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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacgatatcgtgtgggtattatgagagcagaaatttttagtaattctatcaaacatttggtaaatctttctgtgttaattgatcaattgcaatctttcagGTGCACCCAGAAGGAAAATATGTTGTTGATGTCGATAAAAGTATTGATATTACAAAGCTCTCGCCTTCAACAAGAGTTGCTCTTCGAAATGACAGCTATA

Basic information

species Oryza sativa
transcript LOC_Os06g39870.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g39870.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA08G24000.1 (Glycine max), 3'ss of exon 2
-aacgatatcgtgtgggtattatgagagcagaaatttttagtaattctatcaaacatttggtaaatctttctgtgttaattgatcaattgcaatctttcagGTGCACCCAGAAGGAAAATATGTTGTTGATGTCGATAAAAGTATTGATATTACAAAGCTCTCGCCTTCAACAAGAGTTGCTCTTCGAAATGACAGCTATA
  | |  |  || | | | | |  | |   |  ||  | | ||||   |    |        ||       |||| | |||  ||  || |  |  ||||||| |||||||||||||||||||| |||||| | || ||||||||||| ||||||||| |  | || || || |||||||| ||||| || ||||| ||| 
ttatg-caatgtttagttctgaaaacacacgtcatcctaattaataaaacaggatcaaaaccaagatcaattgtgctgatttttcctttactcttcttcagGTCCACCCAGAAGGAAAATATGTCGTTGATATTGACAAAAGTATTGACATTACAAAGATTACTCCATCCACTAGAGTTGCACTTCGCAACGACAGTTATG

upper sequence: LOC_Os06g39870.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 2
aacgatatcgtgtgggtattatgagagcagaaatttttagtaattctatcaaac---atttggt--aaatctttctgtgttaattgatcaattgcaatctttcagGTGCACCCAGAAGGAAAATATGTTGTTGATGTCGATAAAAGTATTGATATTACAAAGCTCTCGCCTTCAACAAGAGTTGCTCTTCGAAATGACAGCTATA
    ||    |||     || ||| |  ||| |  | |   || |  || ||||   ||    |  ||       |||| | |||  ||  || || |  ||||||| ||||||||||||||||||||||||||  | || |||| |||||| ||||||||| |  | || || || |||||||| || || || ||||| ||| 
--ttatgcaatgttta-gttctgaaa--agacacatctgtcaaattaataaaactggatcaaatccaagatcaattgtgctgatttttcctttacacttcttcagGTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATTACAAAGATTACTCCATCCACTAGAGTTGCACTCCGCAACGACAGTTATG

upper sequence: LOC_Os06g39870.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT5G19990.1 (Arabidopsis thaliana), 3'ss of exon 2
aacgatatcgtgtgggtattatgagagcagaaatttttagtaattctatcaaacatttggtaaatctttctgtgttaattgatca-attgcaatctttcagGTGCACCCAGAAGGAAAATATGTTGTTGATGTCGATAAAAGTATTGATATTACAAAGCTCTCGCCTTCAACAAGAGTTGCTCTTCGAAATGACAGCTATA
                        |     |  |||||  | ||  | |      ||     ||  |   |||    |  | | | | | | || || ||||| || ||||| || || |||||||||||| | || |||||||| || ||||| ||  || | || ||||| |||||||||||||| ||||| |||||| 
------------------------gtatgaatcttttttattatcatgtttgtatttctacgaacatagttgtcagtaaggcttacactcccattttccagGTTCATCCAGAGGGGAAGTATGTTGTTGATATTGACAAAAGTATAGACATTACGAAAATCACTCCATCAACGAGAGTTGCTCTTCGTAATGATAGCTATG

upper sequence: LOC_Os06g39870.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv04s0008g04690.t01 (Vitis vinifera), 3'ss of exon 2
aacgatatcgtgtgggtattatgagagcagaaatttttagtaattctatcaaacatttg--gtaaatctttctgtgttaattgatcaa---ttgcaatctttcagGTGCACCCAGAAGGAAAATATGTTGTTGATGTCGATAAAAGTATTGATATTACAAAGCTCTCGCCTTCAACAAGAGTTGCTCTTCGAAATGACAGCTATA
     | ||       |  | | |  || |||   ||||  |||  | | |   ||     || | |     ||  ||   |||| |    || |    ||| |||| || |||||||| || |||||||||||| | ||||| |  || || || || ||| || | ||||||||  ||||||||||||| |||||||||||| 
--atttctctaccattttcttttacggctgaa---tttaacaatgttgtgatgtatgaaatgtgagttcagatgatttggctgataatattttccttctttttagGTTCATCCAGAAGGGAAGTATGTTGTTGATATTGATAAGAACATAGACATCACTAAGATCACACCTTCAACCCGAGTTGCTCTTCGCAATGACAGCTATG

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|58612276|gb|CK039988.1|CK039988
EST:     CAAGGTTATGGGCAAGTCCAAGGTTCTAGTGAAG                         GTGCACCCAGAAGGAAAATATGTTGTTGATGTCGATAAAAGTATTGATATT
genomic: CAAGGTTATGGGCAAGTCCAAGGTTCTAGTGAAGgtacatatcc ... aatctttcagGTGCACCCAGAAGGAAAATATGTTGTTGATGTCGATAAAAGTATTGATATT
EST: gi|29655700|gb|CB651975.1|CB651975
EST:     ATGTTGGTGAGGTTGTCAAGGTTATGGGCAAGTCCAAGGTTCTAGTGAAG                         GTGCACCCAGAAGGAAAATATGTTGTTGATGTCGATAAAAGTATTGATATT
genomic: ATGTTGGTGAGGTTGTCAAGGTTATGGGCAAGTCCAAGGTTCTAGTGAAGgtacatatcc ... aatctttcagGTGCACCCAGAAGGAAAATATGTTGTTGATGTCGATAAAAGTATTGATATT
EST: gi|89172082|gb|CI721141.1|CI721141
EST:     ATGTTGGTGAGGTTGTCAAGGTTATGGGCAAGTCCAAGGTTCTAGTGAAG                         GTGCACCCAGAAGGAAAATATGTNGTCGATGTCGATAAAAGTATCGATAT
genomic: ATGTTGGTGAGGTTGTCAAGGTTATGGGCAAGTCCAAGGTTCTAGTGAAGgtacatatcc ... aatctttcagGTGCACCCAGAAGGAAAATATGTTGTTGATGTCGATAAAAGTATTGATAT
EST: gi|88669214|gb|CI719352.1|CI719352
EST:     ATGTTGGTGAGGTTGTCAAGGTTATGGGCAAGTCCAAGGTTCTAGTGAAG                         GTGCACCCAGAAGGAAAATATGTTGTTGATGTCGATAAAAGTATTGATATT
genomic: ATGTTGGTGAGGTTGTCAAGGTTATGGGCAAGTCCAAGGTTCTAGTGAAGgtacatatcc ... aatctttcagGTGCACCCAGAAGGAAAATATGTTGTTGATGTCGATAAAAGTATTGATATT
EST: gi|88672636|gb|CI726752.1|CI726752
EST:     ATGTTGGTGAGGTTGTCAAGGTTATGGGCAAGTCCAAGGTTCTAGTGAAG                         GTGCACCCACAAGGAAAATATGTNGTNGATGTCGATAAAAGTATTGATATC
genomic: ATGTTGGTGAGGTTGTCAAGGTTATGGGCAAGTCCAAGGTTCTAGTGAAGgtacatatcc ... aatctttcagGTGCACCCAGAAGGAAAATATGTTGTTGATGTCGATAAAAGTATTGATATT
EST: gi|88667640|gb|CI722379.1|CI722379
EST:     ATGTTGGTGAGGTTGTCAAGGTTATGGGCAAGTCCAAGGTTCTAGTGAAG                         GTGCACCCAGAAGGAAAATATGTGGTTGATG
genomic: ATGTTGGTGAGGTTGTCAAGGTTATGGGCAAGTCCAAGGTTCTAGTGAAGgtacatatcc ... aatctttcagGTGCACCCAGAAGGAAAATATGTTGTTGATG
EST: gi|88692546|gb|CI736121.1|CI736121
EST:     ATGTTGGTGAGGTTGTCAAGGTTATGGGCAAGTCCAAGGTTCTAGTGAAG                         GTGCACCCAGAAGGAAAATATGTCGTTGATGTCGATAA
genomic: ATGTTGGTGAGGTTGTCAAGGTTATGGGCAAGTCCAAGGTTCTAGTGAAGgtacatatcc ... aatctttcagGTGCACCCAGAAGGAAAATATGTTGTTGATGTCGATAA
EST: gi|88334119|gb|CI641170.1|CI641170
EST:     ATGTTGGTGAGGTTGTCAAGGTTATGGGCAAGTCCAAGGTTCTAGTGAAG                         GTGCACCCAGAAGGAAAATATGTTGTTGATGTCGATAAAAGTATTGATATT
genomic: ATGTTGGTGAGGTTGTCAAGGTTATGGGCAAGTCCAAGGTTCTAGTGAAGgtacatatcc ... aatctttcagGTGCACCCAGAAGGAAAATATGTTGTTGATGTCGATAAAAGTATTGATATT
EST: gi|88688166|gb|CI731742.1|CI731742
EST:     ATGTTGGTGAGGTTGTCAAGGTTATGGGCAAGTCCAAGGTTCTAGTGAAG                         GTGCACCCAGAAGGAAAATATGTTGTTGATGTC
genomic: ATGTTGGTGAGGTTGTCAAGGTTATGGGCAAGTCCAAGGTTCTAGTGAAGgtacatatcc ... aatctttcagGTGCACCCAGAAGGAAAATATGTTGTTGATGTC
EST: gi|88671979|gb|CI726095.1|CI726095
EST:     ATGTTGGTGAGGTTGTCCAGGTTATGGGCAAGTCCAAGGTTCTAGTGAAG                         GTGCACCCAGAAGGAAAATATGTTGTCGATGTCGATAAAAGTATCGATATT
genomic: ATGTTGGTGAGGTTGTCAAGGTTATGGGCAAGTCCAAGGTTCTAGTGAAGgtacatatcc ... aatctttcagGTGCACCCAGAAGGAAAATATGTTGTTGATGTCGATAAAAGTATTGATATT
EST: gi|88908591|gb|CI713149.1|CI713149
EST:     ATGTTGGTGAGGTTGTCAAGGTTATGGGCAAGTCCAAGGTTCTAGTGAAG                         GTGCACCCAGAAGGAAAATATGTTGTTGATGTCG
genomic: ATGTTGGTGAGGTTGTCAAGGTTATGGGCAAGTCCAAGGTTCTAGTGAAGgtacatatcc ... aatctttcagGTGCACCCAGAAGGAAAATATGTTGTTGATGTCG
EST: gi|88670889|gb|CI725005.1|CI725005
EST:     ATGTTGGTGAGGTTGTCAAGGTTATGGGCAAGTCCAAGGTTCTAGTGAAG                         GTGCACCCAGAAGGAAAATATGTTGTTGATGTCGATA
genomic: ATGTTGGTGAGGTTGTCAAGGTTATGGGCAAGTCCAAGGTTCTAGTGAAGgtacatatcc ... aatctttcagGTGCACCCAGAAGGAAAATATGTTGTTGATGTCGATA
EST: gi|88391263|gb|CI595517.1|CI595517
EST:     TGTTGGTGAGGTTGTCAAGGTTATGGGCAAGTC-AAGGTTCCTAGTGAAG                         GTGGACCCAGAAGGAAAATATGTTGTTGATGTCGATAAAAGTATTGATAT
genomic: TGTTGGTGAGGTTGTCAAGGTTATGGGCAAGTCCAAGGTTC-TAGTGAAGgtacatatcc ... aatctttcagGTGCACCCAGAAGGAAAATATGTTGTTGATGTCGATAAAAGTATTGATAT
EST: gi|88676270|gb|CI730383.1|CI730383
EST:     ATGTTGGTGAGGTTGTCAAGGTTATGGGCAAGTCCAAGGTTCTACTGAAG                         GTGCACCCAGAAGGAAAATATGT
genomic: ATGTTGGTGAGGTTGTCAAGGTTATGGGCAAGTCCAAGGTTCTAGTGAAGgtacatatcc ... aatctttcagGTGCACCCAGAAGGAAAATATGT
EST: gi|88337057|gb|CI628143.1|CI628143
EST:     ATGTTGGTGAGGTTGTCAAGGTTATGGGCAAGTCCAAGGTTCTAGTGAAG                         GTGCACCCAGAAGGAAAATATGTTGTTGATGTCGATAAAAGTATTGATATT
genomic: ATGTTGGTGAGGTTGTCAAGGTTATGGGCAAGTCCAAGGTTCTAGTGAAGgtacatatcc ... aatctttcagGTGCACCCAGAAGGAAAATATGTTGTTGATGTCGATAAAAGTATTGATATT
EST: gi|88676783|gb|CI730896.1|CI730896
EST:     ATGTTGGTGAGGTTGTCAAGGTTATGGGCAAGTCCAAGGTTCTAGTGAAG                         GTGCACCCAGAAGGAAAATATGTNGTTGATGTCGAT
genomic: ATGTTGGTGAGGTTGTCAAGGTTATGGGCAAGTCCAAGGTTCTAGTGAAGgtacatatcc ... aatctttcagGTGCACCCAGAAGGAAAATATGTTGTTGATGTCGAT
EST: gi|88671588|gb|CI725704.1|CI725704
EST:     ATGTTGGTGAGGTTGTCAAGGTTATGGGCAAGTCCAAGGTTCTAGTGAAG                         GTGCACCCAGAAGGAAAATATGTTGTTGATGT
genomic: ATGTTGGTGAGGTTGTCAAGGTTATGGGCAAGTCCAAGGTTCTAGTGAAGgtacatatcc ... aatctttcagGTGCACCCAGAAGGAAAATATGTTGTTGATGT
EST: gi|88324402|gb|CI566215.1|CI566215
EST:     ATGTTGGTGAGGTTGTCAAGGTTATGGGCAAGTCCAAGGTTCTAGTGAAG                         GTGCACCCAGAAGGAAAATATGTTTGTTGATGTCGATAAAAGTATTGATAT
genomic: ATGTTGGTGAGGTTGTCAAGGTTATGGGCAAGTCCAAGGTTCTAGTGAAGgtacatatcc ... aatctttcagGTGCACCCAGAAGGAAAATATGTT-GTTGATGTCGATAAAAGTATTGATAT
EST: gi|88345698|gb|CI630966.1|CI630966
EST:     ATGTTGGTGAGGTTGTCAAGGTTATGGGCAAGTCCAAGGTTCTAGTGAAG                         GTGCACCCAGAAGGAAAATATGTTGTTGATGTCGATAAAAGTATTGATATT
genomic: ATGTTGGTGAGGTTGTCAAGGTTATGGGCAAGTCCAAGGTTCTAGTGAAGgtacatatcc ... aatctttcagGTGCACCCAGAAGGAAAATATGTTGTTGATGTCGATAAAAGTATTGATATT

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: 42 (upstream exon), 72 (downstream exon)
Score: 6

TTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATGTTGGTGAGGTTGTCAAGGTTATGGGCAAGTCCAAGGTTCTAGTGAAGgtacatatcc ... aatctttcagGTGCACCCAGAAGGAAAATATGTTGTTGATGTCGATAAAAGTATTGATATTACAAAGCTCTCGCCTTCAACAAGAGTTGCTCTTCGAAATGACAGCTATA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatcaaacatttggtaaatctttctgtgttaattgatcaattgcaatctttcagGTGCACCCAGAAGGAAAATATGTTGTTGATGTCGATAAAAGTATTGATATTACAAAGCTCTCGCCTTCAACAAGAGTTGCTCTTCGAAATGACAGCTATA
                                               tctttc  CT-rich tract
                             ttaattgatcaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacgatatcgtgtgggtattatgagagcagaaatttttagtaattctatcaaacatttggtaaatctttctgtgttaattgatcaattgcaatctttcagGTGCACCCAGAAGGAAAATATGTTGTTGATGTCGATAAAAGTATTGATATTACAAAGCTCTCGCCTTCAACAAGAGTTGCTCTTCGAAATGACAGCTATA

- - - - - - - - - - - - -agcagaa
- - - - - - - - - - - - - - - - - - - - - - - - tcaaaca