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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgacaaaacagcataaagattttattaggcgggtgaactgcatccatatactgtgccactgatattccttgactgaaatcttcatcccagGCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCT

Basic information

species Oryza sativa
transcript LOC_Os03g01850.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g01850.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G008327_T01 (Zea mays), 3'ss of exon 6
gtatgacaaaacagcataaagattttattaggcgggtg----aactgcatc-catatactgtgcca---ctgatattccttgactgaaat-------------cttcatcccagGCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCT
   | |   ||||||||||  ||||   | |||   ||    || |||||    ||| ||   |||   || | | ||  ||  ||  ||             || |||  ||||  || |||||  | ||||| | ||||||||||||||| |||||||||||||||
--gtaaggcaacagcataagcatttcgctgggcacatgtggcaagtgcattgtgtatcctcatccatagcttacaatctgtgtttgtcatatatatccgatgcctccattacagGACCTGGCAACAGTAGTCCCAAATCTTGACCCTGCTGGGTTGGACCTTCTCTCT
















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|33803869|gb|CF327809.1|CF327809
EST:     TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAG                         GCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
genomic: TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAGgtatgacaaa ... ttcatcccagGCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
EST: gi|88268788|gb|CI378723.1|CI378723
EST:     TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAG                         GCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
genomic: TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAGgtatgacaaa ... ttcatcccagGCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
EST: gi|3766971|gb|AU031081.1|AU031081
EST:     TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAG                         GCTCTTGCAANTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
genomic: TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAGgtatgacaaa ... ttcatcccagGCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
EST: gi|29662032|gb|CB658307.1|CB658307
EST:     TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAG                         GCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
genomic: TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAGgtatgacaaa ... ttcatcccagGCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
EST: gi|88559037|gb|CI489575.1|CI489575
EST:     TTTCCCCAAGTGGCAGGCACAG                         GCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGNTTTGGACCTTCTC
genomic: TTTCCCCAAGTGGCAGGCACAGgtatgacaaa ... ttcatcccagGCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
EST: gi|88253212|gb|CI351838.1|CI351838
EST:     TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAG                         GCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
genomic: TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAGgtatgacaaa ... ttcatcccagGCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
EST: gi|88978284|gb|CI384727.1|CI384727
EST:     TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAG                         GCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
genomic: TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAGgtatgacaaa ... ttcatcccagGCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
EST: gi|86885548|gb|CI318699.1|CI318699
EST:     TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAG                         GCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
genomic: TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAGgtatgacaaa ... ttcatcccagGCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
EST: gi|89196147|gb|CI397149.1|CI397149
EST:     TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAG                         GCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
genomic: TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAGgtatgacaaa ... ttcatcccagGCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
EST: gi|88437700|gb|CI531259.1|CI531259
EST:     TTAGCTCATTACCTGAGTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAG                         GCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
genomic: TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAGgtatgacaaa ... ttcatcccagGCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
EST: gi|88488941|gb|CI426212.1|CI426212
EST:     TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAG                         GCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
genomic: TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAGgtatgacaaa ... ttcatcccagGCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
EST: gi|88509819|gb|CI437325.1|CI437325
EST:     TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAG                         GCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
genomic: TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAGgtatgacaaa ... ttcatcccagGCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
EST: gi|88437696|gb|CI531255.1|CI531255
EST:     TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAG                         GCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
genomic: TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAGgtatgacaaa ... ttcatcccagGCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
EST: gi|38482398|gb|CF966438.1|CF966438
EST:     TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAG                         GCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
genomic: TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAGgtatgacaaa ... ttcatcccagGCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
EST: gi|66915263|gb|CX102111.1|CX102111
EST:     TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAG                         GCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
genomic: TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAGgtatgacaaa ... ttcatcccagGCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
EST: gi|88522726|gb|CI450366.1|CI450366
EST:     TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAG                         GCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
genomic: TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAGgtatgacaaa ... ttcatcccagGCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC

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: 57 (upstream exon), 45 (downstream exon)
Score: 13

GGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAGgtatgacaaa ... ttcatcccagGCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactgcatccatatactgtgccactgatattccttgactgaaatcttcatcccagGCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCT
                                           tcttcatccc  CT-rich tract
          atatact  TA-rich tract