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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatcatagcagtgcagacctgatgttcccttgacttttacatattccttacatgagcaaactgggactaatgctttcttcttcactcacttaatttccagTTCTTCATTGTATTGTCGTGCACAATTGCTGTTGGGACCAATCTAAGCCAGTTCATATGCATTGGAAGATTCACAGCTGTCTCATTTCAAGTTCTAGGCC

Basic information

species Oryza sativa
transcript LOC_Os02g40090.4
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g40090.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G089630_T01 (Zea mays), 3'ss of exon 6
-tatcatagcagtgcagacctgatgttcccttgacttttacatattccttacatgagcaaactgggactaatgctttcttcttcactcacttaa-tttccagTTCTTCATTGTATTGTCGTGCACAATTGCTGTTGGGACCAATCTAAGCCAGTTCATATGCATTGGAAGATTCACAGCTGTCTCATTTCAAGTTCTAGGCC
  |||       |  | |    |  ||  |||  ||||     |  | | ||   | |   |   |||| ||  |||     ||||    ||   ||| |||||||| || || |||||||||| ||||||||| |||||||| |||||||||||||||||||| ||||||||||| || ||||| || ||||| ||||| |
agatccatttgcttgatattataaattttcttt-ctttgctgcaagcttgac-caacctggccaagacttattgttttcctgtcacatgttttccttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCTGTCGGGACCAACCTAAGCCAGTTCATATGCATCGGAAGATTCACGGCCGTCTCGTTCCAAGTCCTAGGTC

upper sequence: LOC_Os02g40090.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G823629_T03 (Zea mays), 3'ss of exon 5
tatcatagcagtgcagacctgatgttcccttgacttttacatattccttacatgagcaaactgggactaatgctttcttcttcactcacttaatttccagTTCTTCATTGTATTGTCGTGCACAATTGCTGTTGGGACCAATCTAAGCCAGTTCATATGCATTGGAAGATTCACAGCTGTCTCATTTCAAGTTCTAGGCC
|||   | | |        |     |       |||   |  |  | | ||         |  |   || |  |||||| |    |   ||  ||| |||||||| || || |||||||||| |||||| |||||||| ||||||||||| ||||||||||| |||||||||||||| ||||| || ||||| |||||||
tatttgatctgcttgatgttataaattttcattcttcggcgcaaacttgacgaacctgggcatgacttactattttcttatcacatgttttccttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCCGTTGGGACGAATCTAAGCCAATTCATATGCATCGGAAGATTCACAGCCGTCTCGTTCCAAGTCCTAGGCC

upper sequence: LOC_Os02g40090.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA10G36620.1 (Glycine max), 3'ss of exon 4
tatcatagcagtgcagacctgatgttcccttgacttttacatattccttacatgagca--aactgggactaatgctttcttcttcactcacttaatttccagTTCTTCATTGTATTGTCGTGCACAATTGCTGTTGGGACCAATCTAAGCCAGTTCATATGCATTGGAAGATTCACAGCTGTCTCATTTCAAGTTCTAGGCC
| | | | |  |  ||| |  |  |     ||| ||  | ||    |||   |    |   ||   ||| ||   | |  | ||   |       ||  ||| | |||||  |  |||| ||||| || || ||||||||||| || ||||| || || || ||||| |||||||| |||||||| || ||||| |||||||
tgtaaaaac--tatagaacaaaattgagaatgaattacaaattgatcttttgttgatattgaccttgaccaagtttcttatattttgtgttggctttggcagATTTTCATATTTATGTCATGCACTATAGCAGTTGGGACCAACCTCAGCCAATTTATCTGTATTGGCAGATTCACTGCTGTCTCTTTCCAAGTACTAGGCC

upper sequence: LOC_Os02g40090.4 (Oryza sativa), 3'ss of exon 5
lower sequence: AT4G09810.1 (Arabidopsis thaliana), 3'ss of exon 5
tatcatagcagtgcagacctgatgttcccttgacttttacatattcct-tacatgagcaaactgggactaatgctttcttcttcactcacttaat-------ttccagTTCTTCATTGTATTGTCGTGCACAATTGCTGTTGGGACCAATCTAAGCCAGTTCATATGCATTGGAAGATTCACAGCTGTCTCATTTCAAGTTCTAGGCC
      || || |      | |  ||   |    | | | ||     |  ||||   |      | | |  |   ||  | |||| | ||||  |        | ||| | || ||     | ||||||||||| ||  | ||||| || || ||||||||||| ||||| || ||||||||||| || ||||| ||||| || ||||
------agaagggtgattatcaccttttttctgttatcaaatgggtttgcacatcgactctaatgaattgtt--ctttgtattcaataacttggtgatgattctgcagATGTTTATAACCCTCTCGTGCACAATAGCAATCGGGACAAACCTGAGCCAGTTCATCTGCATCGGGAGATTCACAGCAGTGTCATTCCAAGTCCTGGGCC

upper sequence: LOC_Os02g40090.4 (Oryza sativa), 3'ss of exon 5
lower sequence: AT1G34020.1 (Arabidopsis thaliana), 3'ss of exon 5
tatcatagcagtgcagacc--tgatgttcccttgacttttacatattccttacatgagcaaactgggactaatgctttcttcttcactcacttaatttc-cagTTCTTCATTGTATTGTCGTGCACAATTGCTGTTGGGACCAATCTAAGCCAGTTCATATGCATTGGAAGATTCACAGCTGTCTCATTTCAAGTTCTAGGCC
  |  |     | || |||  |  | |   ||| |     |    | |  |||||         |  ||| || |   | |  |   || || ||||   ||| | || ||     ||||||||||||| ||  |||| ||||| |||||||||||||| ||||| ||||||||||||||||| || || ||||| || || |
cttagttaacttacaaaccatttctctgtgcttaaggccaaaccgtgctgtacatacatgg-tagaaacttattcgaacctaat--gtccctgaattctgcagCTGTTTATAACCCTGTCGTGCACAATAGCGATTGGAACCAACCTAAGCCAGTTCATCTGCATCGGAAGATTCACAGCTGTATCGTTCCAAGTGCTGGGAC

upper sequence: LOC_Os02g40090.4 (Oryza sativa), 3'ss of exon 5
lower sequence: AT4G39390.1 (Arabidopsis thaliana), 3'ss of exon 5
--------------------------------------------------------------tatcatagcagtgcagacctgatgttccc-ttgacttttacatattcc-ttacatgagcaaactg------------ggactaatgctttct---tcttcactcacttaatttc-----cagTTCTTCATTGTATTGTCGTGCACAATTGCTGTTGGGACCAATCTAAGCCAGTTCATATGCATTGGAAGATTCACAGCTGTCTCATTTCAAGTTCTAGGCC
                                                              |   |    |||| ||   |  |  ||      | |   |  |||||| |  || || |  | ||            ||| |  |  || ||      |  || ||  |||||      ||||||||| |  || | |||||||  || || |||||||||||||| ||||| ||||| || |||||||||||||| || || || || ||||| || || |
gtaaagtttcttctccgtttctttacaaagtctcctacgattcaaaacagagcaatgagtatttggaacatagtgtagtattagtagtcataccaattcgcatttattccatctcaagaactgattgttatactctgttggatttgtctttcctaagctctatctaacacaattttttgggcagTTCTTCTTAATACTCTCGTGCAGTATCGCGGTTGGGACCAATCTCAGCCAATTCATCTGTATTGGAAGATTCACGGCGGTGTCTTTCCAAGTACTTGGTC

upper sequence: LOC_Os02g40090.4 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv18s0072g00080.t01 (Vitis vinifera), 3'ss of exon 4
tatcatagcagtgcagacctgatgttcccttgacttttacat-attccttacatgagcaaactgggactaatgctttcttcttcactcacttaatttccagTTCTTCATTGTATTGTCGTGCACAATTGCTGTTGGGACCAATCTAAGCCAGTTCATATGCATTGGAAGATTCACAGCTGTCTCATTTCAAGTTCTAGGCC
  | |      |  ||  |   |  | ||| |  || | | |   |  ||   |   |||    |  ||    ||| | || |   ||      ||| ||| | || ||  |  | || || || || || || |||||||| || |||||||||||||||||||| ||||||||||||||||| |||||||| || ||||
ggtgaatttcctctagttcactttattcctagcattgtgccttgctatttgtctttacaagaatgatctctcacttgcctcgttg-tcttggcttttgcagATATTTATAATCCTTTCATGTACTATCGCGGTAGGGACCAACCTCAGCCAGTTCATATGCATTGGTAGATTCACAGCTGTCTCCTTTCAAGTACTTGGCC

upper sequence: LOC_Os02g40090.4 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv07s0031g01860.t01 (Vitis vinifera), 3'ss of exon 5
tatcatagcagtgcagacctgatgttcccttg-acttttacatattccttacat-gagcaaactgggactaatgctttcttcttcactcacttaatttcc---agTTCTTCATTGTATTGTCGTGCACAATTGCTGTTGGGACCAATCTAAGCCAGTTCATATGCATTGGAAGATTCACAGCTGTCTCATTTCAAGTTCTAGGCC
    |||    |      || || |||        |||| |||  | ||   || |    |  | ||| |  ||||      ||  | |||||  || ||   || | |||||  |  |||| ||||||||||| || || ||||| || ||||| ||||| || |||||||||||||| || || || || |||||  | || |
---tatattcatttt--tctcatattcatgcatgtttttgcatcctgctcgtatcgtatcatttaggaatgctgctgatgatttgccccactttgttccctgcagATGTTCATCATTCTGTCCTGCACAATTGCGGTAGGAACCAACCTCAGCCAATTCATCTGTATTGGAAGATTCACTGCAGTGTCCTTCCAAGTGATTGGGC

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|29639689|gb|CB644698.1|CB644698
EST:     GGCTGACCAATAGAAGAGTTGATACTTTCAATTACACAACAATAGTTACG                         TTCTTCATTGTATTGTCGTGCACAATTGCTGTTGGGACCAATCTAAGCCAG
genomic: GGCTGACCAATAGAAGAGTTGATACTTTCAATTACACAACAATAGTTACGgtatgtgatt ... taatttccagTTCTTCATTGTATTGTCGTGCACAATTGCTGTTGGGACCAATCTAAGCCAG
EST: gi|88965552|gb|CI011719.1|CI011719
EST:     ATACTTTCAATTACACAACAATAGTTACG                         TTCTTCATTGTATTGTCGTGCACAATTGCTGTTGGGACCAATCTAAGCCAG
genomic: ATACTTTCAATTACACAACAATAGTTACGgtatgtgatt ... taatttccagTTCTTCATTGTATTGTCGTGCACAATTGCTGTTGGGACCAATCTAAGCCAG
EST: gi|29639690|gb|CB644699.1|CB644699
EST:     GGCTGACCAATAGAAGAGTTGATACTTTCAATTACACAACAATAGTTACG                         TTCTTCATTGTATTGTCGTGCACAATTGCTGTTGGGACCAATCTAAGCCAG
genomic: GGCTGACCAATAGAAGAGTTGATACTTTCAATTACACAACAATAGTTACGgtatgtgatt ... taatttccagTTCTTCATTGTATTGTCGTGCACAATTGCTGTTGGGACCAATCTAAGCCAG
EST: gi|88228513|gb|CI227993.1|CI227993
EST:     AACAATAGTTACG                         TTCTTCATTGTATTGTCGTGCACAATTGCTGTTGGGACCAATCTAAGCCAG
genomic: AACAATAGTTACGgtatgtgatt ... taatttccagTTCTTCATTGTATTGTCGTGCACAATTGCTGTTGGGACCAATCTAAGCCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttacatgagcaaactgggactaatgctttcttcttcactcacttaatttccagTTCTTCATTGTATTGTCGTGCACAATTGCTGTTGGGACCAATCTAAGCCAGTTCATATGCATTGGAAGATTCACAGCTGTCTCATTTCAAGTTCTAGGCC
                         tgctttcttcttcact  CT-rich tract
                                          acttaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatcatagcagtgcagacctgatgttcccttgacttttacatattccttacatgagcaaactgggactaatgctttcttcttcactcacttaatttccagTTCTTCATTGTATTGTCGTGCACAATTGCTGTTGGGACCAATCTAAGCCAGTTCATATGCATTGGAAGATTCACAGCTGTCTCATTTCAAGTTCTAGGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - cagtgca
- - - - - - - - -cctgatg
- - - - - - - - - - - - - - - - - - - - - - - - - catgagc