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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtctaaaaggatttcttacattattagatggttctggcaactaaccgtttgcctttctccagTTCTTGCGGGAGCAAGCTGCTCTTTCTGCTGCTGAAATAACTGCCGACGCCGTTAATAACTTTGTTGCCGATCTTGAAGATGAAAGTGACTATGAGCAGT

Basic information

species Oryza sativa
transcript LOC_Os03g22160.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g22160.1 (Oryza sativa), 3'ss of exon 20
lower sequence: GRMZM2G353147_T01 (Zea mays), 3'ss of exon 19
------------gtaagtctaaaaggatttcttacattattagatggttctggcaactaaccgtttgcctttctccagTTCTTGCGGGAGCAAGCTGCTCTTTCTGCTGCTGAAATAACTGCCGACGCCGTTAATAACTTTGTTGCCGATCTTGAAGATGAAAGTGACTATGAGCAGT
             | | |  ||     |||| |||  || ||||  | | ||| || ||| | ||| | | ||   |||||||  ||||||||||||||||||||||||||||||| ||||| ||||| |||||||  |||||||| ||||||||||||||||||||   |||||  |
gtatgtggtactatcatttaaatctattttcctacgataatagacagct-tggtaattaatcttttccttatc---agTTCTTAAGGGAGCAAGCTGCTCTTTCTGCTGCTGAAATTACTGCTGACGCAGTTAATAGTTTTGTTGCTGATCTTGAAGATGAAAGTGATAGTGAGCTTT
















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|88676576|gb|CI730689.1|CI730689
EST:     GTGCAAGACACAAAATTATGAAA                         TTCTTGCGGGAGCAAGCTGCTCTTTCTGCTGCTGAAATAACTGCCGACGCC
genomic: GTGCAAGACACAAAATTATGAAAgtaagtctaa ... ctttctccagTTCTTGCGGGAGCAAGCTGCTCTTTCTGCTGCTGAAATAACTGCCGACGCC
EST: gi|88905382|gb|CI712681.1|CI712681
EST:     GTGCAAGACACAAAATTATGAAA                         TTCTTGCGGGAGCAAGCTGCTCTTTCTGCTGCTGAAATAACTGCCGACGCC
genomic: GTGCAAGACACAAAATTATGAAAgtaagtctaa ... ctttctccagTTCTTGCGGGAGCAAGCTGCTCTTTCTGCTGCTGAAATAACTGCCGACGCC
EST: gi|88667031|gb|CI719167.1|CI719167
EST:     GTGCAAGACACAAAATTATGAAA                         TTCTTGCGGGAGCAAGCTGCTCTTTCTGCTGCTGAAATAACTGCCGACGCC
genomic: GTGCAAGACACAAAATTATGAAAgtaagtctaa ... ctttctccagTTCTTGCGGGAGCAAGCTGCTCTTTCTGCTGCTGAAATAACTGCCGACGCC
EST: gi|88665731|gb|CI715887.1|CI715887
EST:     GTGCAAGACACAAAATTATGAAA                         TTCTTGCGGGAGCAAGCTGCTCTTTCTGCTGCTGAAATAACTGCCGACGCC
genomic: GTGCAAGACACAAAATTATGAAAgtaagtctaa ... ctttctccagTTCTTGCGGGAGCAAGCTGCTCTTTCTGCTGCTGAAATAACTGCCGACGCC
EST: gi|88672319|gb|CI726435.1|CI726435
EST:     GTGCAAGACACAAAATTATGAAA                         TTCTTGCGGGAGCAAGCTGCTCTTTCTGCTGCTGAAATAACTGCCGACGCC
genomic: GTGCAAGACACAAAATTATGAAAgtaagtctaa ... ctttctccagTTCTTGCGGGAGCAAGCTGCTCTTTCTGCTGCTGAAATAACTGCCGACGCC
EST: gi|88670310|gb|CI724426.1|CI724426
EST:     GTGCAAGACACAAAATTATGAAA                         TTCTTGCGGGAGCAAGCTGCTCTTTCTGCTGCTGAAATAACTGCCGACGCC
genomic: GTGCAAGACACAAAATTATGAAAgtaagtctaa ... ctttctccagTTCTTGCGGGAGCAAGCTGCTCTTTCTGCTGCTGAAATAACTGCCGACGCC
EST: gi|88673296|gb|CI725921.1|CI725921
EST:     GTGCAAGACACAAAATTATGAAA                         TTCTTGCGGGAGCAAGCTGCTCTTTCTGCTGCTGAAATAACTGCCGACGCC
genomic: GTGCAAGACACAAAATTATGAAAgtaagtctaa ... ctttctccagTTCTTGCGGGAGCAAGCTGCTCTTTCTGCTGCTGAAATAACTGCCGACGCC
EST: gi|88669082|gb|CI720039.1|CI720039
EST:     GTGCAAGACACAAAATTATGAAA                         TTCTTGCGGGAGCAAGCTGCTCTTTCTGCTGCTGAAATAACTGGCGACGCC
genomic: GTGCAAGACACAAAATTATGAAAgtaagtctaa ... ctttctccagTTCTTGCGGGAGCAAGCTGCTCTTTCTGCTGCTGAAATAACTGCCGACGCC
EST: gi|88673957|gb|CI728070.1|CI728070
EST:     GTGCAAGACACAAAATTATGAAA                         TTCTTGCGGGAGCAAGCTGCTCTTTCTGCTGCTGAAATAACTGCCGACGCC
genomic: GTGCAAGACACAAAATTATGAAAgtaagtctaa ... ctttctccagTTCTTGCGGGAGCAAGCTGCTCTTTCTGCTGCTGAAATAACTGCCGACGCC
EST: gi|88668265|gb|CI723004.1|CI723004
EST:     GTGCAAGACACAAAATTATGAAA                         TTCTTGCGGGAGCAAGCTGCTCTTTCTGCTGCTGAAATAACTGCCGACGCC
genomic: GTGCAAGACACAAAATTATGAAAgtaagtctaa ... ctttctccagTTCTTGCGGGAGCAAGCTGCTCTTTCTGCTGCTGAAATAACTGCCGACGCC
EST: gi|88908643|gb|CI713201.1|CI713201
EST:     GTGCAAGACACAAAATTATGAAA                         TTCTTGCGGGAGCAAGCTGCTCTTTCTGCTGCTGAAATAACTGCCGACGCC
genomic: GTGCAAGACACAAAATTATGAAAgtaagtctaa ... ctttctccagTTCTTGCGGGAGCAAGCTGCTCTTTCTGCTGCTGAAATAACTGCCGACGCC
EST: gi|88954855|gb|CI720256.1|CI720256
EST:     GTGCAAGACACAAAATTATGAAA                         TTCTTGCGGGAGCAAGCTGCTCTTTCTGCTGCTGAAATAACTGCCGACGCC
genomic: GTGCAAGACACAAAATTATGAAAgtaagtctaa ... ctttctccagTTCTTGCGGGAGCAAGCTGCTCTTTCTGCTGCTGAAATAACTGCCGACGCC
EST: gi|88973071|gb|CI717600.1|CI717600
EST:     GTGCAAGACACAAAATTATGAAA                         TTCTTGCGGGAGCAAGCTGCTCTTTCTGCTGCTGAAATAACTGCCGACGCC
genomic: GTGCAAGACACAAAATTATGAAAgtaagtctaa ... ctttctccagTTCTTGCGGGAGCAAGCTGCTCTTTCTGCTGCTGAAATAACTGCCGACGCC
EST: gi|88666683|gb|CI718819.1|CI718819
EST:     GTGCAAGACACAAAATTATGAAA                         TTCTTGCGGGAGCAAGCTGCTCTTTCTGCTGCTGAAATAACTGCCGACGCC
genomic: GTGCAAGACACAAAATTATGAAAgtaagtctaa ... ctttctccagTTCTTGCGGGAGCAAGCTGCTCTTTCTGCTGCTGAAATAACTGCCGACGCC
EST: gi|88672750|gb|CI726866.1|CI726866
EST:     GTGCAAGACACAAAATTATGAAA                         TTCTTGCGGGAGCAAGCTGCTCTTTCTGCTGCTGAAATAACTGCCGACGCC
genomic: GTGCAAGACACAAAATTATGAAAgtaagtctaa ... ctttctccagTTCTTGCGGGAGCAAGCTGCTCTTTCTGCTGCTGAAATAACTGCCGACGCC
EST: gi|88972491|gb|CI717231.1|CI717231
EST:     GTGCAAGACACAAAATTATGAAA                         TTCTTGCGGGAGCAAGCTGCTCTTTCTGCTGCTGAAATAACTGCCGACGCC
genomic: GTGCAAGACACAAAATTATGAAAgtaagtctaa ... ctttctccagTTCTTGCGGGAGCAAGCTGCTCTTTCTGCTGCTGAAATAACTGCCGACGCC
EST: gi|88973814|gb|CI718222.1|CI718222
EST:     GTGCAAGACACAAAATTATGAAA                         TTCTTGCGGGAGCAAGCTGCTCTTTCTGCTGCTGAAATAACTGCCGACGCC
genomic: GTGCAAGACACAAAATTATGAAAgtaagtctaa ... ctttctccagTTCTTGCGGGAGCAAGCTGCTCTTTCTGCTGCTGAAATAACTGCCGACGCC
EST: gi|88973710|gb|CI718138.1|CI718138
EST:     GTGCAAGACACAAAATTATGAAA                         TTCTTGCGGGAGCAAGCTGCTCTTTCTGCTGCTGAAATAACTGCCGACGCC
genomic: GTGCAAGACACAAAATTATGAAAgtaagtctaa ... ctttctccagTTCTTGCGGGAGCAAGCTGCTCTTTCTGCTGCTGAAATAACTGCCGACGCC
EST: gi|88973510|gb|CI717938.1|CI717938
EST:     GTGCAAGACACAAAATTATGAAA                         TTCTTGCGGGAGCAAGCTGCTCTTTCTGCTGCTGAAATAACTGCCGACGCC
genomic: GTGCAAGACACAAAATTATGAAAgtaagtctaa ... ctttctccagTTCTTGCGGGAGCAAGCTGCTCTTTCTGCTGCTGAAATAACTGCCGACGCC
EST: gi|109974372|gb|DT806873.1|DT806873
EST:     AGTGGCTTCAACATGCGAAAACTCGCAGTGCAAGACACAAAATTATGAAA                         TTCTTGCGGGAGCAAGCCGCTCTTTCTGCTGCTGAAATAACTGCCGACGCC
genomic: AGTGGCTTCAACATGCGAAAACTCGCAGTGCAAGACACAAAATTATGAAAgtaagtctaa ... ctttctccagTTCTTGCGGGAGCAAGCTGCTCTTTCTGCTGCTGAAATAACTGCCGACGCC
EST: gi|66922942|gb|CX109790.1|CX109790
EST:     AGTGGCTTCAACATGCGAAAACTCGCAGTGCAAGACACAAAATTATGAAA                         TTCTTGCGGGAGCAAGCCGCTCTTTCTGCTGCTGAAATAACTGCCGACGCC
genomic: AGTGGCTTCAACATGCGAAAACTCGCAGTGCAAGACACAAAATTATGAAAgtaagtctaa ... ctttctccagTTCTTGCGGGAGCAAGCTGCTCTTTCTGCTGCTGAAATAACTGCCGACGCC

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: 45 (upstream exon), 72 (downstream exon)
Score: 32

AAATTATCTGCTAAATATGCATTCCAGCGTCACCAGCAGTGGCTTCAACATGCGAAAACTCGCAGTGCAAGACACAAAATTATGAAAgtaagtctaa ... ctttctccagTTCTTGCGGGAGCAAGCTGCTCTTTCTGCTGCTGAAATAACTGCCGACGCCGTTAATAACTTTGTTGCCGATCTTGAAGATGAAAGTGACTATGAGCAGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggatttcttacattattagatggttctggcaactaaccgtttgcctttctccagTTCTTGCGGGAGCAAGCTGCTCTTTCTGCTGCTGAAATAACTGCCGACGCCGTTAATAACTTTGTTGCCGATCTTGAAGATGAAAGTGACTATGAGCAGT
                               aactaac  putative branch site (score: 32)
                                     ccgtttgcctttctcc  CT-rich tract
     ttcttacattatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtctaaaaggatttcttacattattagatggttctggcaactaaccgtttgcctttctccagTTCTTGCGGGAGCAAGCTGCTCTTTCTGCTGCTGAAATAACTGCCGACGCCGTTAATAACTTTGTTGCCGATCTTGAAGATGAAAGTGACTATGAGCAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG