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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGCGGCAAATAAAAACAAGCCAACTGAGGTTGTAAACATACTAGTCACAAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAGgtgctttactacctattttaacacctgttacctcaatttttacacttgcttgcttttcttctgttctcaagactgcatgttcaattcatttttcattttt...

Basic information

species Oryza sativa
transcript LOC_Os07g39630.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g39630.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G066051_T01 (Zea mays), 5'ss of exon 10
TTTGCGGCAAATAAAAACAAGCCAACTGAGGTTGTAAACATACTAGTCACAAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAGgtgctttactacctattttaacacctgtt---acctcaatttttacacttgcttgcttttcttctgttctcaagactgcatgttcaattcatttttcattttt---
||||| || ||||||||||| ||  ||||||| || |||||||| ||||| ||  |||||||||| || || |||||||| |||||||||||||||||||||   |    ||||  ||||||  | |||      |    ||    |  | ||  |  | | |  | | |  || | |   ||||| ||   ||||||        
TTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTCACCAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACAAAGgtatat----acctgctttaacttccgtttgtgtgtttgcttgcttatctactcacagtaccttaggtgtggagtc-gtg-gttcagttatattttcagccgcctg
















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|88384250|gb|CI551176.1|CI551176
EST:     CTCCGATTTTTTGCCGGATTCAAGATTGACAAAG                         AGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
genomic: CTCCGATTTTTTGCCGGATTCAAGATTGACAAAGgtgctttact ... ggtttatcagAGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
EST: gi|88270962|gb|CI386817.1|CI386817
EST:     AAACCGAAGCAAGCTTCTCCCATTTTTTGCCGGATTCAAGATTGACAAAG                         AGGATGAGCACTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
genomic: AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAGgtgctttact ... ggtttatcagAGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
EST: gi|88438508|gb|CI543612.1|CI543612
EST:     CCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAG                         AGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
genomic: CCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAGgtgctttact ... ggtttatcagAGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
EST: gi|88365751|gb|CI545610.1|CI545610
EST:     CAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAG                         AGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
genomic: CAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAGgtgctttact ... ggtttatcagAGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
EST: gi|88219747|gb|CI219307.1|CI219307
EST:     AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAG                         AGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
genomic: AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAGgtgctttact ... ggtttatcagAGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
EST: gi|88456733|gb|CI544670.1|CI544670
EST:     AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAG                         AGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
genomic: AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAGgtgctttact ... ggtttatcagAGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
EST: gi|38473913|gb|CF958045.1|CF958045
EST:     AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAG                         AGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
genomic: AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAGgtgctttact ... ggtttatcagAGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
EST: gi|88467436|gb|CI537078.1|CI537078
EST:     AACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAG                         AGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
genomic: AACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAGgtgctttact ... ggtttatcagAGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
EST: gi|58598860|gb|CK009388.1|CK009388
EST:     AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAG                         AGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
genomic: AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAGgtgctttact ... ggtttatcagAGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
EST: gi|86528760|gb|CI168966.1|CI168966
EST:     AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAG                         AGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
genomic: AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAGgtgctttact ... ggtttatcagAGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
EST: gi|29675062|gb|CB671337.1|CB671337
EST:     AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAG                         AGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
genomic: AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAGgtgctttact ... ggtttatcagAGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
EST: gi|58601029|gb|CK011557.1|CK011557
EST:     CCGGATTCAAGATTGACAAAG                         AGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
genomic: CCGGATTCAAGATTGACAAAGgtgctttact ... ggtttatcagAGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
EST: gi|89170955|gb|CI040232.1|CI040232
EST:     AACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAG                         AGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
genomic: AACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAGgtgctttact ... ggtttatcagAGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
EST: gi|218481593|gb|FG960934.1|FG960934
EST:     AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAG                         AGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
genomic: AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAGgtgctttact ... ggtttatcagAGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
EST: gi|88283565|gb|CI405011.1|CI405011
EST:     AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAG                         AGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
genomic: AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAGgtgctttact ... ggtttatcagAGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
EST: gi|29673566|gb|CB669841.1|CB669841
EST:     AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAG                         AGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
genomic: AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAGgtgctttact ... ggtttatcagAGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
EST: gi|86500993|gb|CI143626.1|CI143626
EST:     AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAG                         AGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
genomic: AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAGgtgctttact ... ggtttatcagAGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
EST: gi|88226063|gb|CI225979.1|CI225979
EST:     AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAG                         AGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
genomic: AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAGgtgctttact ... ggtttatcagAGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
EST: gi|86495340|gb|CI137973.1|CI137973
EST:     AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAG                         AGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
genomic: AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAGgtgctttact ... ggtttatcagAGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
EST: gi|38481075|gb|CF965164.1|CF965164
EST:     AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAG                         AGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
genomic: AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAGgtgctttact ... ggtttatcagAGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
EST: gi|88214576|gb|CI214425.1|CI214425
EST:     AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAG                         AGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
genomic: AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAGgtgctttact ... ggtttatcagAGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
EST: gi|29673647|gb|CB669922.1|CB669922
EST:     AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAG                         AGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
genomic: AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAGgtgctttact ... ggtttatcagAGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
EST: gi|89170800|gb|CI040077.1|CI040077
EST:     AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAG                         AGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
genomic: AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAGgtgctttact ... ggtttatcagAGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
EST: gi|88490037|gb|CI427309.1|CI427309
EST:     AACCGAAGCAAGCTTCTCCGATTTTTTGCCGGAGTTCAAGATTGACAAAG                         AGGATGGACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
genomic: AACCGAAGCAAGCTTCTCCGATTTTTTGCCGGA-TTCAAGATTGACAAAGgtgctttact ... ggtttatcagAGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
EST: gi|29679531|gb|CB675806.1|CB675806
EST:     AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAG                         AGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
genomic: AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAGgtgctttact ... ggtttatcagAGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
EST: gi|88442558|gb|CI544125.1|CI544125
EST:     AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAG                         AGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
genomic: AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAGgtgctttact ... ggtttatcagAGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
EST: gi|87008328|gb|CI301086.1|CI301086
EST:     AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAG                         AGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
genomic: AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAGgtgctttact ... ggtttatcagAGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
EST: gi|29664684|gb|CB660959.1|CB660959
EST:     AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAG                         AGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
genomic: AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAGgtgctttact ... ggtttatcagAGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
EST: gi|25799534|gb|CA755495.1|CA755495
EST:     AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACNAAG                         AGGATGAACAGTTCGAGGCAGACNAAGAGCAGGTCATAAAGGAGATATCTG
genomic: AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAGgtgctttact ... ggtttatcagAGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
EST: gi|88434926|gb|CI549123.1|CI549123
EST:     AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAG                         AGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
genomic: AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAGgtgctttact ... ggtttatcagAGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
EST: gi|29656023|gb|CB652298.1|CB652298
EST:     AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAG                         AGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
genomic: AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAGgtgctttact ... ggtttatcagAGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
EST: gi|66915714|gb|CX102562.1|CX102562
EST:     AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAG                         AGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
genomic: AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAGgtgctttact ... ggtttatcagAGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
EST: gi|29660229|gb|CB656504.1|CB656504
EST:     AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAG                         AGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
genomic: AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAGgtgctttact ... ggtttatcagAGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
EST: gi|86426306|gb|CI071403.1|CI071403
EST:     AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAG                         AGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
genomic: AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAGgtgctttact ... ggtttatcagAGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
EST: gi|86253232|gb|CI058157.1|CI058157
EST:     AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAG                         AGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
genomic: AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAGgtgctttact ... ggtttatcagAGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
EST: gi|88323015|gb|CI548109.1|CI548109
EST:     AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAG                         AGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG
genomic: AAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAGgtgctttact ... ggtttatcagAGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTG

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: 75 (upstream exon), 74 (downstream exon)
Score: 124

TTTGCGGCAAATAAAAACAAGCCAACTGAGGTTGTAAACATACTAGTCACAAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAGgtgctttact ... ggtttatcagAGGATGAACAGTTCGAGGCAGACAAAGAGCAGGTCATAAAGGAGATATCTGCACTTTAGTGTCCTTCTGTATACCTCGCGGAGGCTTTTGGTCAATGCGT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTGCGGCAAATAAAAACAAGCCAACTGAGGTTGTAAACATACTAGTCACAAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACAAAGgtgctttactacctattttaacacctgttacctcaatttttacacttgcttgcttttcttctgttctcaagactgcatgttcaattcatttttcattttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT