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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATACGGATCGTGCGCGACGGCTCGGGACTTCGAGATTTACGCGGCGCATGCCACATTCGAGGACCCGCTTATGCGAGCTCATGGgtacgtctacgtttgtttcctcaccatcgatccatcatatctcttcttctttggcaaggcctttccatcccctgttctccgaaagaacagtgtttcgtgg...

Basic information

species Oryza sativa
transcript LOC_Os01g73500.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g73500.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G167758_T02 (Zea mays), 5'ss of exon 1
----------------ATACGGATCGTGCGCGACGGCTCGGGACTTCGAGATTTACGCGGCGCATGCCACATTCGAGGACCCGCTTATGCGAGCTCATGGgtacgtctacgt------ttgtttcctcaccatcgatc--catcatatctcttcttctttggcaaggcctttccatcccc--tgttctccgaaagaacagtgtttcgtgg
                ||| |||||||  |||||||| ||||||||||||||||||||| |  |||| || || ||||||||||| ||||||||||| |||||||||  |||      | || || || |  ||  ||  | || |   |    | |     || |||     || |  |  | | |          |||| |      |
TGCTGTGCTGGTGAAGATATGGATCGTCTGCGACGGCACGGGACTTCGAGATTTACGCGCCAAATGCGACGTTTGAGGACCCGCTCATGCGAGCTCACGGgtacgtcgtcgtccagtctcgtctcttctctgtctgtcgtcgtcgtcgttggcatccacctccatggctccatcagcatcattatgcgttactgatccagtatgctacag

upper sequence: LOC_Os01g73500.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G167758_T01 (Zea mays), 5'ss of exon 2
ATACGGATCGTGCGCGACGGCTCGGGACTTCGAGATTTACGCGGCGCATGCCACATTCGAGGACCCGCTTATGCGAGCTCATGGgtacgtctacgt------ttgtttcctcaccatcgatc--catcatatctcttcttctttggcaaggcctttccatcccc--tgttctccgaaagaacagtgtttcgtgg
||| |||||||  |||||||| ||||||||||||||||||||| |  |||| || || ||||||||||| ||||||||||| |||||||||  |||      | || || || |  ||  ||  | || |   |    | |     || |||     || |  |  | | |          |||| |      |
ATATGGATCGTCTGCGACGGCACGGGACTTCGAGATTTACGCGCCAAATGCGACGTTTGAGGACCCGCTCATGCGAGCTCACGGgtacgtcgtcgtccagtctcgtctcttctctgtctgtcgtcgtcgtcgttggcatccacctccatggctccatcagcatcattatgcgttactgatccagtatgctacag
















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|88571055|gb|CI662428.1|CI662428
EST:     ATTTACGCGGCGCATGCCACATTCGAGGACCCGCTTATGCGAGCTCATGG                         GGTTAAGCAGATCANATCGGCCTTCTACACACTCCCCAAG
genomic: ATTTACGCGGCGCATGCCACATTCGAGGACCCGCTTATGCGAGCTCATGGgtacgtctac ... ttcattccagGGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAG
EST: gi|33662848|gb|CF293815.1|CF293815
EST:     ATTTACGCGGCGCATGCCACATTCGAGGACCCGCTTATGCGAGCTCATGG                         GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAG
genomic: ATTTACGCGGCGCATGCCACATTCGAGGACCCGCTTATGCGAGCTCATGGgtacgtctac ... ttcattccagGGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAG
EST: gi|33683454|gb|CF311693.1|CF311693
EST:     ATTTACGCGGCGCATGCCACATTCGAGGACCCGCTTATGCGAGCTCATGG                         GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAG
genomic: ATTTACGCGGCGCATGCCACATTCGAGGACCCGCTTATGCGAGCTCATGGgtacgtctac ... ttcattccagGGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAG
EST: gi|33659979|gb|CF290946.1|CF290946
EST:     ATTTACGCGGCGCATGCCACATTCGAGGACCCGCTTATGCGAGCTCATGG                         GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAG
genomic: ATTTACGCGGCGCATGCCACATTCGAGGACCCGCTTATGCGAGCTCATGGgtacgtctac ... ttcattccagGGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAG
EST: gi|55430712|gb|CV728357.1|CV728357
EST:     ATTTACGCGGCGCATGCCACATTCGAGGACCCGCTTATGCGAGCTCATGG                         GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAG
genomic: ATTTACGCGGCGCATGCCACATTCGAGGACCCGCTTATGCGAGCTCATGGgtacgtctac ... ttcattccagGGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAG
EST: gi|88344530|gb|CI637215.1|CI637215
EST:     ATTTACGCGGCGCATGCCACATTCGAGGACCCGCTTATGCGAGCTCATGG                         GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAG
genomic: ATTTACGCGGCGCATGCCACATTCGAGGACCCGCTTATGCGAGCTCATGGgtacgtctac ... ttcattccagGGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAG
EST: gi|25803799|gb|CA759760.1|CA759760
EST:     A-TTACGCGGCGCATGCCATATTCGAGGACCCGCTTATGCGAGCTCATGG                         GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAG
genomic: ATTTACGCGGCGCATGCCACATTCGAGGACCCGCTTATGCGAGCTCATGGgtacgtctac ... ttcattccagGGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAG
EST: gi|33665646|gb|CF296613.1|CF296613
EST:     ATTTACGCGGCGCATGCCACATTCGAGGACCCGCTTATGCGAGCTCATGG                         GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAG
genomic: ATTTACGCGGCGCATGCCACATTCGAGGACCCGCTTATGCGAGCTCATGGgtacgtctac ... ttcattccagGGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAG
EST: gi|38475002|gb|CF959135.1|CF959135
EST:     ATTTACGCGGCGCATGCCACATTCGAGGACCCGCTTATGCGAGCTCATGG                         GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAG
genomic: ATTTACGCGGCGCATGCCACATTCGAGGACCCGCTTATGCGAGCTCATGGgtacgtctac ... ttcattccagGGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAG
EST: gi|88340926|gb|CI637086.1|CI637086
EST:     ATTTACGCGGCGCATGCCACATTCGAGGACCCGCTTATGCGAGCTCATGG                         GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAG
genomic: ATTTACGCGGCGCATGCCACATTCGAGGACCCGCTTATGCGAGCTCATGGgtacgtctac ... ttcattccagGGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAG
EST: gi|33659959|gb|CF290926.1|CF290926
EST:     ATTTACGCGGCGCATGCCACATTCGAGGACCCGCTTATGCGAGCTCATGG                         GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAG
genomic: ATTTACGCGGCGCATGCCACATTCGAGGACCCGCTTATGCGAGCTCATGGgtacgtctac ... ttcattccagGGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAG
EST: gi|88290458|gb|CI665247.1|CI665247
EST:     ATTTACGCGGCGCATGCCACATTCGAGGACCCGCTTATGCGAGCTCATGG                         GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAG
genomic: ATTTACGCGGCGCATGCCACATTCGAGGACCCGCTTATGCGAGCTCATGGgtacgtctac ... ttcattccagGGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAG
EST: gi|33659939|gb|CF290906.1|CF290906
EST:     ATTTACGCGGCGCATGCCACATTCGAGGACCCGCTTATGCGAGCTCATGG                         GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAG
genomic: ATTTACGCGGCGCATGCCACATTCGAGGACCCGCTTATGCGAGCTCATGGgtacgtctac ... ttcattccagGGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAG
EST: gi|66916268|gb|CX103116.1|CX103116
EST:     ATTTACGCGGCGCATGCCACATTCGAGGACCCGCTTATGCGAGCTCATGG                         GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAG
genomic: ATTTACGCGGCGCATGCCACATTCGAGGACCCGCTTATGCGAGCTCATGGgtacgtctac ... ttcattccagGGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAG
EST: gi|88327415|gb|CI645201.1|CI645201
EST:     ATTTACGCGGCGCATGCCACATTCGAGGACCCGCTTATGCGAGCTCATGG                         GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAG
genomic: ATTTACGCGGCGCATGCCACATTCGAGGACCCGCTTATGCGAGCTCATGGgtacgtctac ... ttcattccagGGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAG
EST: gi|2428527|gb|C72990.1|C72990
EST:     ATTTACGCGGCGCATGCCACATTCGAGGACCCGCTTATGCGAGCTCATGG                         GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAG
genomic: ATTTACGCGGCGCATGCCACATTCGAGGACCCGCTTATGCGAGCTCATGGgtacgtctac ... ttcattccagGGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAG
EST: gi|88689446|gb|CI733022.1|CI733022
EST:     ATTTACGCGGCGCATGCCACATTCGAGGACCCGCTTATGCGAGCTCATGG                         GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAG
genomic: ATTTACGCGGCGCATGCCACATTCGAGGACCCGCTTATGCGAGCTCATGGgtacgtctac ... ttcattccagGGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAG

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: 69 (upstream exon), 40 (downstream exon)
Score: 22

ATACGGATCGTGCGCGACGGCTCGGGACTTCGAGATTTACGCGGCGCATGCCACATTCGAGGACCCGCTTATGCGAGCTCATGGgtacgtctac ... ttcattccagGGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATACGGATCGTGCGCGACGGCTCGGGACTTCGAGATTTACGCGGCGCATGCCACATTCGAGGACCCGCTTATGCGAGCTCATGGgtacgtctacgtttgtttcctcaccatcgatccatcatatctcttcttctttggcaaggcctttccatcccctgttctccgaaagaacagtgtttcgtgg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctcacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catcccc