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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCACAGTTGAATGAGCACACTAAACTCTCTATGCTAAGGAATGCAACTTGGACTTTATCGAACTTCTGCAGAGGAAAACCACAGCCATCATTTGAACAGgtttggacaaagtttctttgtactctactgtagttagtagggaaagacagttccttaacatgatgtttattgggtgtcaatag

Basic information

species Oryza sativa
transcript LOC_Os01g14950.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g14950.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G091119_T02 (Zea mays), 5'ss of exon 5
AGCACAGTTGAATGAGCACACTAAACTCTCTATGCTAAGGAATGCAACTTGGACTTTATCGAACTTCTGCAGAGGAAAACCACAGCCATCATTTGAACAGgtt-tggacaaagtttctttgtactctactgtagttagtagggaaagacagttccttaacatgatgtttattgggtgtcaatag
||| ||||||||||||||  | || ||||| ||| | |||||||| || |||||| | || ||||| ||||| ||||| ||||||||||||||||| |||||  | |||||   ||||||     ||  | |     |||      |  | |   | |||||| | ||  |||  ||| |  ||
AGCCCAGTTGAATGAGCATGCGAAGCTCTCCATGTTGAGGAATGCCACCTGGACTCTGTCCAACTTTTGCAGGGGAAAGCCACAGCCATCATTTGATCAGgtcgtagacaagacttctttaattgcttttct-----gtaacagtggttactaaataaacatgttattctttgactgtta-cag

upper sequence: LOC_Os01g14950.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G088231_T01 (Zea mays), 5'ss of exon 5
AGCACAGTTGAATGAGCACACTAAACTCTCTATGCTAAGGAATGCAACTTGGACTTTATCGAACTTCTGCAGAGGAAAACCACAGCCATCATTTGAACAGgttt-ggacaaagtttctttgtactctactgtagttagtagggaaagacagttccttaacatgatgtttattgggtgtcaatag
||| ||||||||||||||   ||| ||||| |||||  ||||||| || |||||||| || ||||||||||| ||||||||||||||||||||||| |||||||   ||||   ||||||  |||    |   || | |  || |    | |  || |||||| |  |  |||| ||| | |||
AGCCCAGTTGAATGAGCATGTTAAGCTCTCCATGCTGCGGAATGCCACCTGGACTTTGTCTAACTTCTGCAGGGGAAAACCACAGCCATCATTTGATCAGgttttaaacaagacttcttttaactgcttttctgtaactgtggta----actaactaaacatgtttatctttggctgtta-tag

upper sequence: LOC_Os01g14950.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA03G39210.1 (Glycine max), 5'ss of exon 6
AGCACAGTTGAATGAGCACACTAAACTCTCTATGCTAAGGAATGCAACTTGGACTTTATCGAACTTCTGCAGAGGAAAACCACAGCCATCATTTGAACAGgtttg--gacaaagtttctttgtactctactgtagttagtagggaaagacagttccttaacatgatgtttattgggtgtcaatag---------------
 ||||| |||||||||||  | || || ||||||||||| ||||| || |||||  ||||||| |||||||| || |||||||||||  | ||||| ||||| ||  |  |    ||   ||  ||  | | |      |  ||        ||| |     |  | || |||  |    || |                
GGCACAATTGAATGAGCATGCCAAGCTTTCTATGCTAAGAAATGCTACCTGGACACTATCGAATTTCTGCAGGGGGAAACCACAGCCTGCTTTTGATCAGgtatgatgttatgaattgcatgatcttaaatattaaagttttggctccttccttcatctttttattcttcattttgctataaaataaaatatctctcatg

upper sequence: LOC_Os01g14950.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA19G41770.1 (Glycine max), 5'ss of exon 5
AGCACAGTTGAATGAGCACACTAAACTCTCTATGCTAAGGAATGCAACTTGGACTTTATCGAACTTCTGCAGAGGAAAACCACAGCCATCATTTGAACAGgtttggacaaagtttctttgtactctactgtagttagtagggaaa----gacag-ttccttaacatgatgtttattgggtgtca-atag------------
 ||||| |||||||||||  | || || ||||||||||| ||||| || |||||  ||||||| |||||||| || |||||||||||  | ||||| ||||| || |   |  |  | || | |  |  ||  | | ||  |||     | ||  ||||||    |  |  || ||   | | | ||||            
GGCACAATTGAATGAGCATGCCAAGCTTTCTATGCTAAGAAATGCTACCTGGACACTATCGAATTTCTGCAGGGGGAAACCACAGCCTGCTTTTGATCAGgtatgaagttatctgttatgcattgcatggtc-taaatattgaagttttggcaccttccttcgtctttttattcttcattttgatatagaataaaatattt

upper sequence: LOC_Os01g14950.1 (Oryza sativa), 5'ss of exon 5
lower sequence: AT1G02690.1 (Arabidopsis thaliana), 5'ss of exon 5
AGCACAGTTGAATGAGCACACTAAACTCTCTATGCTAAGGAATGCAACTTGGACTTTATCGAACTTCTGCAGAGGAAAACCACAGCCATCATTTGAACAGgttt----ggacaaagtttctttgtactctactgtagttagtagggaaagacagttccttaacatga---tgt-ttattgggtgtcaatag---
 || || ||  |||||||  | || ||||| ||||| |||||||| || ||||| ||||| || ||||||||||| || || |||||  |||||||||||||||    | | | |   | | |  || | | |  |  |  |        || |||  |||| ||||   ||| | ||||  | |    ||   
GGCTCAATTCCATGAGCATTCAAAGCTCTCCATGCTGAGGAATGCTACATGGACATTATCAAATTTCTGCAGAGGGAAGCCGCAGCCTGCATTTGAACAGgtttccttgcatataagatatataaac-caatttgaagtgttttttctcaactgtttattaatatgagaatgtgtcattgcatttgttgagcag

upper sequence: LOC_Os01g14950.1 (Oryza sativa), 5'ss of exon 5
lower sequence: AT1G02690.2 (Arabidopsis thaliana), 5'ss of exon 5
AGCACAGTTGAATGAGCACACTAAACTCTCTATGCTAAGGAATGCAACTTGGACTTTATCGAACTTCTGCAGAGGAAAACCACAGCCATCATTTGAACAGgttt----ggacaaagtttctttgtactctactgtagttagtagggaaagacagttccttaacatga---tgt-ttattgggtgtcaatag
 || || ||  |||||||  | || ||||| ||||| |||||||| || ||||| ||||| || ||||||||||| || || |||||  |||||||||||||||    | | | |   | | |  || | | |  |  |  |        || |||  |||| ||||   ||| | ||||  | |    ||
GGCTCAATTCCATGAGCATTCAAAGCTCTCCATGCTGAGGAATGCTACATGGACATTATCAAATTTCTGCAGAGGGAAGCCGCAGCCTGCATTTGAACAGgtttccttgcatataagatatataaac-caatttgaagtgttttttctcaactgtttattaatatgagaatgtgtcattgcatttgttgag

upper sequence: LOC_Os01g14950.1 (Oryza sativa), 5'ss of exon 5
lower sequence: AT4G16143.1 (Arabidopsis thaliana), 5'ss of exon 4
AGCACAGTTGAATGAGCACACTAAACTCTCTATGCTAAGGAATGCAACTTGGACTTTATCGAACTTCTGCAGAGGAAAACCACAGCCATCATTTGAACAGgtttggacaaagtttctttgtactctactgtagttagtagggaaagacagttccttaacatgatgtttattgggtgtcaatag---
  | ||||||||||||||  |||||||||| ||||| || ||||| ||||||||  | || || |||||||| || || ||||||||  | ||||| ||||||||       || || |   ||  |     |     ||   |||  ||||  |     | ||  || |    | | ||||    
CTCTCAGTTGAATGAGCATGCTAAACTCTCGATGCTGAGAAATGCTACTTGGACCCTCTCTAATTTCTGCAGGGGCAAGCCACAGCCTCCCTTTGACCAGgtttgtctctcattcctat---cttaatctctgcccaaagatgaagg-agtttttctttttaattcttgtgatctcttaataacag

upper sequence: LOC_Os01g14950.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv05s0077g01430.t01 (Vitis vinifera), 5'ss of exon 5
AGCACAGTTGAATGAGCACACTAAACTCTCTATGCTAAGGAATGCAACTTGGACTTTATCGAACTTCTGCAGAGGAAAACCACAGCCATCATTTGAACAGgtt-------tggacaaag--tttctttgtactctactgtagttagtagggaaagacagttccttaacatgatgtttattgggtgtcaatag---------------------------
||||||||||||||||||  | ||||| || |||||||| ||||| || |||||| |||| |||||||||||||| || || |||||| ||||||| ||||||       ||  ||  |  ||  || | | || |   | |      |       |   | |   | ||  |  ||  ||| ||||  |||                           
AGCACAGTTGAATGAGCATGCCAAACTTTCAATGCTAAGAAATGCCACATGGACTCTATCAAACTTCTGCAGAGGCAAGCCTCAGCCACCATTTGATCAGgttgttgctttgatcattgcattgtttaggattcaagcattgcatcccgtctctccctccttccctaaattttactttgtggttgtctgtagcagtttttaaaccttttgaaattgcag

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|29662761|gb|CB659036.1|CB659036
EST:     GGACTTTATCGAACTTCTGCAGAGGAAAACCACAGCCATCATTTGTACAG                         ACTACGCCTGCTCTTCCAGCACTGGCACGGCTTATT
genomic: GGACTTTATCGAACTTCTGCAGAGGAAAACCACAGCCATCATTTGAACAGgtttggacaa ... gtgtcaatagACTAGGCCTGCTCTTCCAGCACTGGCACGGCTTATT
EST: gi|88761467|gb|CI771023.1|CI771023
EST:     GGACTTTATCGAACTTCTGCAGAGGAAAACCACAGCCATCATTTGAACAG                         ACTAGGCCTGCTCTTCCAGCACTGGCACGGCTTATTCACTC
genomic: GGACTTTATCGAACTTCTGCAGAGGAAAACCACAGCCATCATTTGAACAGgtttggacaa ... gtgtcaatagACTAGGCCTGCTCTTCCAGCACTGGCACGGCTTATTCACTC
EST: gi|58608932|gb|CK036965.1|CK036965
EST:     GGACTTTATCGAACTTCTGCAGAGGAAAACCACAGCCATCATTTGAACAG                         ACTAGGCCTGCTCTTCCAGCACTGGCACGGCTTATTCACTCCAATGATGAG
genomic: GGACTTTATCGAACTTCTGCAGAGGAAAACCACAGCCATCATTTGAACAGgtttggacaa ... gtgtcaatagACTAGGCCTGCTCTTCCAGCACTGGCACGGCTTATTCACTCCAATGATGAG
EST: gi|218502437|gb|FG957283.1|FG957283
EST:     GGACTTTATCGAACTTCTGCAGAGGAAAACCACAGCCATCATTTGAACAG                         ACTAGGCCTGCTCTTCCAGCACTGGCACGGCTTATTCACTCC
genomic: GGACTTTATCGAACTTCTGCAGAGGAAAACCACAGCCATCATTTGAACAGgtttggacaa ... gtgtcaatagACTAGGCCTGCTCTTCCAGCACTGGCACGGCTTATTCACTCC
EST: gi|86851083|gb|CI311301.1|CI311301
EST:     GGACTTTATCGAACTTCTGCAGAGGAAAACCACAGCCATCATTTGAACAG                         ACTAGGCCTGCTCTTCCAGCACTGGCACGGCTTATTCACTCCAATGATGAG
genomic: GGACTTTATCGAACTTCTGCAGAGGAAAACCACAGCCATCATTTGAACAGgtttggacaa ... gtgtcaatagACTAGGCCTGCTCTTCCAGCACTGGCACGGCTTATTCACTCCAATGATGAG
EST: gi|218497818|gb|FG965121.1|FG965121
EST:     GGACTTTATCGAACTTCTGCAGAGGAAAACCACAGCCATCATTTGAACAG                         ACTAGGCCTGCTCTTCCAGCACTGGCACGGCTTATTCACTCCAATGATGAG
genomic: GGACTTTATCGAACTTCTGCAGAGGAAAACCACAGCCATCATTTGAACAGgtttggacaa ... gtgtcaatagACTAGGCCTGCTCTTCCAGCACTGGCACGGCTTATTCACTCCAATGATGAG
EST: gi|55411455|gb|CV723831.1|CV723831
EST:     GGACTTTATCGAACTTCTGCAGAGGAAAACCACAGCCATCATTTGAACAG                         ACTAGGCCTGCTCTTCCAGCACTGGCACGGCTTATTCACTCCAATGATGAG
genomic: GGACTTTATCGAACTTCTGCAGAGGAAAACCACAGCCATCATTTGAACAGgtttggacaa ... gtgtcaatagACTAGGCCTGCTCTTCCAGCACTGGCACGGCTTATTCACTCCAATGATGAG
EST: gi|2443054|gb|C74825.1|C74825
EST:     GGACTTTATCGAACTTCTGCAGAGGAAAACCACAGCCATCATTTGAACAG                         ACTAGGCCTGCTCTTCCAGCACTGGCACGGCTTATTCACTCCAATGATGAG
genomic: GGACTTTATCGAACTTCTGCAGAGGAAAACCACAGCCATCATTTGAACAGgtttggacaa ... gtgtcaatagACTAGGCCTGCTCTTCCAGCACTGGCACGGCTTATTCACTCCAATGATGAG
EST: gi|29662174|gb|CB658449.1|CB658449
EST:     GGACTTTATCGAACTTCTGCAGAGGAAAACCACAGCCATCATTTGAACAG                         ACTAGGCCTGCTCTTCCAGCA
genomic: GGACTTTATCGAACTTCTGCAGAGGAAAACCACAGCCATCATTTGAACAGgtttggacaa ... gtgtcaatagACTAGGCCTGCTCTTCCAGCA
EST: gi|58588691|gb|CF986999.1|CF986999
EST:     GGACTTTATCGAACTTCTGCAGAGGAAAACCACAGCCATCATTTGAACAG                         ACTAGGCCTGCTCTTCCAGCACTGGCACGGCTTATTCACTCCAATGATGAG
genomic: GGACTTTATCGAACTTCTGCAGAGGAAAACCACAGCCATCATTTGAACAGgtttggacaa ... gtgtcaatagACTAGGCCTGCTCTTCCAGCACTGGCACGGCTTATTCACTCCAATGATGAG
EST: gi|29640361|gb|CB645370.1|CB645370
EST:     GGACTTTATCGAACTTCTGCAGAGGAAAACCACAGCCATCATTTGAACAG                         ACTAGGCCTGCTCTTCCAGCACTGGCACGGCTTATTCACTCCAATGATGAG
genomic: GGACTTTATCGAACTTCTGCAGAGGAAAACCACAGCCATCATTTGAACAGgtttggacaa ... gtgtcaatagACTAGGCCTGCTCTTCCAGCACTGGCACGGCTTATTCACTCCAATGATGAG
EST: gi|29643710|gb|CB648717.1|CB648717
EST:     GGACTTTATCGAACTTCTGCAGAGGAAAACCACAGCCATCATTTGAACAG                         ACTAGGCCTGCTCTTCCAGCACTGGCACGGCTTATTCACTCCAATGATGAG
genomic: GGACTTTATCGAACTTCTGCAGAGGAAAACCACAGCCATCATTTGAACAGgtttggacaa ... gtgtcaatagACTAGGCCTGCTCTTCCAGCACTGGCACGGCTTATTCACTCCAATGATGAG
EST: gi|66912883|gb|CX099731.1|CX099731
EST:     GGACTTTATCGAACTTCTGCAGAGGAAAACCACAGCCATCATTTGAACAG                         ACTAGGCCTGCTCTTCCAGCACTGGCACGGCTTATTCACTCCAATGATGAG
genomic: GGACTTTATCGAACTTCTGCAGAGGAAAACCACAGCCATCATTTGAACAGgtttggacaa ... gtgtcaatagACTAGGCCTGCTCTTCCAGCACTGGCACGGCTTATTCACTCCAATGATGAG

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: 74 (upstream exon), 75 (downstream exon)
Score: 117

AGCACAGTTGAATGAGCACACTAAACTCTCTATGCTAAGGAATGCAACTTGGACTTTATCGAACTTCTGCAGAGGAAAACCACAGCCATCATTTGAACAGgtttggacaa ... gtgtcaatagACTAGGCCTGCTCTTCCAGCACTGGCACGGCTTATTCACTCCAATGATGAGGAAGTTCTCACTGATGCGTGCTGGGCTCTTTCATATTTATCTGATGGCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCACAGTTGAATGAGCACACTAAACTCTCTATGCTAAGGAATGCAACTTGGACTTTATCGAACTTCTGCAGAGGAAAACCACAGCCATCATTTGAACAGgtttggacaaagtttctttgtactctactgtagttagtagggaaagacagttccttaacatgatgtttattgggtgtcaatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA