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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAGgtagattgcatgccactgagtttttggctttaagccaattctttcttgttttatttcaaaggactcagaaatgcgagggtatggtttcatcttttgttagtcaactctaattagtttgttttccttctgtatag

Basic information

species Oryza sativa
transcript LOC_Os05g51530.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g51530.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G128995_T01 (Zea mays), 5'ss of exon 5
GTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAGgtagattgca-tgccac----tgagtttttggctttaag---------------cca--attctttcttgttttatttcaaaggactcagaaatgcgagggt--atggtttcatc-ttttgttagtcaact--------ctaattagtttgttttccttctgtatag---
||||||| | ||||||| ||||||||||||||||||||||||||||||||||| ||||||| ||| ||||| |||||  || ||     || || ||  |  |  ||               |||  | | |||| |  ||||||  ||| |   ||| |  ||     |  |||| ||  || |||| |  ||   ||        ||||||||||||   |  |  ||| |     
GTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAGgtaaattgcgctgacatactttgtgtgttcagactctagaggaagtgcttgattccaggactttttccttgtttattgtaaaaggaacaggagagcagaaatgaatggcttactcattttatctgttgcctttcctatactaattagtttggccttttattgtgtgaaag

upper sequence: LOC_Os05g51530.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G128995_T05 (Zea mays), 5'ss of exon 5
GTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAGgtagattgca-tgccac----tgagtttttggctttaag---------------cca--attctttcttgttttatttcaaaggactcagaaatgcgagggt--atggtttcatc-ttttgttagtcaact--------ctaattagtttgttttccttctgtatag--------
||||||| | ||||||| ||||||||||||||||||||||||||||||||||| ||||||| ||| ||||| |||||  || ||     || || ||  |  |  ||               |||  | | |||| |  ||||||  ||| |   ||| |  ||     |  |||| ||  || |||| |  ||   ||        ||||||||||||   |  |  ||| |          
GTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAGgtaaattgcgctgacatactttgtgtgttcagactctagaggaagtgcttgattccaggactttttccttgtttattgtaaaaggaacaggagagcagaaatgaatggcttactcattttatctgttgcctttcctatactaattagtttggccttttattgtgtgaaagcttag

upper sequence: LOC_Os05g51530.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G144372_T01 (Zea mays), 5'ss of exon 5
GTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAGgtagattgcatgccactgagtttttg-----------------gctttaagccaa----------ttctttcttgttttatttcaaaggactcagaaatgcgag-------ggtatg---gtttcatcttttgttagtcaactctaattagtttgttttcc-ttctgtatag-
|| |||| ||||||||| |||||||||||||||||||||||||| |||||||||||||||| ||| ||||| |||||||     |   ||| ||                 | || | |||||          || |  |||||||  ||| ||| |   ||| |  |||         |||||     |||||||| ||| |   |    ||||||||||||| ||   || |||  |  
GTGCGAGCAGCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCAATCAACAGAAAGCAAAGTGGGAGgtaaattgcattgtcatacttttgtgcagaccctggaggaactgtttgatgccaagaccattacgttttcccttgtttattttaaaaaggaacaggagagcggaactggatggtatatccatttcatctgttgctttcctgtactaattagtttgtcttttattgtgtgaaag

upper sequence: LOC_Os05g51530.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G177912_T02 (Zea mays), 5'ss of exon 5
GTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAGgtagattgcatgccactgagtttttggctttaagccaattctttcttgttttatttcaaaggactcagaaatgcgagggtatggtttcatcttttgttagtcaactctaattagtttgttttccttctgtatag
|| |||| ||||||||| || ||||||||||||||||||| ||| |||||||||||||||| ||| |||||  |  ||| |   |     |     ||| ||| ||       ||   | | ||     |  |  |   |  |||    | |     || || | |  | |  || |||                       
GTCCGAGCAGCGGAATATAACAATGTAAGGAGCCAGCTTACTGCAATCAACAGAAAGCAAAGTGGGAGgtat-tgccatacttttatcactagtttttttagcgaaagggcctttagctgagtt-----ggttacgtggtctgag----tagcac--tccttaggtcctgagttcgaatc----------------------

upper sequence: LOC_Os05g51530.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA16G05470.1 (Glycine max), 5'ss of exon 5
GTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAGgtagattgcatgccactgagttt----ttggctttaagccaattctttcttgttttatttcaaagg-actcagaaatgcgagggtatggtttcatcttttgttagtcaactctaattagtttgttttccttctgtatag
||||| |   | || || || ||| |  | || ||||||| ||| |||||| |||||||||||||||||| |  || |||    |  |  |    | |  || ||    | | | |  | |||  || |  |   |||     ||   ||                                                         
GTTCGTGTTTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCTATCAACCGAAAGCAAACTGGAAGgt-gtgtggatgttgttatgactggtatagttttcaaatatagtatgttctatttctttgctgatctacttgactatttcag---------------------------------------------------------

upper sequence: LOC_Os05g51530.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA16G26220.1 (Glycine max), 5'ss of exon 5
GTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAGgtagattgcatgccactgagtttttggctttaagccaattctttcttgttttatttcaaaggactcagaaatgcgagggtatggtttcatcttttgttagtcaactctaattagtttgttttccttctgtatag
||||| |   | || || || ||| |  | || ||||||| ||| |||||| ||||||||||||||||||    || |||  |     || ||| |    |  ||  |   | ||  | || | || |   || ||       |    |    ||   || || ||||                                  
GTTCGTGTTTCCGAGTATAACAATATCCGCAGTCAGCTTAATGCCATCAACCGAAAGCAAACTGGAAGgtg---tgaatgttat----ttattgacc---aatca--tgacttttaatataatacatatttcttagctgacttaaatgacctatttgcctgtttttag----------------------------------

upper sequence: LOC_Os05g51530.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA02G07260.1 (Glycine max), 5'ss of exon 5
GTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAGgtagattgcatgccactgagtttttggctttaagccaattctttcttgttttatttcaaaggactcagaaatgcgagggtatggtttcatcttttgttagtcaactctaattagtttgttttccttctgtatag
||||| |   | || || || ||| |  | || ||||||| ||| |||||| ||||||||||||||||||    || |||  | | |         || ||  ||||  |  |||       || ||   | | || | | |   | |    ||| ||    | || | |   | ||                         
GTTCGTGTTTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCCATCAACCGAAAGCAAACTGGAAGgtg---tgaatgttattta---------ttgaa--caatcatgactt-------tttaatataataagtatttcttagctg-actttaatgacctatttgcctgttttag------------------------

upper sequence: LOC_Os05g51530.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv17s0000g00460.t01 (Vitis vinifera), 5'ss of exon 5
GTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAGgtagattgcat-gccactgagtttttggctttaagccaattctttcttgttttatttcaaaggactcagaaatgcgagggtatggtttcatcttttgttagtcaactctaattagtttgttttccttctgtatag
||||| |  || || || || |||||| | || ||||||| ||| || |||||||||||||||||||||||  ||| ||     |||   |  |      ||   | |||    |  |   | || | |  | |      |||  |   |    |  ||   |    | ||||                              
GTTCGTGTTGCTGAGTATAACAATGTACGCAGTCAGCTTAATGCCATAAACAGAAAGCAAACTGGAAGgta--ttgaattattgctgtaatcatcaacagaaattatttcaactt--tccaaatttataaaaattttgtttgcctgt-cagaaataaataaataaacattcaa------------------------------

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|29656670|gb|CB652945.1|CB652945
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAG                         CTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAGgtagattgca ... ttctgtatagCTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCAC
EST: gi|29662007|gb|CB658282.1|CB658282
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAG                         CTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAGgtagattgca ... ttctgtatagCTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCAC
EST: gi|29612869|gb|CB617882.1|CB617882
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAG                         CTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAGgtagattgca ... ttctgtatagCTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCAC
EST: gi|58667113|gb|CK055799.1|CK055799
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAG                         CTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCA
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAGgtagattgca ... ttctgtatagCTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCA
EST: gi|58666270|gb|CK054956.1|CK054956
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAG                         CTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAGgtagattgca ... ttctgtatagCTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCAC
EST: gi|218479849|gb|FG959490.1|FG959490
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAG                         CTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAGgtagattgca ... ttctgtatagCTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCAC
EST: gi|218498003|gb|FG943208.1|FG943208
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAG                         CTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAGgtagattgca ... ttctgtatagCTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCAC
EST: gi|58686384|gb|CK075071.1|CK075071
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAG                         CTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAGgtagattgca ... ttctgtatagCTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCAC
EST: gi|58594698|gb|CF993006.1|CF993006
EST:     ATAATGCTCAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAG                         CTTAGCAGTTCGTGATCTTGGCCAATCTGGTAAAACCAGAGGATATGGTCA
genomic: ATAATG-TAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAGgtagattgca ... ttctgtatagCTTAGCAGTTCGTGATCTTT-CCAATCTGGTAAAACCAGAGGATATGGTCA
EST: gi|58600826|gb|CK011354.1|CK011354
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAG                         CTTAGCAGTTCGTGATCTT
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAGgtagattgca ... ttctgtatagCTTAGCAGTTCGTGATCTT
EST: gi|29613101|gb|CB618114.1|CB618114
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAG                         CTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAGgtagattgca ... ttctgtatagCTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCAC
EST: gi|58596246|gb|CK006774.1|CK006774
EST:     CATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAG                         CTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAGgtagattgca ... ttctgtatagCTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCAC
EST: gi|58688997|gb|CK077684.1|CK077684
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAG                         CTTAGCAGTTCGTGATCTTTCCAATCTGGTAA
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAGgtagattgca ... ttctgtatagCTTAGCAGTTCGTGATCTTTCCAATCTGGTAA
EST: gi|25802832|gb|CA758793.1|CA758793
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAG                         CTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAGgtagattgca ... ttctgtatagCTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCAC
EST: gi|27578007|gb|CB000702.1|CB000702
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAG                         CTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAGgtagattgca ... ttctgtatagCTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCAC
EST: gi|29613962|gb|CB618975.1|CB618975
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAG                         CTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAGgtagattgca ... ttctgtatagCTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCAC

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: 72 (upstream exon), 75 (downstream exon)
Score: 66

GTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAGgtagattgca ... ttctgtatagCTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCACATCAGAACATCTAGTGACACTCCTTGCAGTTGTTCCTAAGTACTCTCAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAGgtagattgcatgccactgagtttttggctttaagccaattctttcttgttttatttcaaaggactcagaaatgcgagggtatggtttcatcttttgttagtcaactctaattagtttgttttccttctgtatag

- - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG