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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATGAATGCTCCTGTTATGGTCGAGCTTGAAGGGGAGACTGATCCACTTGAGgtaaagttccgatttcagttttctagacatagacttcttcaattaatacaagtctgcacaaaatgtcaccttctatatttccttgagctcttcatttcta...

Basic information

species Oryza sativa
transcript LOC_Os07g27930.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g27930.1 (Oryza sativa), 5'ss of exon 4
lower sequence: AT2G04630.1 (Arabidopsis thaliana), 5'ss of exon 4
CATGAATGCTCCTGTTATGGTCGAGCTTGAAGGGGAGACTGATCCACTTGAGgtaaagttccgatttcagttttctagacatagacttcttcaattaatacaagtctgcacaaa-atgtcaccttctatatttccttgagctcttcatttcta-
||||||||||||||||||||| ||| | || || ||||||||||||||||||||    | ||   |||  | || | |   |   | |  |   | | || | ||    |   | |||     || | |  ||  |||     ||    |  | 
CATGAATGCTCCTGTTATGGTTGAGTTGGAGGGTGAGACTGATCCACTTGAGgtg--ttgccttcttccttcttgttgtgtttttcatgatttgtcagtaaatgttgatatgtatatgaacatttgtgttgtttattgtatgatttggcttaag

upper sequence: LOC_Os07g27930.1 (Oryza sativa), 5'ss of exon 4
lower sequence: AT5G51940.1 (Arabidopsis thaliana), 5'ss of exon 4
CATGAATGCTCCTGTTATGGTCGAGCTTGAAGGGGAGACTGATCCACTTGAGgtaaagttccgatttcagttttctagacatagacttcttcaatta-atacaagtctgcacaaaatgtcaccttctatatttccttgagctcttcatttcta
||||||||||||||| ||||| ||||| || || ||||||||||||||||||||    || |     |    |||| |   | |  || |  | |||  |   |||   |  | |    ||  |    || ||  ||  | | |  |||    
CATGAATGCTCCTGTCATGGTTGAGCTAGAGGGTGAGACTGATCCACTTGAGgtgtgcttac-----ctaccttcttgttgttggtttttgaagttatgtctcagtaaacttatatgaacatttgagctaatttattatgatttggattcag-
















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|89168501|gb|CI038855.1|CI038855
EST:     TGAATGCTCCTGTTATGGTCGAGCTTGAAGGGGAGACTGATCCACTTGAG                         ATTGCCATGAAAGAATTGAGAGCACGCAAGATCCCTTTCACAATCAGGCGG
genomic: TGAATGCTCCTGTTATGGTCGAGCTTGAAGGGGAGACTGATCCACTTGAGgtaaagttcc ... gaaatttcagATTGCCATGAAAGAATTGAGAGCACGCAAGATCCCTTTCACAATCAGGCGG
EST: gi|89168685|gb|CI038537.1|CI038537
EST:     CGAGCTTGAAGGGGAGACTGATCCACTTGAG                         ATTGCCATGAAAGAATTGAGAGCACGCAAGATCCCTTTCACGATCAGGCGG
genomic: CGAGCTTGAAGGGGAGACTGATCCACTTGAGgtaaagttcc ... gaaatttcagATTGCCATGAAAGAATTGAGAGCACGCAAGATCCCTTTCACAATCAGGCGG
EST: gi|58590685|gb|CF988993.1|CF988993
EST:     TGAATGCTCCTGTTATGGTTGAGCTTGAAGGGGAGACTGATCCACTTGAG                         ATTGCCATGAAAGAATTGAGAGCACGCAAGATCCCTTTCACAATCAGGCGG
genomic: TGAATGCTCCTGTTATGGTCGAGCTTGAAGGGGAGACTGATCCACTTGAGgtaaagttcc ... gaaatttcagATTGCCATGAAAGAATTGAGAGCACGCAAGATCCCTTTCACAATCAGGCGG
EST: gi|88435819|gb|CI513958.1|CI513958
EST:     TGAATGCTCCTGTTATGGTCGAGCTTGAAGGGGAGACTGATCCACTTGAG                         ATTGCCATGAAAGAATTGAGAGCACGCAAGATCCCTTTCACAATCAGGCGG
genomic: TGAATGCTCCTGTTATGGTCGAGCTTGAAGGGGAGACTGATCCACTTGAGgtaaagttcc ... gaaatttcagATTGCCATGAAAGAATTGAGAGCACGCAAGATCCCTTTCACAATCAGGCGG
EST: gi|33659391|gb|CF282004.1|CF282004
EST:     TGAATGCTCCTGTTATGGTCGAGCTTGAAGGGGAGACTGATCCACTTGAG                         ATTGCCATGAAAGAATTGAGAGCACGCAAGATCCCTTTCACAATCAGGCGG
genomic: TGAATGCTCCTGTTATGGTCGAGCTTGAAGGGGAGACTGATCCACTTGAGgtaaagttcc ... gaaatttcagATTGCCATGAAAGAATTGAGAGCACGCAAGATCCCTTTCACAATCAGGCGG
EST: gi|88958855|gb|CI381658.1|CI381658
EST:     TGAATGCTCCTGTTATGGTCGAGCTTGAAGGGGAGACTGATCCACTTGAG                         ATTGCCATGAAAGAATTGAGAGCACGCAAGATCCCTTTCACAATCAGGCGG
genomic: TGAATGCTCCTGTTATGGTCGAGCTTGAAGGGGAGACTGATCCACTTGAGgtaaagttcc ... gaaatttcagATTGCCATGAAAGAATTGAGAGCACGCAAGATCCCTTTCACAATCAGGCGG
EST: gi|88286132|gb|CI515256.1|CI515256
EST:     TGAATGCTCCTGTTATGGTCGAGCTTGAAGGGGAGACTGATCCACTTGAG                         ATTGCCATGAAAGAATTGAGAGCACGCAAGATCCCTTTCACAATCAGGCGG
genomic: TGAATGCTCCTGTTATGGTCGAGCTTGAAGGGGAGACTGATCCACTTGAGgtaaagttcc ... gaaatttcagATTGCCATGAAAGAATTGAGAGCACGCAAGATCCCTTTCACAATCAGGCGG
EST: gi|88259548|gb|CI363841.1|CI363841
EST:     TGAGTGCTCCTGTTATGTTCGAGCTTGAAGGGGAGACTGATCCACTTGAG                         ATTGCCATGAAAGAATTGAGAGCACGCAAGATCCCTTTCACAATCAGGCGG
genomic: TGAATGCTCCTGTTATGGTCGAGCTTGAAGGGGAGACTGATCCACTTGAGgtaaagttcc ... gaaatttcagATTGCCATGAAAGAATTGAGAGCACGCAAGATCCCTTTCACAATCAGGCGG
EST: gi|88555714|gb|CI485991.1|CI485991
EST:     TGAATGCTCCTTTTATGGTCGAGCTTGAAGGGGAGACTGATCCACGTGAG                         ATTGCCATGAAAGAATTGAGAGCACGCAAGATCCCTTTCACAATCAGGCGG
genomic: TGAATGCTCCTGTTATGGTCGAGCTTGAAGGGGAGACTGATCCACTTGAGgtaaagttcc ... gaaatttcagATTGCCATGAAAGAATTGAGAGCACGCAAGATCCCTTTCACAATCAGGCGG
EST: gi|88419886|gb|CI516335.1|CI516335
EST:     TGAATGCTCCTGTTATGTTCGAGCTTGAAGGGGAGACTGATCCACTTGAG                         ATTGCCATGAAAGAATTGAGAGCACGCAAGATCCCTTTCACAATCAGGCGG
genomic: TGAATGCTCCTGTTATGGTCGAGCTTGAAGGGGAGACTGATCCACTTGAGgtaaagttcc ... gaaatttcagATTGCCATGAAAGAATTGAGAGCACGCAAGATCCCTTTCACAATCAGGCGG
EST: gi|325493780|gb|JG458304.1|JG458304
EST:     TGAATGCTCCTGTTATGGTCGAGCTTGAAGGGGAGACTGATCCACTTGAG                         ATTGCCATGAAAGAACTGAGAGCACGCA
genomic: TGAATGCTCCTGTTATGGTCGAGCTTGAAGGGGAGACTGATCCACTTGAGgtaaagttcc ... gaaatttcagATTGCCATGAAAGAATTGAGAGCACGCA
EST: gi|86867542|gb|CI337921.1|CI337921
EST:     TGAATGCTCCTGTTATGGTCGAGCTTGAAGGGGAGACTGATCCACTTGAG                         ATTGCCATGAAAGAATTGAGAGCACGCAAGATCCCTTTCACAATCAGGCGG
genomic: TGAATGCTCCTGTTATGGTCGAGCTTGAAGGGGAGACTGATCCACTTGAGgtaaagttcc ... gaaatttcagATTGCCATGAAAGAATTGAGAGCACGCAAGATCCCTTTCACAATCAGGCGG
EST: gi|38476890|gb|CF961023.1|CF961023
EST:     TGAATGCTCCTGTTATGGTCGAGCTTGAAGGGGAGACTGATCCACTTGAG                         ATTGCCATGAAAGAATTGAGAGCACGCAAGATCCCTTTCACAATCAGGCGG
genomic: TGAATGCTCCTGTTATGGTCGAGCTTGAAGGGGAGACTGATCCACTTGAGgtaaagttcc ... gaaatttcagATTGCCATGAAAGAATTGAGAGCACGCAAGATCCCTTTCACAATCAGGCGG
EST: gi|88541223|gb|CI468481.1|CI468481
EST:     TGAATGCTCCTGTTATGGTCGAGCTTGAAGGGGAGACTNATCCACTTGAG                         ATTGCCATGAAAGAATTGAGAGCACGCAAGATCCCTTTCACAATCAGGCGG
genomic: TGAATGCTCCTGTTATGGTCGAGCTTGAAGGGGAGACTGATCCACTTGAGgtaaagttcc ... gaaatttcagATTGCCATGAAAGAATTGAGAGCACGCAAGATCCCTTTCACAATCAGGCGG
EST: gi|13165597|gb|AU174394.1|AU174394
EST:     TGAATGCTCCTGTTATGGTCGAGCTTGAAGGGGAGACTGATCCACTTGAG                         ATTGCCATGAAAGAATTGAGAGCACGCAAGATCCCTTTCACAATCAGGCGG
genomic: TGAATGCTCCTGTTATGGTCGAGCTTGAAGGGGAGACTGATCCACTTGAGgtaaagttcc ... gaaatttcagATTGCCATGAAAGAATTGAGAGCACGCAAGATCCCTTTCACAATCAGGCGG
EST: gi|88549482|gb|CI479375.1|CI479375
EST:     TGAATGCTCCTGTTATGGTCGAGCTTGAAGGGGAGACTGATCCACTTGAG                         ATTGCCATGAAAGAATTGAGAGCACCCAANATCCCTTTCACAATCAGGCGG
genomic: TGAATGCTCCTGTTATGGTCGAGCTTGAAGGGGAGACTGATCCACTTGAGgtaaagttcc ... gaaatttcagATTGCCATGAAAGAATTGAGAGCACGCAAGATCCCTTTCACAATCAGGCGG
EST: gi|88992556|gb|CI035639.1|CI035639
EST:     TGAATGCTCCTGTTATGGTCGAGCTTGAAGGGGAGACTGATCCACTTGAG                         ATTGCCATGAAAGAATTGAGAGCACGCAAGATCCCTTTCACAATCAGGCGG
genomic: TGAATGCTCCTGTTATGGTCGAGCTTGAAGGGGAGACTGATCCACTTGAGgtaaagttcc ... gaaatttcagATTGCCATGAAAGAATTGAGAGCACGCAAGATCCCTTTCACAATCAGGCGG

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), 34 (downstream exon)
Score: 84

CATGAATGCTCCTGTTATGGTCGAGCTTGAAGGGGAGACTGATCCACTTGAGgtaaagttcc ... gaaatttcagATTGCCATGAAAGAATTGAGAGCACGCAAGATCCCTTTCACAATCAGGCGGTATTTACCTGATGGAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATGAATGCTCCTGTTATGGTCGAGCTTGAAGGGGAGACTGATCCACTTGAGgtaaagttccgatttcagttttctagacatagacttcttcaattaatacaagtctgcacaaaatgtcaccttctatatttccttgagctcttcatttcta

- - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - TTGAAG