctgatatgaccgacagtaatatcctt-tgttatactaattcaagtatgactgttctatatcatatgctttggat-------
 ||| |||||||||||||| ||||||||||||||||||||||||| | ||| |||| |  |||||| |||| |||| || |||||||||  ||||||||||||||       |  || ||||  ||     ||| | | | | |  | ||| | | | | || | |   ||||  |  |||   | ||| |  || | | |       
GTATAATTCACCTGGGCAAGTTTTTGTTGCTTTTGAAAAGCCAGAGCGTGTACCTGTTGTTGGGAAGTTTTTAAATTTGTTGAAGTTTACAGTTAAAGAGgtaaaca-----taatggtgtttcatgt--gtataatctataatcttctccctgtatcagac-agtaatagtaatatagtttgttttcaaaaactgtagtttgttaag

upper sequence: LOC_Os03g12590.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GLYMA12G04820.1 (Glycine max), 5'ss of exon 16
TTATGATTCACCTGGGCAAATTTTTGTTGCTTTTGAAAAGCCAGAACATGTTCCTGCTACTGGGAAATTTTCAAATGTGCTGAAGTTTATTGTTAAAGAGgtaaatgtttccttctgctgttgga----------tcctgatatgaccgacagtaatatcctttgt-tatactaattcaagtatgactgttctatatcatatgctttggat--------------------------------------------------------------------------------------
||||||||||||||||||||  ||||| |||||||| ||||| ||     | ||   | |||| |||||||| ||||| ||||| ||||||||||||||||||  |||  ||||   |  | |||          |  |  | || || |     | | || | || ||||  |      ||||   |      |      |  |||   |                                                                                      
TTATGATTCACCTGGGCAAACATTTGTGGCTTTTGAGAAGCCTGAGGGATTGCCAATTGCTGGAAAATTTTCGAATGTTCTGAAATTTATTGTTAAAGAGgtacttgtcccctttatccttgggaagcattgtggtttttctttgtcctagtcctagacccctggtatatatcacgaagtgtatatttcaagcgtggagcttattttatttttctctggcacggaatttgtggaaaataaaacaataatatttttgtggaaatctaatcactgcttcatgtattggatattgaccag
















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|58695561|gb|CK084248.1|CK084248
EST:     TTCCTGCTACTGGGAAATTTTCAAATGTGCTGAAGTTTATTGTTAAAGAG                         GTTGACACATCTACAGGGGAAGTTGATGAGGATGGTGTGGAGGATGAATAC
genomic: TTCCTGCTACTGGGAAATTTTCAAATGTGCTGAAGTTTATTGTTAAAGAGgtaaatgttt ... caattctcagGTTGACACATCTACAGGGGAAGTTGATGAGGATGGTGTGGAGGATGAATAC
EST: gi|218498611|gb|FG960368.1|FG960368
EST:     TTCCTGCTACTGGGAAA-TTTCAAATGTGCTGAAGTTTATTGTTAAAGAG                         GTTGACACATCTACAGGGGAAGTTGATGAGGATGGTGTGGAGGATGAATAC
genomic: TTCCTGCTACTGGGAAATTTTCAAATGTGCTGAAGTTTATTGTTAAAGAGgtaaatgttt ... caattctcagGTTGACACATCTACAGGGGAAGTTGATGAGGATGGTGTGGAGGATGAATAC
EST: gi|33656418|gb|CF279032.1|CF279032
EST:     TTCCTGCTACTGGGAAATTTTCAAATGTGCTGAAGTTTATTGTTAAAGAG                         GTTGACACATCTACAGGGGAAGTTGATGAGGATGGTGTGGAGGATGAATAC
genomic: TTCCTGCTACTGGGAAATTTTCAAATGTGCTGAAGTTTATTGTTAAAGAGgtaaatgttt ... caattctcagGTTGACACATCTACAGGGGAAGTTGATGAGGATGGTGTGGAGGATGAATAC
EST: gi|58663414|gb|CK052100.1|CK052100
EST:     TTCCTGCTACTGGGAAATTTTCAAATGTGCTGAAGTTTATTGTTAAAGAG                         GTTGACACATCTACAGGGGAAGTTGATGAGGATGGTGTGGAGGATGAATAC
genomic: TTCCTGCTACTGGGAAATTTTCAAATGTGCTGAAGTTTATTGTTAAAGAGgtaaatgttt ... caattctcagGTTGACACATCTACAGGGGAAGTTGATGAGGATGGTGTGGAGGATGAATAC
EST: gi|14571493|gb|BI118861.1|BI118861
EST:     TTCCTGCTACTGGGAAATTTTCAAATGTGCTGAAGTTTATTGTTAAAGAG                         GTTGACACATCTACAGGGGAAGTTGATGAGGATGGTGTGGAGGATGAATAC
genomic: TTCCTGCTACTGGGAAATTTTCAAATGTGCTGAAGTTTATTGTTAAAGAGgtaaatgttt ... caattctcagGTTGACACATCTACAGGGGAAGTTGATGAGGATGGTGTGGAGGATGAATAC
EST: gi|86478723|gb|CI121356.1|CI121356
EST:     TTCCTGCTACTGGGAAATTGTCAAATGTGCTAAAGTTTATTGTTAAAGAG                         GTTGACACATCTACAGGGGAAGTTGATGAGGATGGTGTGGAGGATGAATAC
genomic: TTCCTGCTACTGGGAAATTTTCAAATGTGCTGAAGTTTATTGTTAAAGAGgtaaatgttt ... caattctcagGTTGACACATCTACAGGGGAAGTTGATGAGGATGGTGTGGAGGATGAATAC
EST: gi|58654518|gb|CK043198.1|CK043198
EST:     TTCCTGCTACTGGGAAATTTTCAAATGTGCTGAAGTTTATTGTTAAAGAG                         GTTGACACATCTACAGGGGAAGTTGATGAGGATGGTGTGGAGGATGAATAC
genomic: TTCCTGCTACTGGGAAATTTTCAAATGTGCTGAAGTTTATTGTTAAAGAGgtaaatgttt ... caattctcagGTTGACACATCTACAGGGGAAGTTGATGAGGATGGTGTGGAGGATGAATAC
EST: gi|58667540|gb|CK056226.1|CK056226
EST:     TTCCTGCTACTGGGAAATTTTCAAATGTGCTGAAGTTTATTGTTAAAGAG                         GTTGACACATCTACAGGGGAAGTTGATGAGGATGGTGTGGAGGATGAATAC
genomic: TTCCTGCTACTGGGAAATTTTCAAATGTGCTGAAGTTTATTGTTAAAGAGgtaaatgttt ... caattctcagGTTGACACATCTACAGGGGAAGTTGATGAGGATGGTGTGGAGGATGAATAC
EST: gi|427768|gb|D23905.1|D23905
EST:     TTCCTGCTACTGGGAAATTTTCAAATGTGCTGAAGTTTATTGTTAAAGAG                         GTTGACACATCTACAGGGGAAGTTGATGAGGATGGTGTGGAGGATGAATAC
genomic: TTCCTGCTACTGGGAAATTTTCAAATGTGCTGAAGTTTATTGTTAAAGAGgtaaatgttt ... caattctcagGTTGACACATCTACAGGGGAAGTTGATGAGGATGGTGTGGAGGATGAATAC

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: 74 (upstream exon), 61 (downstream exon)
Score: 43

TTATGATTCACCTGGGCAAATTTTTGTTGCTTTTGAAAAGCCAGAACATGTTCCTGCTACTGGGAAATTTTCAAATGTGCTGAAGTTTATTGTTAAAGAGgtaaatgttt ... caattctcagGTTGACACATCTACAGGGGAAGTTGATGAGGATGGTGTGGAGGATGAATACCAGATCGAAGACCTGGAAATTGTTTCGGCTGATTACATGCTGAGGGTTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTATGATTCACCTGGGCAAATTTTTGTTGCTTTTGAAAAGCCAGAACATGTTCCTGCTACTGGGAAATTTTCAAATGTGCTGAAGTTTATTGTTAAAGAGgtaaatgtttccttctgctgttggatcctgatatgaccgacagtaatatcctttgttatactaattcaagtatgactgttctatatcatatgctttggat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG