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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgtagttgcagtctagcttcttgctttgcatttcaccgagcacctggtgggcgcttgctaatgctcctttttttttctttttttttttttttgcagAAAACAAACCCAGTGGTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGG

Basic information

species Oryza sativa
transcript LOC_Os01g17170.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g17170.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G043109_T01 (Zea mays), 3'ss of exon 1
gttcgtagttgcagtctagcttcttgctttgcatttcaccgagcacctggtgggcgcttgctaatgctcctttttttttctttttttttttttttgcagAAAACAAACCCAGTGGTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGG
|||| |   ||     | ||  ||||| |||| |      |||||  |  | | |  |  ||  ||  | | |  |  |    |  |||| || |||||||||| ||||| || ||||| |||||||||||||||||||||||||| ||||| || || |||||
gttccttcatgtttctttgc--cttgccttgcctcgtctggagcatttcatcgaccat--ctggtgggcgtgtgctgataccctgcttttcttctgcagAAAACTAACCCGGTCGTGGCGGAGATCTTCTCGCTCATGTCCAGGGACGAGGCGCGCCATGCTGG

upper sequence: LOC_Os01g17170.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G081462_T02 (Zea mays), 3'ss of exon 1
gttcgtagttgcagtctagcttcttgctt--tgcatttcaccgagcacctggtgggcgcttgctaatgctcctttttttttctttttttttttttttgcagAAAACAAACCCAGTGGTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGG
       ||| |  ||  ||| ||| |||  ||||||||  ||| | |||||||||||  ||           |  |  | |  |  |||||  | |||||||||| ||||| || ||||| |||||||||||||||||||| ||||| ||||| || || |||||
-------gttcct-tcctgctcctttcttcgtgcatttcctcgaccgcctggtgggcgtgtg-----------tgctgatgccctgctttttcctctgcagAAAACCAACCCGGTCGTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAGGCGCGCCATGCTGG

upper sequence: LOC_Os01g17170.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA03G27380.1 (Glycine max), 3'ss of exon 1
---gttcgtagttgcagtctagcttcttgctttgcatttcaccgagcacctggtgggcgcttgctaatgctcctttttttttcttttttttttttt-ttgcagAAAACAAACCCAGTGGTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGG
    |  |  ||||  |||  | ||  || ||     | |     |||  |  ||| |  ||  |  ||  |   | | || ||||   | ||  | || |||||||| ||||| |||||||||||||| ||||| || ||||| |||||||| ||| |||| |||||
ttcttatgatgttgtggtc--gtttgatgattaattctgctttatgcagttt-tggtcttttattcttggcctgatatattgctttggatgttgatgttacagAAAACCAACCCTGTGGTGGCTGAGATTTTCTCACTGATGTCTAGGGATGAAGCCAGGCATGCTGG

upper sequence: LOC_Os01g17170.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT3G56940.2 (Arabidopsis thaliana), 3'ss of exon 2
gttcgt--agttgcagtctagcttcttgctttgcatttcaccgagcacctggtgggcgcttgctaatgctcctttttttttctttttttttttttttgcagAAAACAAACCCAGTGGTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGG
| || |   || | |||       | ||     | | |    |      |||       ||  |        |||   | | |  | |  |    ||||||||||||||||| || ||||||||||||||||| || ||||| || ||||| ||  | || || ||
gctcattaggtggaagttagagcacatgtgagacttgttgttgtttctttggatcat-tttattggcttgattttgaatctttgatctgatggcattgcagAAAACAAACCCTGTTGTGGCTGAGATCTTCTCTCTTATGTCTAGAGATGAAGCAAGACATGCCGG

upper sequence: LOC_Os01g17170.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S97_248V6.1 (Physcomitrella patens), 3'ss of exon 1
------gttcgtagttgcagtctagcttcttgctttgcatttcaccgagcacctggtgggcgcttgctaatgctcctttttttttctttttttttttttttgcagAAAACAAACCCAGTGGTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGG-----------------------------------
      |||   | |   | | | ||     |||||  || |  |    |  | | |    | ||| ||||| |    ||  || |||   |   | |    ||||| |||||||| |||||||||||||| ||| | || ||||| |||||||| ||| | || |||||                                   
agaaatgttgccactccaattgttgcaaacagcttttgatctttcttctc-tccgat--atgattg-taatgttgaaattgcttccttccatgaatgtga-acagAAGACAAACCCTGTGGTGGCTGAGATTTTCACCCTTATGTCAAGGGATGAAGCCAGACATGCTGGCTTCTTGAACAAGGGACTGTCAGACTTCAACTTGG

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|29662324|gb|CB658599.1|CB658599
EST:     CGGAGTTCTCCGGGTTCCTCCTCTACAAGGAGCTCGGCCGCAGGCTCAAG                         AAAACAAACCCAGTGGTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAG
genomic: CGGAGTTCTCCGGGTTCCTCCTCTACAAGGAGCTCGGCCGCAGGCTCAAGgttcgtagtt ... ttttttgcagAAAACAAACCCAGTGGTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAG
EST: gi|300216174|gb|HO087959.1|HO087959
EST:     CGGGTTCCTCCTCTAC-AGGAGCTCGGCCGCAGGCTCAAG                         AAAACAAACCCAGTGGTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAG
genomic: CGGGTTCCTCCTCTACAAGGAGCTCGGCCGCAGGCTCAAGgttcgtagtt ... ttttttgcagAAAACAAACCCAGTGGTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAG
EST: gi|29672478|gb|CB668753.1|CB668753
EST:     CGGAGTTCTCCGGGTTCCTCCTCTACAAGGAGCTCGGCCGCAGGCTCAAG                         AAAACAAACCCAGTGGTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAG
genomic: CGGAGTTCTCCGGGTTCCTCCTCTACAAGGAGCTCGGCCGCAGGCTCAAGgttcgtagtt ... ttttttgcagAAAACAAACCCAGTGGTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAG
EST: gi|66912779|gb|CX099627.1|CX099627
EST:     CGGAGTTCTCCGGGTTCCTCCTCTACAAGGAGCTCGGCCGCAGGCTCAAG                         AAAACAAACCCAGTGGTGGCTGAGATCTTCTCGCTCATGTCCANGGATGAG
genomic: CGGAGTTCTCCGGGTTCCTCCTCTACAAGGAGCTCGGCCGCAGGCTCAAGgttcgtagtt ... ttttttgcagAAAACAAACCCAGTGGTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAG
EST: gi|38474941|gb|CF959074.1|CF959074
EST:     CGGAGTACTCCGGGTTCCTCCTCTACAAGGAGCTCGGCCGCAGGCTCAAG                         AAAACAAACCCAGTGGTGGCTGAGATCTACTCGCTCATGTCCANGGATGAG
genomic: CGGAGTTCTCCGGGTTCCTCCTCTACAAGGAGCTCGGCCGCAGGCTCAAGgttcgtagtt ... ttttttgcagAAAACAAACCCAGTGGTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAG
EST: gi|29676338|gb|CB672613.1|CB672613
EST:     CGGAGTTCTCCGGGTTCCTCCTCTACAAGGAGCTCGGCCGCAGGCTCAAG                         AAAACAAACCCAGTGGTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAG
genomic: CGGAGTTCTCCGGGTTCCTCCTCTACAAGGAGCTCGGCCGCAGGCTCAAGgttcgtagtt ... ttttttgcagAAAACAAACCCAGTGGTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAG
EST: gi|38471854|gb|CF955985.1|CF955985
EST:     CGGAGTTCTCCGGGTTCCTCCTCTACAAGGAGCTCGGCCGCAGGCTCAAG                         AAAACAAACCCAGTGGTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAG
genomic: CGGAGTTCTCCGGGTTCCTCCTCTACAAGGAGCTCGGCCGCAGGCTCAAGgttcgtagtt ... ttttttgcagAAAACAAACCCAGTGGTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAG
EST: gi|38476267|gb|CF960400.1|CF960400
EST:     CGGAGTTCTCCGGGTTCCTCCTCTACAAGGAGCTCGGCCGCAGGCTCAAG                         AAAACAAACCCAGTGGTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAG
genomic: CGGAGTTCTCCGGGTTCCTCCTCTACAAGGAGCTCGGCCGCAGGCTCAAGgttcgtagtt ... ttttttgcagAAAACAAACCCAGTGGTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAG
EST: gi|38473793|gb|CF957925.1|CF957925
EST:     CGGAGTTCTCCGGGTTCCTCCTCTACAAGGAGCTCGGCCGCAGGCTCAAG                         AAAACAAACCCAGTGGTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAG
genomic: CGGAGTTCTCCGGGTTCCTCCTCTACAAGGAGCTCGGCCGCAGGCTCAAGgttcgtagtt ... ttttttgcagAAAACAAACCCAGTGGTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAG
EST: gi|29619025|gb|CB624037.1|CB624037
EST:     CGGAGTTCTCCGGGTTCCTCCTCTACAAGGAGCTCGGCCGCAGGCTCAAG                         AAAACAAACCCAGTGGTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAG
genomic: CGGAGTTCTCCGGGTTCCTCCTCTACAAGGAGCTCGGCCGCAGGCTCAAGgttcgtagtt ... ttttttgcagAAAACAAACCCAGTGGTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAG
EST: gi|38475252|gb|CF959385.1|CF959385
EST:     GGCCGCAGGCTCAAG                         AAAACAAACCCAGTGGTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAG
genomic: GGCCGCAGGCTCAAGgttcgtagtt ... ttttttgcagAAAACAAACCCAGTGGTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAG
EST: gi|29616676|gb|CB621688.1|CB621688
EST:     CGGAGTTCTCCGGGTTCCTCCTCTACAAGGAGCTCGGCCGCAGGCTCAAG                         AAAACAAACCCAGCGGTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAG
genomic: CGGAGTTCTCCGGGTTCCTCCTCTACAAGGAGCTCGGCCGCAGGCTCAAGgttcgtagtt ... ttttttgcagAAAACAAACCCAGTGGTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAG
EST: gi|38474054|gb|CF958186.1|CF958186
EST:     CGGAGTTCTCCGGGTTCCTCCTCTACAAGGAGCTCGGCCGCAGGCTCAAG                         AAAACAAACCCAGTGGTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAG
genomic: CGGAGTTCTCCGGGTTCCTCCTCTACAAGGAGCTCGGCCGCAGGCTCAAGgttcgtagtt ... ttttttgcagAAAACAAACCCAGTGGTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAG
EST: gi|55409938|gb|CV722314.1|CV722314
EST:     CGGAGTTCTCCGGGTTCCTCCTCTACAAGGAGCTCGGCCGCAGGCTCAAG                         AAAACAAACCCAGTGGTGGCTGAGATCTTC
genomic: CGGAGTTCTCCGGGTTCCTCCTCTACAAGGAGCTCGGCCGCAGGCTCAAGgttcgtagtt ... ttttttgcagAAAACAAACCCAGTGGTGGCTGAGATCTTC
EST: gi|29663604|gb|CB659879.1|CB659879
EST:     CGGAGTTCTCCGGGTTCCTCCTCTACAAGGAGCTCGGCCGCAGGCTCAAG                         AAAACAAACCCAGTGGTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAG
genomic: CGGAGTTCTCCGGGTTCCTCCTCTACAAGGAGCTCGGCCGCAGGCTCAAGgttcgtagtt ... ttttttgcagAAAACAAACCCAGTGGTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAG
EST: gi|2801122|gb|AA754416.1|AA754416
EST:     CGGAGTTCTCCGGGTTCCTCCTCTACAAGGAGCTCGGCCGCA-G-TCAAG                         AAAACAAACCCAGTGGTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAG
genomic: CGGAGTTCTCCGGGTTCCTCCTCTACAAGGAGCTCGGCCGCAGGCTCAAGgttcgtagtt ... ttttttgcagAAAACAAACCCAGTGGTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAG
EST: gi|29620880|gb|CB625891.1|CB625891
EST:     CGGAGTTCTCCGGGTTCCTCCTCTACAAGGAGCTCGGCCGCAGGCTCAAG                         AAAACAAACCCAGTGGTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAG
genomic: CGGAGTTCTCCGGGTTCCTCCTCTACAAGGAGCTCGGCCGCAGGCTCAAGgttcgtagtt ... ttttttgcagAAAACAAACCCAGTGGTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acctggtgggcgcttgctaatgctcctttttttttctttttttttttttttgcagAAAACAAACCCAGTGGTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGG
              tgctaat  putative branch site (score: 2)
            cttgctaatgctcctt  CT-rich tract
                 taatgctccttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgtagttgcagtctagcttcttgctttgcatttcaccgagcacctggtgggcgcttgctaatgctcctttttttttctttttttttttttttgcagAAAACAAACCCAGTGGTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC