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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCTTGAGGTGTTGCGTGAAGACCTCAGAAATTTGTCTTCGCTCGTTGTATTAAACATTAGTCACAACAATATTTCTTCCCTCCCCGCAGCTATTGGAGAgtatgtactggactatccttatttactactccctccggtcatggaaacatatcgtttgtggacatgtttgaagtcactgccttcaaaaccagtttcataa...

Basic information

species Oryza sativa
transcript LOC_Os02g58030.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g58030.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G015090_T01 (Zea mays), 5'ss of exon 2
ACCTTGAGGTGTTGCGTGAAGACCTCAGAAATTTGTCTTCGCTCGTTGTATTAAACATTAGTCACAACAATATTTCTTCCCTCCCCGCAGCTATTGGAGAgtatgtactggactatccttatttactactccctccggtcatggaaacatatcgtt----tgtggacatgtttgaagtcactgccttcaaaaccagtttcataa
| |||||||||||  | |||||||| || || ||||||||||| |||||  |||| || ||||||||||| || |||||||| || |||||||| |||||||||| ||    |||||  |||| || | |  |     | |         ||   |    ||    | |||||   || | | |  |      |||| ||    
ATCTTGAGGTGTTAAGAGAAGACCTTAGGAACTTGTCTTCGCTTGTTGTTCTAAATATAAGTCACAACAAGATATCTTCCCTTCCAGCAGCTATCGGAGAgtatgcacctc-ctatc--tattgacgaatttcattaataaatatgcgccattaatataatgccaccgtgttttttgttaatcctatttcttgcagtctcccg-
















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|58594661|gb|CF992969.1|CF992969
EST:     TAAACATTAGTCACAACAATATTGGGTGCCCTCCCCGCAGCTATTGGAGA                         CCTTCCTTTGCTAAAATCATTGGATGTATCTTCTAATCAAATAAACGCTTT
genomic: TAAACATTAGTCACAACAATATT-TCTTCCCTCCCCGCAGCTATTGGAGAgtatgtactg ... ttccatgcagCCTTCCTTTGCTAAAATCGTTGGATGTATCTTCTAATCAAATAAACGCTTT
EST: gi|88393661|gb|CI621156.1|CI621156
EST:     TTAAACATTAGTCACAACAATATTTCTTCCCTCCCCGCAGCTATTGGAGA                         CCTTCCTTTGCTA
genomic: TTAAACATTAGTCACAACAATATTTCTTCCCTCCCCGCAGCTATTGGAGAgtatgtactg ... ttccatgcagCCTTCCTTTGCTA
EST: gi|88370332|gb|CI587722.1|CI587722
EST:     TTAAACATTAGTCACAACAATATTTCTTCCCTCCCCGCAGCTATTGGAGA                         CCTTCCTTTGCTAAAATCGTTGGATGTATCTTCTAATCAAATAAACGCTTT
genomic: TTAAACATTAGTCACAACAATATTTCTTCCCTCCCCGCAGCTATTGGAGAgtatgtactg ... ttccatgcagCCTTCCTTTGCTAAAATCGTTGGATGTATCTTCTAATCAAATAAACGCTTT
EST: gi|88372250|gb|CI619580.1|CI619580
EST:     TTAAACATTAGTCACAACAATATTTCTTCCCTCCCCGCAGCTATTGGAGA                         CCTTCCTTTGCTAAAATCGTTGGATGTATCTTCTAATCAAATAAAC
genomic: TTAAACATTAGTCACAACAATATTTCTTCCCTCCCCGCAGCTATTGGAGAgtatgtactg ... ttccatgcagCCTTCCTTTGCTAAAATCGTTGGATGTATCTTCTAATCAAATAAAC
EST: gi|88339003|gb|CI677822.1|CI677822
EST:     TTAAACATTAGTCACAACAATATTTCTTCCCTCCCCGCAGCTATTGGAGA                         CCTTCCTTTGCTAA
genomic: TTAAACATTAGTCACAACAATATTTCTTCCCTCCCCGCAGCTATTGGAGAgtatgtactg ... ttccatgcagCCTTCCTTTGCTAA
EST: gi|88315437|gb|CI613706.1|CI613706
EST:     TTAAACATTAGTCACAACAATATTTCTTCCCTCCCCGCAGCTATTGGAGA                         CCTTCCTTTGCTAAAATCGTTGGATGTATCTTCT
genomic: TTAAACATTAGTCACAACAATATTTCTTCCCTCCCCGCAGCTATTGGAGAgtatgtactg ... ttccatgcagCCTTCCTTTGCTAAAATCGTTGGATGTATCTTCT
EST: gi|58669154|gb|CK057840.1|CK057840
EST:     TTAAACATTAGTCACAACAATATTTCTTCCCTCCCCGCAGCTATTGGAGA                         CCTTCCTTTGCTAAAATCATTGGATGTATCTTCTAATCAAATAAACGCTTT
genomic: TTAAACATTAGTCACAACAATATTTCTTCCCTCCCCGCAGCTATTGGAGAgtatgtactg ... ttccatgcagCCTTCCTTTGCTAAAATCGTTGGATGTATCTTCTAATCAAATAAACGCTTT
EST: gi|88355166|gb|CI651869.1|CI651869
EST:     TTAAACATTAGTCACAACAATATTTCTTCCCTCCCCGCAGCTATTGGAGA                         CCTTCCTTTGC
genomic: TTAAACATTAGTCACAACAATATTTCTTCCCTCCCCGCAGCTATTGGAGAgtatgtactg ... ttccatgcagCCTTCCTTTGC
EST: gi|58663247|gb|CK051933.1|CK051933
EST:     TTAAACATTAGTCACAACAATATTTCTTCCCTCCCCGCAGCTATTGGAGA                         CCTTCCTTTGCTAAAATCATTGGATGTATCTTCTAATCAAATAAACGCTTT
genomic: TTAAACATTAGTCACAACAATATTTCTTCCCTCCCCGCAGCTATTGGAGAgtatgtactg ... ttccatgcagCCTTCCTTTGCTAAAATCGTTGGATGTATCTTCTAATCAAATAAACGCTTT

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: 59 (upstream exon), 75 (downstream exon)
Score: 10

ACCTTGAGGTGTTGCGTGAAGACCTCAGAAATTTGTCTTCGCTCGTTGTATTAAACATTAGTCACAACAATATTTCTTCCCTCCCCGCAGCTATTGGAGAgtatgtactg ... ttccatgcagCCTTCCTTTGCTAAAATCGTTGGATGTATCTTCTAATCAAATAAACGCTTTTCCCGAAGAGATTGGTTTTGCGACCGCTTTAGTCAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACCTTGAGGTGTTGCGTGAAGACCTCAGAAATTTGTCTTCGCTCGTTGTATTAAACATTAGTCACAACAATATTTCTTCCCTCCCCGCAGCTATTGGAGAgtatgtactggactatccttatttactactccctccggtcatggaaacatatcgtttgtggacatgtttgaagtcactgccttcaaaaccagtttcataa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccctccg