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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAGCGACGCTTGATGGAGAAAATTCCTGAAATTGTTGCTGTCGAGCCCATTGCTGATGAGGAGACTGGCCTTGAGTTGAACCAGGAGAATATTGAAAAGgtacttgcttatatttctggctaaataaaattatacgcaaaaggtctcttgtagagtacatcatgtcgaagtagcttaagctttaccgtggctaattgat...

Basic information

species Oryza sativa
transcript LOC_Os11g07916.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g07916.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G089317_T02 (Zea mays), 5'ss of exon 2
TGAGCGACGCTTGATGGAGAAAATTCCTGAAATTGTTGCTGTCGAGCCCATTGCTGATGAGGAGACTGGCCTTGAGTTGAACCAGGAGAATATTGAAAAGgtacttgcttatatttctggctaaataaaattatacgcaaaaggtctcttgtagagtacatcatgtcgaagtagcttaagctttaccgtggctaatt--gat-
||| || ||||||||||||||||| || || |||||||| || |||||||||||||||||||| |||||||||||||||||||| ||||| ||||||||||||  || || ||||  |||| |||||    |||  | ||||| || ||||     ||     |   ||||||    | |  |||   ||    |||  ||| 
TGAACGGCGCTTGATGGAGAAAATACCAGAGATTGTTGCAGTTGAGCCCATTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAGgtaaatg-ttctattgttggccaaatatt-ctattggtaaaag-tcacttgattcttatggattactgaagtaaaccaggacttattttgttggattttgatt
















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|86508544|gb|CI151177.1|CI151177
EST:     TTGCTGATGAGGAGACTGGCCTTGAGTTGAACCAGGAGAATATTGAAAAG                         GTACTCGATGAGATTAGGCCATANCCTTTCTGGCACAGGAGGTGGTGAGCT
genomic: TTGCTGATGAGGAGACTGGCCTTGAGTTGAACCAGGAGAATATTGAAAAGgtacttgctt ... cctttattagGTACTCGATGAGATTAGGCCATA-CCTTTCTGGCACAGGAGGTGGTGAGCT
EST: gi|86258572|gb|CI064925.1|CI064925
EST:     TTGCTGATGAGGAGACTGGCCTTGAGTTGAACCAGGAGAATATTGAAAAG                         GTACTCGATGAGATTAGGCCATACCTTTCTGGCACAGGAGGTGGTGAGCTT
genomic: TTGCTGATGAGGAGACTGGCCTTGAGTTGAACCAGGAGAATATTGAAAAGgtacttgctt ... cctttattagGTACTCGATGAGATTAGGCCATACCTTTCTGGCACAGGAGGTGGTGAGCTT
EST: gi|88998301|gb|CI038186.1|CI038186
EST:     TTGCTGATGAGGAGACTGGCCTTGAGTTGAACCAGGAGAATATTGAAAAG                         GTACTCGATGAGATTAGGCCATACCTTTCTGGCACAGGAGGTGGTGAGCTT
genomic: TTGCTGATGAGGAGACTGGCCTTGAGTTGAACCAGGAGAATATTGAAAAGgtacttgctt ... cctttattagGTACTCGATGAGATTAGGCCATACCTTTCTGGCACAGGAGGTGGTGAGCTT
EST: gi|88832583|gb|CI008179.1|CI008179
EST:     TTGCTGATGAGGAGACTGGCCTTGAGTTGAACCAGGAGAATATTGAAAAG                         GTACTCGATGAGATTAGGCCATACCTTTCTGGCACAGGAGGTGGTGAGCTT
genomic: TTGCTGATGAGGAGACTGGCCTTGAGTTGAACCAGGAGAATATTGAAAAGgtacttgctt ... cctttattagGTACTCGATGAGATTAGGCCATACCTTTCTGGCACAGGAGGTGGTGAGCTT
EST: gi|86537734|gb|CI177940.1|CI177940
EST:     TTGCTGATGAGGAGACTGGCCTTGAGTTGAACCAGGAGAATATTGAAAAG                         GTACTCGATGAGATTAGGCCATACCTTTCTGGCACAGGAGGTGGTGAGCTT
genomic: TTGCTGATGAGGAGACTGGCCTTGAGTTGAACCAGGAGAATATTGAAAAGgtacttgctt ... cctttattagGTACTCGATGAGATTAGGCCATACCTTTCTGGCACAGGAGGTGGTGAGCTT
EST: gi|86545098|gb|CI185304.1|CI185304
EST:     CCTTGAGTTGAACCAGGAGAATATTGAAAAG                         GTACTCGATGAGATTAGGCCATACCTTTCTGGCACAGGAGGTGGTGAGCTT
genomic: CCTTGAGTTGAACCAGGAGAATATTGAAAAGgtacttgctt ... cctttattagGTACTCGATGAGATTAGGCCATACCTTTCTGGCACAGGAGGTGGTGAGCTT
EST: gi|86258573|gb|CI064926.1|CI064926
EST:     TTGCTGATGAGGAGACTGGCCTTGAGTTGAACCAGGAGAATATTGAAAAG                         GTACTCGATGAGATTAGGCCATACCTTTCTGGCACAGGAGGTGGTGAGCTT
genomic: TTGCTGATGAGGAGACTGGCCTTGAGTTGAACCAGGAGAATATTGAAAAGgtacttgctt ... cctttattagGTACTCGATGAGATTAGGCCATACCTTTCTGGCACAGGAGGTGGTGAGCTT
EST: gi|88205239|gb|CI205088.1|CI205088
EST:     TTGCTGATGAGGAGACTGGCCTTGAGTTGAACCAGGAGAATATTGAAAAG                         GTACTCGATGAGATTAGGCCATACCTTTCTGGCACAGGAGGTGGTGAGCTT
genomic: TTGCTGATGAGGAGACTGGCCTTGAGTTGAACCAGGAGAATATTGAAAAGgtacttgctt ... cctttattagGTACTCGATGAGATTAGGCCATACCTTTCTGGCACAGGAGGTGGTGAGCTT
EST: gi|86864550|gb|CI344155.1|CI344155
EST:     TTGCTGATGAGGAGACTGGCCTTGAGTTGAACCAGGAGAATATTGAAAAG                         GTACTCGATGAGATTAGGCCATACCTTTCTGGCACAGGAGGTGGTGAGCTT
genomic: TTGCTGATGAGGAGACTGGCCTTGAGTTGAACCAGGAGAATATTGAAAAGgtacttgctt ... cctttattagGTACTCGATGAGATTAGGCCATACCTTTCTGGCACAGGAGGTGGTGAGCTT
EST: gi|86511242|gb|CI153875.1|CI153875
EST:     TTGCTGATGAGGAGACTGGCCTTGAGTTGAACCAGGAGAATATTGAAAAG                         GTACTCGATGAGATTAGGCCATACCTTTCTGGCACAGGAGGTGGTGAGCTT
genomic: TTGCTGATGAGGAGACTGGCCTTGAGTTGAACCAGGAGAATATTGAAAAGgtacttgctt ... cctttattagGTACTCGATGAGATTAGGCCATACCTTTCTGGCACAGGAGGTGGTGAGCTT
EST: gi|88218879|gb|CI216877.1|CI216877
EST:     TTGCTGATGAGGAGACTGGCCTTGAGTTGAACCAGGAGAATATTGAAAAG                         GTACTCGATGAGATTAGGCCATACCTTTCTGGCACAGGAGGTGGTGAGCTT
genomic: TTGCTGATGAGGAGACTGGCCTTGAGTTGAACCAGGAGAATATTGAAAAGgtacttgctt ... cctttattagGTACTCGATGAGATTAGGCCATACCTTTCTGGCACAGGAGGTGGTGAGCTT
EST: gi|88215591|gb|CI215440.1|CI215440
EST:     TTGCTGATGAGGAGACTGGCCTTGAGTTGAACCAGGAGAATATTGAAAAG                         GTACTCGATGAGATTAGGCCATACCTTTCTGGCACAGGAGGTGGTGAGCTT
genomic: TTGCTGATGAGGAGACTGGCCTTGAGTTGAACCAGGAGAATATTGAAAAGgtacttgctt ... cctttattagGTACTCGATGAGATTAGGCCATACCTTTCTGGCACAGGAGGTGGTGAGCTT
EST: gi|13806859|gb|AU181705.1|AU181705
EST:     TTGCTGATGAGGAGACTGGCCTTGAGTTGAACCAGGAGAATATTGAAAAG                         GTACTCGATGAGATTAGGCCATACCTTTNTGGCACAGGAGGTGGTGAGCTT
genomic: TTGCTGATGAGGAGACTGGCCTTGAGTTGAACCAGGAGAATATTGAAAAGgtacttgctt ... cctttattagGTACTCGATGAGATTAGGCCATACCTTTCTGGCACAGGAGGTGGTGAGCTT
EST: gi|88278998|gb|CI399998.1|CI399998
EST:     CCTTGAGTTGAACCAGGAGAATATTGAAAAG                         GTACTCAATGAGATTAGNCCATACCTTTCTGGCACACGAGGTGGTGAGCTT
genomic: CCTTGAGTTGAACCAGGAGAATATTGAAAAGgtacttgctt ... cctttattagGTACTCGATGAGATTAGGCCATACCTTTCTGGCACAGGAGGTGGTGAGCTT
EST: gi|86531069|gb|CI171275.1|CI171275
EST:     TTGCTGATGAGGAGACTGGCCTTGAGTTGAACCAGGAGAATATTGAAAAG                         GTACTCGATGAGATTAGGCCATACCTTTCTGGCACAGGAGGTGGTGAGCTT
genomic: TTGCTGATGAGGAGACTGGCCTTGAGTTGAACCAGGAGAATATTGAAAAGgtacttgctt ... cctttattagGTACTCGATGAGATTAGGCCATACCTTTCTGGCACAGGAGGTGGTGAGCTT
EST: gi|87027922|gb|CI276278.1|CI276278
EST:     TTGCTGATGAGGAGACTGGCCTTGAGTTGAACCAGGAGAATATTGAAAAG                         GTACTCGATGAGATTAGGCCATACCTTTCTGGCACAGGAGGTGGTGAGCTT
genomic: TTGCTGATGAGGAGACTGGCCTTGAGTTGAACCAGGAGAATATTGAAAAGgtacttgctt ... cctttattagGTACTCGATGAGATTAGGCCATACCTTTCTGGCACAGGAGGTGGTGAGCTT
EST: gi|87032192|gb|CI261974.1|CI261974
EST:     TTGCTGATGAGGAGACTGGCCTTGAGTTGAACCAGGAGAATATTGAAAAG                         GTACTCGATGAGATTAGGCCATACCTTTCTGGCACAGGAGGTGGTGAGCTT
genomic: TTGCTGATGAGGAGACTGGCCTTGAGTTGAACCAGGAGAATATTGAAAAGgtacttgctt ... cctttattagGTACTCGATGAGATTAGGCCATACCTTTCTGGCACAGGAGGTGGTGAGCTT
EST: gi|86855056|gb|CI263123.1|CI263123
EST:     TTGCTGATGAGGAGACTGGCCTTGAGTTGAACCAGGAGAATATTGAAAAG                         GTACTCGATGAGATTAGGCCATACCTTTCTGGCACAGGAGGTGGTGAGCTT
genomic: TTGCTGATGAGGAGACTGGCCTTGAGTTGAACCAGGAGAATATTGAAAAGgtacttgctt ... cctttattagGTACTCGATGAGATTAGGCCATACCTTTCTGGCACAGGAGGTGGTGAGCTT
EST: gi|88988204|gb|CI036174.1|CI036174
EST:     TTGCTGATGAGGAGACTGGCCTTGAGTTGAACCAGGAGAATATTGAAAAG                         GTACTCGATGAGATTAGGCCATACCTTTCTGGCACAGGAGGTGGTGAGCTT
genomic: TTGCTGATGAGGAGACTGGCCTTGAGTTGAACCAGGAGAATATTGAAAAGgtacttgctt ... cctttattagGTACTCGATGAGATTAGGCCATACCTTTCTGGCACAGGAGGTGGTGAGCTT
EST: gi|86507179|gb|CI149812.1|CI149812
EST:     TTGCTGATGAGGAGACTGGCCTTGAGTTGAACCAGGAGAATATTGAAAAG                         GTACTCGATGAGATTAGGCCATACCTTTCTGGCACAGGAGGTGGTGAGCTT
genomic: TTGCTGATGAGGAGACTGGCCTTGAGTTGAACCAGGAGAATATTGAAAAGgtacttgctt ... cctttattagGTACTCGATGAGATTAGGCCATACCTTTCTGGCACAGGAGGTGGTGAGCTT
EST: gi|89163879|gb|CI100967.1|CI100967
EST:     TTGCTGATGAGGAGACTGGCCTTGAGTTGAACCAGGAGAATATTGAAAAG                         GTACTCGATGAGATTAGGCCATACCTTTCTGGCACAGGAGGTGGTGAGCTT
genomic: TTGCTGATGAGGAGACTGGCCTTGAGTTGAACCAGGAGAATATTGAAAAGgtacttgctt ... cctttattagGTACTCGATGAGATTAGGCCATACCTTTCTGGCACAGGAGGTGGTGAGCTT
EST: gi|109712798|gb|CI105406.1|CI105406
EST:     TTGCTGATGAGGAGACTGGCCTTGAGTTGAACCAGGAGAATATTGAAAAG                         GTACTCGATGAGATTAGGCCATACCTTTCTGGCACAGGAGGTGGTGAGCTT
genomic: TTGCTGATGAGGAGACTGGCCTTGAGTTGAACCAGGAGAATATTGAAAAGgtacttgctt ... cctttattagGTACTCGATGAGATTAGGCCATACCTTTCTGGCACAGGAGGTGGTGAGCTT

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: 73 (upstream exon), 70 (downstream exon)
Score: 45

TGAGCGACGCTTGATGGAGAAAATTCCTGAAATTGTTGCTGTCGAGCCCATTGCTGATGAGGAGACTGGCCTTGAGTTGAACCAGGAGAATATTGAAAAGgtacttgctt ... cctttattagGTACTCGATGAGATTAGGCCATACCTTTCTGGCACAGGAGGTGGTGAGCTTGAATTCGTTGCGATCGAGGAACCTATCGTCAAGGTTAGGCTTACGGGCC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAGCGACGCTTGATGGAGAAAATTCCTGAAATTGTTGCTGTCGAGCCCATTGCTGATGAGGAGACTGGCCTTGAGTTGAACCAGGAGAATATTGAAAAGgtacttgcttatatttctggctaaataaaattatacgcaaaaggtctcttgtagagtacatcatgtcgaagtagcttaagctttaccgtggctaattgat

- - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaataaa