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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcaatctttcgtccttaacctataatagcctatagctatagatcttgttgattgtgcatgttctgaaatgttcaacaatttgctgcattgactaccatagGCTGTCATAAATGCTGGCATTATTGGTCCTCTGGTGAATCTGCTCCAAACGGCAGAGTTCGATATCAAGAAGGAAGCTGCATGGGCCATCTCAAATGCTA

Basic information

species Oryza sativa
transcript LOC_Os01g14950.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g14950.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G091119_T02 (Zea mays), 3'ss of exon 7
---gcaatctttcgtccttaacctataatagcctatagctatagatcttgttgattgtgcatgttctgaaatgttcaa-caatttgctgcattgactaccatagGCTGTCATAAATGCTGGCATTATTGGTCCTCTGGTGAATCTGCTCCAAACGGCAGAGTTCGATATCAAGAAGGAAGCTGCATGGGCCATCTCAAATGCTA
      || ||||     | ||| ||   |  ||    || |   |    ||| | |   |||||    | || | |  || |||| |    ||| |    ||||||||||||| |||||| ||||| | |||| || || | ||||| |||   |||||||| |||||||||||||| ||||| |||||||||||||| ||||
atttttatttttcacagatgacccatgtcatgct---tctttgccttcatttgttcgaaaatgttagtcattgattactcactttgatatgctgaatttt-tagGCTGTCATAAGTGCTGGTATTATCGCTCCTTTGTTGCAACTGCTTCAAGGAGCAGAGTTTGATATCAAGAAGGAGGCTGCTTGGGCCATCTCAAACGCTA

upper sequence: LOC_Os01g14950.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G088231_T01 (Zea mays), 3'ss of exon 8
gcaatctttcgtccttaacctataatagcctatagctatagatcttgttgattgtgcatgttctgaaatgttcaa-caatttgctgcattgactaccatagGCTGTCATAAATGCTGGCATTATTGGTCCTCTGGTGAATCTGCTCCAAACGGCAGAGTTCGATATCAAGAAGGAAGCTGCATGGGCCATCTCAAATGCTA
 | ||   |  |   ||   | | |   | |    || |   || |||         |||||   || || | |  |  ||||||| | | | |    ||||||||||||| ||| || || || | |||| || || | ||||| ||||| |||||||| |||||||||||||| ||||| |||||||||||||||||||
actattaataatttatattttctcactacatgcttctttgcttcatgtgttcaaaaaatgttagtaattgattactcgctttgctgtactcaatttt-tagGCTGTCATAAGTGCCGGTATCATCGCTCCTTTGTTGCAACTGCTTCAAACAGCAGAGTTTGATATCAAGAAGGAGGCTGCTTGGGCCATCTCAAATGCTA

upper sequence: LOC_Os01g14950.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA10G29000.1 (Glycine max), 3'ss of exon 8
gcaatctttcgtccttaacctataatagcctatagctatagatcttgttga--ttgtgcatgttctgaaatgttcaacaatttgctgcattgactaccatagGCTGTCATAAATGCTGGCATTATTGGTCCTCTGGTGAATCTGCTCCAAACGGCAGAGTTCGATATCAAGAAGGAAGCTGCATGGGCCATCTCAAATGCTA
| |   || | |  ||    ||| |||   || | ||  |  |    ||||  || |   ||   | | ||  ||  |||||      | | |       ||||||| ||  | |||    | |||| |||| |||| |||||||| ||||  || ||||| ||||||||||| |||||||| ||||| |||||||||||||
gtatagttacttgtttgttttatgataat-taaacctccattttcacttgaagttcttattgcaataatattctcttcaattcctgataataa-----gcagGCTGTGATTGAGGCTAATCTAATTGCTCCTTTGGTCAATCTGCTTCAAAATGCTGAGTTTGATATCAAGAAAGAAGCTGCTTGGGCTATCTCAAATGCTA

upper sequence: LOC_Os01g14950.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA03G39210.1 (Glycine max), 3'ss of exon 9
---------------gcaatctt--tcgtccttaacctata-atagcctatagctatagat--cttgttgattgtgcatgt---tctgaaatgttcaa---caatttgctgca----ttgactacc-atagGCTGTCATAAATGCTGGCATTATTGGTCCTCTGGTGAATCTGCTCCAAACGGCAGAGTTCGATATCAAGAAGGAAGCTGCATGGGCCATCTCAAATGCTA
               |   ||||  | ||  |  |  | |  ||    | ||| || |  |    ||||   | ||| | |     | |||| || ||   || ||  || ||     |||| | | | ||| ||| ||  | ||| | || |||| |||| | ||  || |||| ||||  || ||||| ||||||||||| || ||||| ||||| |||||||||||||
gtatagattattttagtggtcttcattgtgttgtatttgtccatcagatgtagttaaatttgatgtgttatctttgcgtttgaacttaaaatcttaaattgcatttctcttcaatttctgacaatctacagGATGTAATTGAGGCTAGTATAATTGCTCCTTTAGTCCATTTGCTTCAAAATGCTGAGTTTGATATCAAGAAAGAGGCTGCTTGGGCAATCTCAAATGCTA

upper sequence: LOC_Os01g14950.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA20G38320.2 (Glycine max), 3'ss of exon 8
gcaatctttcgtccttaacctataatagcctatagctatagatcttgttgattgtgcatgttc---tgaaatgttcaacaatttgctgcattgactaccatagGCTGTCATAAATGCTGGCATTATTGGTCCTCTGGTGAATCTGCTCCAAACGGCAGAGTTCGATATCAAGAAGGAAGCTGCATGGGCCATCTCAAATGCTA
| |   || | |  | |   |||  ||    |    |     ||   || |  || | | ||    | | || |||  |||||      | | |     | ||||||| ||  | |||    | |||| |||| |||| |||||||| ||||  || ||||| ||||||||||| |||||||| ||||| |||||||||||||
gtatagttacttgttcattttatggtaattaaggcttgattttcacttttaaagttcttattgcaataatattttcttcaattcctgataataa-----acagGCTGTGATTGAGGCTAATCTAATTGCTCCTTTGGTCAATCTGCTTCAAAATGCTGAGTTTGATATCAAGAAAGAAGCTGCTTGGGCTATCTCAAATGCTA

upper sequence: LOC_Os01g14950.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA19G41770.1 (Glycine max), 3'ss of exon 8
----------------------gcaatctttcgtccttaacctataatagcctatagctatagatcttgt-tgattgtgcatgttct-gaaatgttcaacaatttgctgcattgactacc--------atagGCTGTCATAAATGCTGGCATTATTGGTCCTCTGGTGAATCTGCTCCAAACGGCAGAGTTCGATATCAAGAAGGAAGCTGCATGGGCCATCTCAAATGCTA
                       || | | | ||  ||  ||   |   |    ||  | | ||| |  | |  |||||  ||  ||  |||| || ||  || |    | || | | |         | ||| ||| ||  | ||| | || |||| |||| | ||  || |||| ||||  || ||||| ||||||||||| || ||||| ||||| |||||||||||||
gtatagattattttaggggtcttcattgtgttgtatttgtccatcagatgtagttaaattttgatgtgttatctttgtgtttgaacttaaaatcttaaattatatttctctttaatttctgacaatctacagGATGTAATTGAGGCTAGTATAATTGCTCCTTTAGTCCATTTGCTTCAAAATGCTGAGTTTGATATCAAGAAAGAGGCTGCTTGGGCAATCTCAAATGCTA

upper sequence: LOC_Os01g14950.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv14s0060g01510.t01 (Vitis vinifera), 3'ss of exon 8
-------gcaatctttcgtccttaacctataatagcctatagctatagatcttgttgattgtgcatgttctgaaatgttcaacaatttgctgcattgactaccatagGCTGTCATAAATGCTGGCATTATTGGTCCTCTGGTGAATCTGCTCCAAACGGCAGAGTTCGATATCAAGAAGGAAGCTGCATGGGCCATCTCAAATGCTA
        |    ||   |  |  |  ||| |||    ||    ||| ||  |   | |  || ||| | | |  | |  |   |||| |   |||         ||||||| ||  | ||   ||| |||||||| || ||  ||||||| ||||  || ||||| ||||||||||| || ||||| ||||| |||||||||||||
catatagactgatttattttgtggatgtatcatatttcattttcatacatgctag-ggtactgaatgatgt-atgtttgtatgtattttcaaaatt-----ttgcagGCTGTAATTGAGGCAAACATAATTGGTCCCCTTGTTCATCTGCTTCAAAATGCTGAGTTTGATATCAAGAAAGAGGCTGCTTGGGCAATCTCAAATGCTA

upper sequence: LOC_Os01g14950.1 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S43_141V6.1 (Physcomitrella patens), 3'ss of exon 9
--gcaatctttcgtccttaacctataatagcctatagctatagatcttgttgattgtgcatg-ttctgaaatgttcaacaat-ttgctg----cattgacta----ccatagGCTGTCATAAATGCTGGCATTATTGGTCCTCTGGTGAATCTGCTCCAAACGGCAGAGTTCGATATCAAGAAGGAAGCTGCATGGGCCATCTCAAATGCTA
   | | ||      ||    |||| ||      | | | ||||| | |||| |         | || || ||      ||| || |||    | | || ||    |   ||||||| ||  | ||   |||||||   ||||| ||   ||||||    || |||||||||||||| |||||||| || || |||||||| ||||| ||||
gtacgaactcaaaatct-gttctatgatcaaactttggtttagatttggttggtcccaatcaatccttaactgagtggtaatgttactgatgtcgtggattattttctgcagGCTGTAATCGACGCCAACATTATTCCACCTCTTGTTTCTCTGCTTGCTACTGCAGAGTTCGATATTAAGAAGGAGGCCGCTTGGGCCATTTCAAACGCTA

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|58673193|gb|CK061879.1|CK061879
EST:     CTTGCTGGACTATTTCAAATATTACTGCTGGTAACAAAGATCAGATACAG                         GCTGTCATAAATGCTGGCATTATTGGTCCTCTGGTGAATCTGCTCCAAACG
genomic: CTTGCTGGACTATTTCAAATATTACTGCTGGTAACAAAGATCAGATACAGgtatgtgtac ... actaccatagGCTGTCATAAATGCTGGCATTATTGGTCCTCTGGTGAATCTGCTCCAAACG
EST: gi|55411455|gb|CV723831.1|CV723831
EST:     CTTGCTGGACTATTTCAAATATTACTGCTGGTAACAAAGATCAGATACAG                         GCTGTCATAAATGCTGGCATTATTGGTCCTCTGGTGAATCTGCT
genomic: CTTGCTGGACTATTTCAAATATTACTGCTGGTAACAAAGATCAGATACAGgtatgtgtac ... actaccatagGCTGTCATAAATGCTGGCATTATTGGTCCTCTGGTGAATCTGCT
EST: gi|29676486|gb|CB672761.1|CB672761
EST:     TGGACTATTTCAAATATTACTGCTGGTAACAAAGATCAGATACAG                         GCTGTCATAAATGCTGGCATTATTGGTCCTCTGGTGAATCTGCTCCAAACG
genomic: TGGACTATTTCAAATATTACTGCTGGTAACAAAGATCAGATACAGgtatgtgtac ... actaccatagGCTGTCATAAATGCTGGCATTATTGGTCCTCTGGTGAATCTGCTCCAAACG
EST: gi|29640361|gb|CB645370.1|CB645370
EST:     CTTGCTGGACTATTTCAAATATTACTGCTGGTAACAAAGATCAGATACAG                         GCTGTCATAAATGCTGGCATTATTGGTCCTCTGGTGAATCTGCTCCAAACG
genomic: CTTGCTGGACTATTTCAAATATTACTGCTGGTAACAAAGATCAGATACAGgtatgtgtac ... actaccatagGCTGTCATAAATGCTGGCATTATTGGTCCTCTGGTGAATCTGCTCCAAACG
EST: gi|66912883|gb|CX099731.1|CX099731
EST:     CTTGCTGGACTATTTCAAATATTACTGCTGGTAACAAAGATCAGATACAG                         GCTGTCATAAATGCTGGCATTATTGGTCCTCTGGTGAATCTGCTCCAAACG
genomic: CTTGCTGGACTATTTCAAATATTACTGCTGGTAACAAAGATCAGATACAGgtatgtgtac ... actaccatagGCTGTCATAAATGCTGGCATTATTGGTCCTCTGGTGAATCTGCTCCAAACG
EST: gi|218501071|gb|FG960845.1|FG960845
EST:     GACTATTTCAAATATTACTGCTGGTAACAAAGATCAGATACAG                         GCTGTCATAAATGCTGGCATTATTGGTCCTCTGGTGAATCTGCTCCAAACG
genomic: GACTATTTCAAATATTACTGCTGGTAACAAAGATCAGATACAGgtatgtgtac ... actaccatagGCTGTCATAAATGCTGGCATTATTGGTCCTCTGGTGAATCTGCTCCAAACG
EST: gi|218505438|gb|FG959801.1|FG959801
EST:     CTTGCTGGACTATTTCAAATATTACTGCTGGTAACAAAGATCAGATACAG                         GCTGTCATAAATGCTGGCATTATTGGTCCTCTGGTGAATCTGCTCCAAACG
genomic: CTTGCTGGACTATTTCAAATATTACTGCTGGTAACAAAGATCAGATACAGgtatgtgtac ... actaccatagGCTGTCATAAATGCTGGCATTATTGGTCCTCTGGTGAATCTGCTCCAAACG
EST: gi|218479493|gb|FG944059.1|FG944059
EST:     CTTGCTGGACTATTTCAAATATTACTGCTGGTAACAAAGATCAGATACAG                         GCTGTCATAAATGCTGGCATTATTGGTCCTCTGGTGAATCTGCTCCAAACG
genomic: CTTGCTGGACTATTTCAAATATTACTGCTGGTAACAAAGATCAGATACAGgtatgtgtac ... actaccatagGCTGTCATAAATGCTGGCATTATTGGTCCTCTGGTGAATCTGCTCCAAACG
EST: gi|58684581|gb|CK073268.1|CK073268
EST:     CTTGCTGGACTATTTCAAATATTACTGCTGGTAACAAAGATCAGATACAG                         GCTGTCATAAATGCTGGCATTATTGGTCCTCTGGTGAATCTGCTCCAAACG
genomic: CTTGCTGGACTATTTCAAATATTACTGCTGGTAACAAAGATCAGATACAGgtatgtgtac ... actaccatagGCTGTCATAAATGCTGGCATTATTGGTCCTCTGGTGAATCTGCTCCAAACG
EST: gi|13806131|gb|AU181373.1|AU181373
EST:     CTTGCTGGACTATTTCAAATATTACTGCTGGTAACAAAGATCAGATACAG                         GCTGTCATAAATGCTGGCATTATTGGTCCTCTGGTGAATCTGCTCCAAACG
genomic: CTTGCTGGACTATTTCAAATATTACTGCTGGTAACAAAGATCAGATACAGgtatgtgtac ... actaccatagGCTGTCATAAATGCTGGCATTATTGGTCCTCTGGTGAATCTGCTCCAAACG
EST: gi|218496280|gb|FG960701.1|FG960701
EST:     C-TGCTGGACTATTTCAAATATTACTGCTGGTAACAAAGATCAGATACAG                         GCTGTCATAAATGCTGGCATTATTGGTCCTCTGGTGAATCTGCTCCAAACG
genomic: CTTGCTGGACTATTTCAAATATTACTGCTGGTAACAAAGATCAGATACAGgtatgtgtac ... actaccatagGCTGTCATAAATGCTGGCATTATTGGTCCTCTGGTGAATCTGCTCCAAACG

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: 75 (upstream exon), 65 (downstream exon)
Score: 84

CCTCCTAAGTCTGTTGACACAAAATCTCAAGAAAAGCATCAAGAAAGAGGCTTGCTGGACTATTTCAAATATTACTGCTGGTAACAAAGATCAGATACAGgtatgtgtac ... actaccatagGCTGTCATAAATGCTGGCATTATTGGTCCTCTGGTGAATCTGCTCCAAACGGCAGAGTTCGATATCAAGAAGGAAGCTGCATGGGCCATCTCAAATGCTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgattgtgcatgttctgaaatgttcaacaatttgctgcattgactaccatagGCTGTCATAAATGCTGGCATTATTGGTCCTCTGGTGAATCTGCTCCAAACGGCAGAGTTCGATATCAAGAAGGAAGCTGCATGGGCCATCTCAAATGCTA
                                        cattgac  putative branch site (score: 84)
                            aacaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaatctttcgtccttaacctataatagcctatagctatagatcttgttgattgtgcatgttctgaaatgttcaacaatttgctgcattgactaccatagGCTGTCATAAATGCTGGCATTATTGGTCCTCTGGTGAATCTGCTCCAAACGGCAGAGTTCGATATCAAGAAGGAAGCTGCATGGGCCATCTCAAATGCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - tgcatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caacaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgca