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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgtcaataagggcatattttatgttctacacaacacttgcatttgacttcgatttgttatagtgcaatgtcctgacattttgactctacctgattgcagCTGAGCTTGCTGTCATCATGTAATTCTGGTGGGGACCCAATTAAGTCTGAAGGCATGGAAAATCTTGGATCTCCACAGAGTTGCCATCTCCCGTTCAT

Basic information

species Oryza sativa
transcript LOC_Os06g45840.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g45840.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G170148_T01 (Zea mays), 3'ss of exon 7
atgtcaataagggcatattttatgttctacacaacacttgcatttgacttcgatttgttatagtgcaatgtcctgacattttgactctacctgattgcagCTGAGCTTGCTGTCATCATGTAATTCTGGTGGGGACCCAATTAAGTCTGAAGGCATGGAAAATCTTGGATCTCCACAGAGTTGCCATCTCCCGTTCAT
                  |  ||| |     | | | | ||||||    |   ||    ||    |  ||   |   ||||  | |   | | | |    |||  ||   |  |||   |  ||  |||||||||||   ||||  |||||||||||||||||| ||||||||| |||||| ||||||| || ||| |
------------------tgcatgattatgtcgatagtggcattttttatattttatgcatgaccctttgcaatagtatttgaattgctcttcacttatactg--ctcttttccatatagCTATGGTGGTGGGGACCATGTTAAACCTGAAGGCATGGAAAATCATGGATCTCCTCAGAGTGGCCATCTTCCATTCCT

upper sequence: LOC_Os06g45840.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G057408_T03 (Zea mays), 3'ss of exon 1
atgtcaataagggcatattttatgttctaca--caacacttgcatttgacttcgatttgttatagtgcaatgtcctgacattttgactctacctgattgcagCTGAGCTTGCTGTCATCATGTAATTCTGGTGG---GGACCCAATTAAGTCTGAAGGCATGGAAAATCTTGGATCTCCACAGAGTTGCCATCTCCCGTTCAT
 ||  | |||  |    ||||||||   | |     || | | | ||          || | |  | |||  | |||||   || || ||  ||||||||||| ||| ||||| ||||||| ||  | ||||||   |||||   | || ||||||| ||||||||||||||||||||| |||||| ||||||| || | |  
ttgagactaaaagttgtttttatgtatgatagtttgcagtagtacttatacatatactgctcttttccaaaatgctgactgatttacact--ctgattgcagCGGAGGTTGCTATCATCATATAGCTATGGTGGCGCGGACCATGTCAAATCTGAAGCCATGGAAAATCTTGGATCTCCTCAGAGTGGCCATCTTCCATCCC-
















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|218486576|gb|FG956240.1|FG956240
EST:     TGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAACTTTGCGGCACAT                         CTGAGCTTGCTGTCATCATGTAATTCTGGTGGGGACCCAATTAAGTCTGAA
genomic: TGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAACTTTGCGGCACATgtaagttgtt ... ctgattgcagCTGAGCTTGCTGTCATCATGTAATTCTGGTGGGGACCCAATTAAGTCTGAA
EST: gi|218500576|gb|FG960552.1|FG960552
EST:     TGATGAGATATCTGTCCATGAACTTAACTAGCCCCAACTTTGCGGCACAT                         CTGAGCTTGCTGTCATCATGTAATTCTGGTGGGGACCCAATTAAGTCTGAA
genomic: TGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAACTTTGCGGCACATgtaagttgtt ... ctgattgcagCTGAGCTTGCTGTCATCATGTAATTCTGGTGGGGACCCAATTAAGTCTGAA
EST: gi|38474825|gb|CF958958.1|CF958958
EST:     TGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAACTTTGCGGCACAT                         CTGAGCTTGCTGTCATCATGTAATTCTGGTGGGGACCCAATTAAGTCTGAA
genomic: TGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAACTTTGCGGCACATgtaagttgtt ... ctgattgcagCTGAGCTTGCTGTCATCATGTAATTCTGGTGGGGACCCAATTAAGTCTGAA
EST: gi|88688887|gb|CI732463.1|CI732463
EST:     TGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAACTTTGCGGCACAT                         CTGAGCTTGCTGTCATCATGTAATTCTGGTGGGGACCCAATTAAGTCTGAA
genomic: TGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAACTTTGCGGCACATgtaagttgtt ... ctgattgcagCTGAGCTTGCTGTCATCATGTAATTCTGGTGGGGACCCAATTAAGTCTGAA
EST: gi|27545921|gb|CA764047.2|CA764047
EST:     TGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAACTTTGCGGCACAT                         CTGAGCTTGCTGTCATCATGTAATTCTGGTGGGGACCCAATTAAGTCTGAA
genomic: TGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAACTTTGCGGCACATgtaagttgtt ... ctgattgcagCTGAGCTTGCTGTCATCATGTAATTCTGGTGGGGACCCAATTAAGTCTGAA
EST: gi|218489538|gb|FG952484.1|FG952484
EST:     TGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAACTTTGCGGCACAT                         CTGAGCTTGCTGTCATCATGTAATTCTGGTGGGGACCCAATTAAGTCTGAA
genomic: TGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAACTTTGCGGCACATgtaagttgtt ... ctgattgcagCTGAGCTTGCTGTCATCATGTAATTCTGGTGGGGACCCAATTAAGTCTGAA
EST: gi|218481447|gb|FG951027.1|FG951027
EST:     TGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAACTTTGCGGCACAT                         CTGAGCTTGCTGTCATCATGTAATTCTGGTGGGGACC-AATTAAGTCTGAA
genomic: TGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAACTTTGCGGCACATgtaagttgtt ... ctgattgcagCTGAGCTTGCTGTCATCATGTAATTCTGGTGGGGACCCAATTAAGTCTGAA
EST: gi|29637643|gb|CB642652.1|CB642652
EST:     TGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAACTTTGCGGCACAT                         CTGAGCTTGCTGTCATCATGTAATTCTGGTGGGGACCCAATTAAGTCTGAA
genomic: TGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAACTTTGCGGCACATgtaagttgtt ... ctgattgcagCTGAGCTTGCTGTCATCATGTAATTCTGGTGGGGACCCAATTAAGTCTGAA
EST: gi|89177323|gb|CI250772.1|CI250772
EST:     GATGAGAAATCTGTCCATGAACTGT-ACTAGCCCCAACTTTGCGGCACAT                         CTGAGCTTGCTGTCATCATGTAATTCTGGTGGGGACCCAATTAAGTCTGAA
genomic: GATGAGAAATCTGTCCATGAACT-TAACTAGCCCCAACTTTGCGGCACATgtaagttgtt ... ctgattgcagCTGAGCTTGCTGTCATCATGTAATTCTGGTGGGGACCCAATTAAGTCTGAA
EST: gi|88689244|gb|CI732820.1|CI732820
EST:     TGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAACTTTGCGGCACAT                         CTGAGCTTGCTGTCATCATGTAATTCTGGTGGGGACCCAATTAAGTCTGAA
genomic: TGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAACTTTGCGGCACATgtaagttgtt ... ctgattgcagCTGAGCTTGCTGTCATCATGTAATTCTGGTGGGGACCCAATTAAGTCTGAA
EST: gi|88689640|gb|CI733216.1|CI733216
EST:     TGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAACTTTGCGGCACAT                         CTGAGCTTGCTGTCATCATGTAATTCTGGTGGGGACCCAATTAAGTCTGAA
genomic: TGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAACTTTGCGGCACATgtaagttgtt ... ctgattgcagCTGAGCTTGCTGTCATCATGTAATTCTGGTGGGGACCCAATTAAGTCTGAA
EST: gi|88691348|gb|CI733931.1|CI733931
EST:     TGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAACTTTGCGGCACAT                         CTGAGCTTGCTGTCATCATGTAATTCTGGTGGGGACCCAATTAAGTCTGAA
genomic: TGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAACTTTGCGGCACATgtaagttgtt ... ctgattgcagCTGAGCTTGCTGTCATCATGTAATTCTGGTGGGGACCCAATTAAGTCTGAA
EST: gi|27334389|gb|CA882840.1|CA882840
EST:     TGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAGCTTTGCGGCACAT                         CTGAGCTTGCTGTCAGCATGTAATTCTGGTGGGGACCCAATTAAGTCTGAA
genomic: TGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAACTTTGCGGCACATgtaagttgtt ... ctgattgcagCTGAGCTTGCTGTCATCATGTAATTCTGGTGGGGACCCAATTAAGTCTGAA
EST: gi|218494859|gb|FG953214.1|FG953214
EST:     TGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAACTTTGCGGCACAT                         CTGAGCTTGCTGTCATCATGTAATTCTGGTGGGGACCCAATTAAGTCTGAA
genomic: TGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAACTTTGCGGCACATgtaagttgtt ... ctgattgcagCTGAGCTTGCTGTCATCATGTAATTCTGGTGGGGACCCAATTAAGTCTGAA

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: 70 (upstream exon), 58 (downstream exon)
Score: 16

GTACTACTGCTGATGAGAAATCTGTCCATGAACTTAACTAGCCCCAACTTTGCGGCACATgtaagttgtt ... ctgattgcagCTGAGCTTGCTGTCATCATGTAATTCTGGTGGGGACCCAATTAAGTCTGAAGGCATGGAAAATCTTGGATCTCCACAGAGTTGCCATCTCCCGTTCAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacttcgatttgttatagtgcaatgtcctgacattttgactctacctgattgcagCTGAGCTTGCTGTCATCATGTAATTCTGGTGGGGACCCAATTAAGTCTGAAGGCATGGAAAATCTTGGATCTCCACAGAGTTGCCATCTCCCGTTCAT
                                       ctctacct  CT-rich tract
       atttgttata  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgtcaataagggcatattttatgttctacacaacacttgcatttgacttcgatttgttatagtgcaatgtcctgacattttgactctacctgattgcagCTGAGCTTGCTGTCATCATGTAATTCTGGTGGGGACCCAATTAAGTCTGAAGGCATGGAAAATCTTGGATCTCCACAGAGTTGCCATCTCCCGTTCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - -ttatgtt
- - - - - - - - - - - - - ctacaca
- - - - - - - - - - - - - - - - - -acttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctgaca