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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatccgcacaaccccgttccccatccccatctcctctcatagctcagccgacttgtaaagatctgttgtttttctactcttcttgttcttgatatgtttggcttatacatcgtttgctcgatttggctttcagCTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG

Basic information

species Oryza sativa
transcript LOC_Os01g68710.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g68710.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G031204_T01 (Zea mays), 3'ss of exon 1
gtatccgcacaaccccgttccccatccccatctcctctcatagctcagccgacttgtaaagatctgttgtttttctactcttcttgttcttgatatgtttggcttatacatcgtttgctcgatttggctttcagCTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
                                      |   |   |   |      |||   |  |    ||| |     ||      |  || | |||   ||  |   |       | |         |||| ||||||||||||||| | || ||||| |||||||||||||| || |||
----------------------------------acggcgccgagtaaagggtccaaaaatgacattaaaattttttagggtccaaacgtgaatttttttccgttgaaggaccaaaatgcaaaaaattcggcagCGTCGGCCAAGAAGTCCAGCGACGTCACCGAGCTTCAGATCGGCGTCAAG

upper sequence: LOC_Os01g68710.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G153991_T01 (Zea mays), 3'ss of exon 1
gtatccgcacaaccccgttccccatccccatctcctc-tcatagctcagccgacttgtaaagatctgttgtttttctactcttcttgttcttgatatgtttggcttatacatcgtttgctcg-atttggctttcagCTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
||  |       |       |  | | | ||| |||  ||| ||| |  ||| |    | ||   || |  ||       |   ||   |||||  || |   ||| |  | |  ||||| |   || |  | |||| ||||||||||||||||| || ||||| |||||||||||||| || |||
gtgacgcagggtctttacctctaaactcgatcgccttgtcagagc-cgtccgcccctcacagccttgctcctt-------cccgtttgccttgacgtgctctccttttgaaaccattgcttgtgatttgtatgcagCGTCGGCCAAGAAGTCCGGCGACGTCACCGAGCTTCAGATCGGCGTCAAG
















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|88723075|gb|CI746585.1|CI746585
EST:     CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCG                         CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
genomic: CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCGgtatccgcac ... tggctttcagCTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
EST: gi|55440369|gb|CV733494.1|CV733494
EST:     CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCG                         CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCATAACTGNGTGAAG
genomic: CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCGgtatccgcac ... tggctttcagCTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
EST: gi|88723491|gb|CI747001.1|CI747001
EST:     CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCG                         CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
genomic: CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCGgtatccgcac ... tggctttcagCTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
EST: gi|55409944|gb|CV722320.1|CV722320
EST:     CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCG                         CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
genomic: CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCGgtatccgcac ... tggctttcagCTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
EST: gi|88723609|gb|CI747119.1|CI747119
EST:     CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCG                         CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
genomic: CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCGgtatccgcac ... tggctttcagCTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
EST: gi|88722134|gb|CI745461.1|CI745461
EST:     CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCG                         CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
genomic: CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCGgtatccgcac ... tggctttcagCTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
EST: gi|568861|gb|D39710.1|D39710
EST:     CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCG                         CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
genomic: CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCGgtatccgcac ... tggctttcagCTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
EST: gi|33659572|gb|CF282185.1|CF282185
EST:     CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCG                         CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
genomic: CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCGgtatccgcac ... tggctttcagCTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
EST: gi|88344739|gb|CI624390.1|CI624390
EST:     CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCG                         CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
genomic: CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCGgtatccgcac ... tggctttcagCTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
EST: gi|88723542|gb|CI747052.1|CI747052
EST:     CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCG                         CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
genomic: CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCGgtatccgcac ... tggctttcagCTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
EST: gi|55436954|gb|CV731666.1|CV731666
EST:     CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCG                         CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
genomic: CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCGgtatccgcac ... tggctttcagCTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
EST: gi|58589883|gb|CF988191.1|CF988191
EST:     CCTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGG-CCTCATCCTGACCG                         CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
genomic: CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCGgtatccgcac ... tggctttcagCTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
EST: gi|11171677|gb|AU163906.1|AU163906
EST:     TTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGNCGGCCNTCATCNTGACCG                         CTTCGGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
genomic: CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCGgtatccgcac ... tggctttcagCTTC-GGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
EST: gi|55433322|gb|CV729734.1|CV729734
EST:     CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCG                         CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
genomic: CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCGgtatccgcac ... tggctttcagCTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
EST: gi|88726773|gb|CI750428.1|CI750428
EST:     CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCG                         CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
genomic: CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCGgtatccgcac ... tggctttcagCTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
EST: gi|55413431|gb|CV725807.1|CV725807
EST:     CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCG                         CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTG-AN
genomic: CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCGgtatccgcac ... tggctttcagCTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
EST: gi|2442348|gb|C74119.1|C74119
EST:     CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCG                         CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
genomic: CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCGgtatccgcac ... tggctttcagCTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
EST: gi|55414253|gb|CV726629.1|CV726629
EST:     CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCG                         CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTTTGATCGGTGTGAAG
genomic: CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCGgtatccgcac ... tggctttcagCTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
EST: gi|55412950|gb|CV725326.1|CV725326
EST:     CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCG                         CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
genomic: CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCGgtatccgcac ... tggctttcagCTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
EST: gi|88827090|gb|CI777655.1|CI777655
EST:     CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCG                         CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
genomic: CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCGgtatccgcac ... tggctttcagCTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
EST: gi|2442460|gb|C74231.1|C74231
EST:     CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCG                         CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
genomic: CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCGgtatccgcac ... tggctttcagCTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
EST: gi|27547036|gb|CA765286.2|CA765286
EST:     CATCCTGACCG                         CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
genomic: CATCCTGACCGgtatccgcac ... tggctttcagCTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
EST: gi|55441436|gb|CV734038.1|CV734038
EST:     CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCG                         CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
genomic: CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCGgtatccgcac ... tggctttcagCTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
EST: gi|33685240|gb|CF313479.1|CF313479
EST:     CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCG                         CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
genomic: CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCGgtatccgcac ... tggctttcagCTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
EST: gi|55413109|gb|CV725485.1|CV725485
EST:     CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCG                         CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
genomic: CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCGgtatccgcac ... tggctttcagCTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
EST: gi|51946051|gb|CV152392.1|CV152392
EST:     CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCG                         CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
genomic: CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCGgtatccgcac ... tggctttcagCTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
EST: gi|163928575|gb|EG711160.1|EG711160
EST:     CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCG                         CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
genomic: CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCGgtatccgcac ... tggctttcagCTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
EST: gi|428562|gb|D24714.1|D24714
EST:     CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCG                         CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTNAAG
genomic: CTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCGgtatccgcac ... tggctttcagCTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG

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: 65 (upstream exon), 59 (downstream exon)
Score: 62

GTACTGGAGAAGCGAATGGGGAAGCGTCAGCAGCAGCGGCGGCTCGTCCGCTTCGCCGTCGCCGCCGCCGTCGTTGTCGCGGCGGCCCTCATCCTGACCGgtatccgcac ... tggctttcagCTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcttgttcttgatatgtttggcttatacatcgtttgctcgatttggctttcagCTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG
        tcttgat  putative branch site (score: 62)
                                                ctttc  putative PPT
             atatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatccgcacaaccccgttccccatccccatctcctctcatagctcagccgacttgtaaagatctgttgtttttctactcttcttgttcttgatatgtttggcttatacatcgtttgctcgatttggctttcagCTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT