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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgctactaatcatttgttcctctcacattgccatgtgagttgcactttgtgtatactccagaatgtaagtctttcccctcttggtggctttgtttttcagGTAGTAACAGTAGGAAAATTTCAAGGAGGTGGAGCCTTCAATGTCATCCCTGATTCTGTTACAATTGGTGGCACCTTCCGAGCCTTTTTAAAAGAGAGTT

Basic information

species Oryza sativa
transcript LOC_Os01g37960.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g37960.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G090779_T01 (Zea mays), 3'ss of exon 3
-tgctactaatcatttgttcctctcacattgccatgtgagttgcactttgtgtatactccagaatgtaagtctttcccctcttggtggctttgtttttcagGTAGTAACAGTAGGAAAATTTCAAGGAGGTGGAGCCTTCAATGTCATCCCTGATTCTGTTACAATTGGTGGCACCTTCCGAGCCTTTTTAAAAGAGAGTT
 |  |  |  |   |||  |||    || |      | | || ||||    |||  |  |   ||||   | |||       |     || |||| | ||||| || ||||| ||||| |||||||||||||||||||||||||| ||||||||||| || || || ||||||||||||||||||||| | ||||||||||
gtatttttgttatgttgaaccttaggcaatttatccttatttacactcca-gtagtccactttatgtttttttttatttggatccattctgtgttgtgcagGTTGTGACAGTTGGAAAGTTTCAAGGAGGTGGAGCCTTCAATGTGATCCCTGATTCGGTAACTATAGGTGGCACCTTCCGAGCCTTTCTGAAAGAGAGTT

upper sequence: LOC_Os01g37960.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA07G01570.1 (Glycine max), 3'ss of exon 3
tgctact-aatcatttgttcctctcacattgccatgtgagttgcactttgtgtatactccagaatgtaagtctttcccct-cttggtggctttgttttt-cagGTAGTAACAGTAGGAAAATTTCAAGGAGGTGGAGCCTTCAATGTCATCCCTGATTCTGTTACAATTGGTGGCACCTTCCGAGCCTTTTTAAAAGAGAGTT
|  || | |  ||   |     ||    |  | | |    ||||   | || |||  |    |   |  || | | || | | |   |  | |||     |||||  | ||| | | |||  | ||||||||||  || |||||||| || || |||| ||| ||||||||||||||||||||||| ||||  | ||| || |
tattatttagacagaagaaaggcttgattctcgaaggattttgc---tagtttatggtgacaatcctctgtatctaccttacataaagtatatgtccccacagGTTTTGACAATTGCAAAGCTCCAAGGAGGTGATGCTTTCAATGTTATTCCAGATTATGTCACAATTGGTGGCACCTTCCGAGCTTTTTCTAGAGAAAGAT

upper sequence: LOC_Os01g37960.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA08G21080.1 (Glycine max), 3'ss of exon 4
tgctact-aatcatttgttcctctcacattgccatgtgagttgcactttgtgtatactccagaatgtaagtctttcccctcttggtggctttgtttttcagGTAGTAACAGTAGGAAAATTTCAAGGAGGTGGAGCCTTCAATGTCATCCCTGATTCTGTTACAATTGGTGGCACCTTCCGAGCCTTTTTAAAAGAGAGTT
   || | || ||   |          ||| |     || ||    | | | |     | |   | |   |||| |     |      | |       |||||  | ||| | | |||  | ||||||||||  || |||||||| || || |||| ||| |||||||||||||| |||||||| ||||  | ||| |  |
-attatttaaacagaagaaaaggcttgattcctgaaggactttacttgtttatggtgacaatcctctgtatcttccttaaataaagtacatgtccccacagGTTTTGACAATTGCAAAGCTCCAAGGAGGTGATGCTTTCAATGTTATTCCAGATTATGTCACAATTGGTGGCACTTTCCGAGCTTTTTCTAGAGAAACAT

upper sequence: LOC_Os01g37960.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA08G21040.1 (Glycine max), 3'ss of exon 3
tgctactaatcatttgttcctctcacattgccatgtgagttgcactttgtgtatactccagaatgtaagtctttcccctcttggtggctttgttttt-cagGTAGTAACAGTAGGAAAATTTCAAGGAGGTGGAGCCTTCAATGTCATCCCTGATTCTGTTACAATTGGTGGCACCTTCCGAGCCTTTTTAAAAGAGAGTT
  || |  || ||||   | | | | |   |    |          |||| |||| |    |   | | |  |  |   | |      | |||   | ||||| || |||||   |||  ||||||||||||  || |||||||| || ||||||| ||  |||||||||||||||| ||| |  |||   ||  | ||  
-actgccgattatttaaacatatgaaaggcctgaatcctgaaggacttgtttatagtgacaatcatcatttgtgtcttccatacataatatgtcaatgcagGTTGTCACAGTTTCAAAGATTCAAGGAGGTGATGCATTCAATGTTATTCCTGATTATGCCACAATTGGTGGCACCTACCGTGGTTTTACTAATAAAAGCA

upper sequence: LOC_Os01g37960.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA07G01580.1 (Glycine max), 3'ss of exon 3
tgctactaatcatttgttcctctcac--attgccatgtgagtt--gcactttgtgtatactccagaatgtaagtctttcccctcttggtggctttgtttttcagGTAGTAACAGTAGGAAAATTTCAAGGAGGTGGAGCCTTCAATGTCATCCCTGATTCTGTTACAATTGGTGGCACCTTCCGAGCCTTTTTAAAAGAGAGTT
     || || ||||   |   | |   |  ||   ||   |   | |||||   | |        |      ||| |  | |       |  |    |  ||||| || ||||| |  || || ||||||||||| || |||||||| || || |||| ||| ||||||||||||||||| ||||| ||||  | ||| |  |
----gctgattatttaaacagatgatgaaaggcttggttcctcaaggactttacttgtttatggtgacaatcctctgtgtcttacataaagtatgtcctcacagGTTGTGACAGTTGCTAAGTTCCAAGGAGGTGGTGCATTCAATGTTATTCCAGATTATGTCACAATTGGTGGCACCTTTCGAGCTTTTTCTAGAGAAAAAT

upper sequence: LOC_Os01g37960.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA15G02560.1 (Glycine max), 3'ss of exon 3
tgctactaatcatttgttcctctcacattgccatgtgagttgcactttgtgtatactccagaatgtaagtctttcccctcttggtggctt------tgtttttcagGTAGTAACAGTAGGAAAATTTCAAGGAGGTGGAGCCTTCAATGTCATCCCTGATTCTGTTACAATTGGTGGCACCTTCCGAGCCTTTTTAAAAGAGAGTT
    | | || ||    |    | | |  ||| |||     | | |   |   |  |   | |   || ||||     ||||  |  | |      | ||   ||||| || || |||||||| |||||||||||||| || |||||||| || || || ||||| ||||||||||||||||||||||| |||| |||||| || |
---aaatgattatcgaatatgatgaaa--gccttgtttccagaaataattaattgtttatggagacaa-tcttctgtgtcttcctaacataaagaatattgcacagGTTGTGACTGTAGGAAAGTTTCAAGGAGGTGGTGCTTTCAATGTTATTCCAGACTCTGTCACAATTGGTGGCACCTTCCGAGCTTTTTCAAAAGAAAGCT

upper sequence: LOC_Os01g37960.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA13G42880.1 (Glycine max), 3'ss of exon 3
----tgctactaatcatttgttcctctcacattgccatgtgagttgcactttgtgtatactccagaatgtaagtctttcccctcttggtggctttgtttttcagGTAGTAACAGTAGGAAAATTTCAAGGAGGTGGAGCCTTCAATGTCATCCCTGATTCTGTTACAATTGGTGGCACCTTCCGAGCCTTTTTAAAAGAGAGTT
       || | |  || || |     |   || ||||      | || ||| |    |    |   ||   ||||| ||   | |   |  | |      ||||| || || |||||||||||||| |||||||| || |||||||| || || || |||||| |||||||||||||||||||||| |||| |||||| || |
aaatgattattga--atatgataaagccttgtttccataaataattcattttttaaggagataatcttggttgtctt-cctaacataaagaatat-ccccacagGTCGTCACTGTAGGAAAATTTCAGGGAGGTGGTGCTTTCAATGTTATTCCAGACTCTGTTGCAATTGGTGGCACCTTCCGAGCTTTTTCAAAAGAAAGCT

upper sequence: LOC_Os01g37960.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA08G21030.1 (Glycine max), 3'ss of exon 3
tgctactaatcatttgttcctctcacattgccatgtga-gttgcactttgt-gtatactccagaatgtaagtctttcccctcttggtggctttgtttttcagGTAGTAACAGTAGGAAAATTTCAAGGAGGTGGAGCCTTCAATGTCATCCCTGATTCTGTTACAATTGGTGGCACCTTCCGAGCCTTTTTAAAAGAGAGTT
      | || |||  | | | |   ||  |||    | | ||      |  | |   || |   | | || ||| |     | |   ||||       ||||| || || ||||||||||| |||||||||   || ||||||||||| || |||||||| |||||||| |||||||||||||| |||| |||||| || |
-aagtgtgattattactgcttattgaat-accacaaaatgctgtttcaagaagcactttcaatcttctgagccttcctaaaatagaaagcttctccacacagGTTGTGACTGTAGGAAAATTCCAAGGAGGTAATGCATTCAATGTCATTCCAGATTCTGTCACAATTGGAGGCACCTTCCGAGCTTTTTCAAAAGAAAGCT

upper sequence: LOC_Os01g37960.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv09s0002g02630.t01 (Vitis vinifera), 3'ss of exon 3
tgctactaatcatttgttcctctcacattgccatgtgagttgcactttgtgtatactccagaatgtaagtctttcccct-cttggtggctttgtttttcagGTAGTAACAGTAGGAAAATTTCAAGGAGGTGGAGCCTTCAATGTCATCCCTGATTCTGTTACAATTGGTGGCACCTTCCGAGCCTTTTTAAAAGAGAGTT
  || ||    ||   ||| |   | | |      |   |||          | | | |   || ||      ||     | |     |||  |||| |||||||| || || | |||||| ||||||||||| || |||||||| || || |||||||| || || |||||||||||  ||||||||| ||| || ||  
-tcttctgtcaatacattcattggaaaatttggctttttttggttccatgaaacattaccttatttatcaaactcattgacctaaaaccttcattttgcagGTAGTTACGGTTGCAAAATTCCAAGGAGGTGGTGCATTCAATGTTATTCCAGATTCTGTAACCATCGGTGGCACCTTTAGAGCCTTTTCAAAGGAAAGCA

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|58688291|gb|CK076978.1|CK076978
EST:     TAAGCCTTCAGCAACTTGTTTCCCGGGAAGCTGATCCCCTAGACTCACAG                         GTAGTAACAGTAGGAAAATTTCAAGGAGGTGGAGCCTTCAATGTCATCCCT
genomic: TAAGCCTTCAGCAACTTGTTTCCCGGGAAGCTGATCCCCTAGACTCACAGgtgagttact ... tgtttttcagGTAGTAACAGTAGGAAAATTTCAAGGAGGTGGAGCCTTCAATGTCATCCCT
EST: gi|58587717|gb|CF986025.1|CF986025
EST:     TTCCCGGGAAGCTGATCCCCTAGACTCACAG                         GTAGTAACAGTAGGAAAATTTCAAGGAGGTGGAGCCTTCAATGTCATCCCT
genomic: TTCCCGGGAAGCTGATCCCCTAGACTCACAGgtgagttact ... tgtttttcagGTAGTAACAGTAGGAAAATTTCAAGGAGGTGGAGCCTTCAATGTCATCCCT
EST: gi|426822|gb|D22895.1|D22895
EST:     TAAGCCTTCAGCAACTTGTTTCCCGGGAAGCTGATCCCCTAGACTCACAG                         GTAGTAACAGTAGGANAATTTCAAGGAGGTGGAGCCTTCAATGTCATCCCT
genomic: TAAGCCTTCAGCAACTTGTTTCCCGGGAAGCTGATCCCCTAGACTCACAGgtgagttact ... tgtttttcagGTAGTAACAGTAGGAAAATTTCAAGGAGGTGGAGCCTTCAATGTCATCCCT
EST: gi|58681864|gb|CK070551.1|CK070551
EST:     AGCCTTCAGCAACTTGTTTCCCGGTGAAGCTGATTCCCCTAAACTCACAG                         GTAGTAACAGTAGGAAAATTTCAAGGAGGTGGAGCCTTCAATGTCATCCCT
genomic: AGCCTTCAGCAACTTGTTTCCCGG-GAAGCTGA-TCCCCTAGACTCACAGgtgagttact ... tgtttttcagGTAGTAACAGTAGGAAAATTTCAAGGAGGTGGAGCCTTCAATGTCATCCCT
EST: gi|218497348|gb|FG955372.1|FG955372
EST:     TAAGCCTTCAGCAACTTGTTTCCCGGGAAGCTGATCCCCTAGACTCACAG                         GTAGTAACAGTAGGAAAATTTCAAGGAGGTGGAGCCTTCAATGTCATCCCT
genomic: TAAGCCTTCAGCAACTTGTTTCCCGGGAAGCTGATCCCCTAGACTCACAGgtgagttact ... tgtttttcagGTAGTAACAGTAGGAAAATTTCAAGGAGGTGGAGCCTTCAATGTCATCCCT
EST: gi|58590412|gb|CF988720.1|CF988720
EST:     TAAGCCTTCAGCAACTTGTTTCCCGGGAAGCTGATCCCCTAGACTCACAG                         GTAGTAACAGTAGGAAAATTTCAAGGAGGTGGAGCCTTCAATGTCATCCCT
genomic: TAAGCCTTCAGCAACTTGTTTCCCGGGAAGCTGATCCCCTAGACTCACAGgtgagttact ... tgtttttcagGTAGTAACAGTAGGAAAATTTCAAGGAGGTGGAGCCTTCAATGTCATCCCT
EST: gi|58588534|gb|CF986842.1|CF986842
EST:     TAAGCCTTCAGCAACTTGTTTCCCGGGAAGCTGATCCCCTAGACTCACAG                         GTAGTAACAGTAGGAAAATTTCAAGGAGGTGGAGCCTTCAATGTGGTCCCT
genomic: TAAGCCTTCAGCAACTTGTTTCCCGGGAAGCTGATCCCCTAGACTCACAGgtgagttact ... tgtttttcagGTAGTAACAGTAGGAAAATTTCAAGGAGGTGGAGCCTTCAATGTCATCCCT
EST: gi|86496037|gb|CI138670.1|CI138670
EST:     AAGCTGATCCCCTAGACTCACAG                         GTAGTAACAGTAGGAAAATTTCAAGGAGGTGGAGCCTTCAATGTCATCCCT
genomic: AAGCTGATCCCCTAGACTCACAGgtgagttact ... tgtttttcagGTAGTAACAGTAGGAAAATTTCAAGGAGGTGGAGCCTTCAATGTCATCCCT
EST: gi|25778006|gb|CA752758.1|CA752758
EST:     TAAGCCTTCAGCAACTTGTTTCCCGGGAAGCTGATCCCCTAGACTCACAG                         GTAGTAACAGTAGGAAAATTTCAAGGAGGTGGAGCCTTCAATGTCATCCCT
genomic: TAAGCCTTCAGCAACTTGTTTCCCGGGAAGCTGATCCCCTAGACTCACAGgtgagttact ... tgtttttcagGTAGTAACAGTAGGAAAATTTCAAGGAGGTGGAGCCTTCAATGTCATCCCT
EST: gi|38473362|gb|CF957494.1|CF957494
EST:     TAAGCCTTCAGCAACTTGTTTCCCGGGAAGCTGATCCCCTAGACTCACAG                         GTAGTAACAGTAGGAAAATTTCAAGGAGGTGGAGCCTTCAATGTCATCCCT
genomic: TAAGCCTTCAGCAACTTGTTTCCCGGGAAGCTGATCCCCTAGACTCACAGgtgagttact ... tgtttttcagGTAGTAACAGTAGGAAAATTTCAAGGAGGTGGAGCCTTCAATGTCATCCCT
EST: gi|58684058|gb|CK072745.1|CK072745
EST:     TAAGCCTTCAGCAACTTGTTTCCCGGGAAGCTGATCCCCTAGACTCACAG                         GTAGTAACAGTAGGAAAATTTCAAGGAGGTGGAGCCTTCAATGTCATCCCT
genomic: TAAGCCTTCAGCAACTTGTTTCCCGGGAAGCTGATCCCCTAGACTCACAGgtgagttact ... tgtttttcagGTAGTAACAGTAGGAAAATTTCAAGGAGGTGGAGCCTTCAATGTCATCCCT

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: 73 (upstream exon), 70 (downstream exon)
Score: 53

ACTTCCCCACCACACTATAGATCCAATACTGGCTGCATCAAATGTTATTGTAAGCCTTCAGCAACTTGTTTCCCGGGAAGCTGATCCCCTAGACTCACAGgtgagttact ... tgtttttcagGTAGTAACAGTAGGAAAATTTCAAGGAGGTGGAGCCTTCAATGTCATCCCTGATTCTGTTACAATTGGTGGCACCTTCCGAGCCTTTTTAAAAGAGAGTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtgtatactccagaatgtaagtctttcccctcttggtggctttgtttttcagGTAGTAACAGTAGGAAAATTTCAAGGAGGTGGAGCCTTCAATGTCATCCCTGATTCTGTTACAATTGGTGGCACCTTCCGAGCCTTTTTAAAAGAGAGTT
                                          ctttgtttttc  CT-rich tract
                                           tttgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgctactaatcatttgttcctctcacattgccatgtgagttgcactttgtgtatactccagaatgtaagtctttcccctcttggtggctttgtttttcagGTAGTAACAGTAGGAAAATTTCAAGGAGGTGGAGCCTTCAATGTCATCCCTGATTCTGTTACAATTGGTGGCACCTTCCGAGCCTTTTTAAAAGAGAGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
tgctact
- - - - -tcatttg
- - - - - - - - - - - - - - - -catgtga
- - - - - - - - - - - - - - - - - - - - tgcactt