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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTATGCTAAGTTTGGATTTGATTTTATAGAGAAGAGCAACCAAATAGGCCCACTGTTCCACAACATCGCGCTGCAGCAATACATCCTGCTTTGCGCACAGgtaataaaagaacatctaatttcatgcttagctggatttgtagaaaatttcttgctgtaacttggaaattctctagtgtttacttgacacttgaatggtaaatctgattcgtgttccaaatcacgcag

Basic information

species Oryza sativa
transcript LOC_Os01g53600.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g53600.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G158562_T03 (Zea mays), 5'ss of exon 11
TTATGCTAAGTTTGGATTTGATTTTATAGAGAAGAGCAACCAAATAGGCCCACTGTTCCACAACATCGCGCTGCAGCAATACATCCTGCTTTGCGCACAGgtaataaaagaacatctaatttcatgcttagctggatttgtagaaaatttcttgctgtaacttggaaattctctagtgtttacttgacacttgaatggtaaatctgattcgtgttccaaatcacgcag
 ||||| ||||||||||||||||||||| |  ||||||||||||| |||||||| ||||| ||||| || ||||| ||||||||||| |||||  | |||||    |   ||| |  |||   ||  |||  |  || || |||   ||| |  ||  ||  || |||||||  | ||    |||   |      |    |  ||                       
CTATGCGAAGTTTGGATTTGATTTTATACAACAGAGCAACCAAATTGGCCCACTCTTCCATAACATTGCCCTGCAACAATACATCCTACTTTGTTCTCAGgtg---aggtaactttgaatacaata-ttattttcatatgcagagt-tttatcactagaatgtg-aaattctgcaatgccgtcttattatagttgttaccaccctc----------------------
















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|88546723|gb|CI474392.1|CI474392
EST:     CACAACATCGCGCTNCAGCAATACATCCTGCTTTGCGCACAG                         GTGCTGGATGGAGGGTTGAGGGATAAGCCTGGGAAGAACAGAGATCACTAC
genomic: CACAACATCGCGCTGCAGCAATACATCCTGCTTTGCGCACAGgtaataaaag ... aatcacgcagGTGCTGGATGGAGGGTTGAGGGATAAGCCTGGGAAGAACAGAGATCACTAC
EST: gi|88291434|gb|CI530024.1|CI530024
EST:     CACTGTTCCACAACATCGCGCTGCAGCAATACATCCTGCTTTGCGCACAG                         GTGGCTGGATGGAGGGTTGAGGGATAAGGCTGGGAAGAACAGAGATCACTA
genomic: CACTGTTCCACAACATCGCGCTGCAGCAATACATCCTGCTTTGCGCACAGgtaataaaag ... aatcacgcagGT-GCTGGATGGAGGGTTGAGGGATAAGCCTGGGAAGAACAGAGATCACTA
EST: gi|88384218|gb|CI548559.1|CI548559
EST:     GCTTTGCGCACAG                         GTGCTGGATGGAGGGTTGAGGGATAAGCCTGGGAAGAACAGAGATCACTAC
genomic: GCTTTGCGCACAGgtaataaaag ... aatcacgcagGTGCTGGATGGAGGGTTGAGGGATAAGCCTGGGAAGAACAGAGATCACTAC
EST: gi|86497703|gb|CI140336.1|CI140336
EST:     CACTGTTCCACAACATCGCGCTGCAGCAATACATCCTGCTTTGCGCACAG                         GTGCTGGATGGAGGGTTGGGGGATAAGCCTGGGAAGAACAGAGATCACTAC
genomic: CACTGTTCCACAACATCGCGCTGCAGCAATACATCCTGCTTTGCGCACAGgtaataaaag ... aatcacgcagGTGCTGGATGGAGGGTTGAGGGATAAGCCTGGGAAGAACAGAGATCACTAC
EST: gi|86600638|gb|CI356395.1|CI356395
EST:     CACTGTTCCACAACATCGCGCTGCAGCAATACATCCTGCTTTGCGCACAG                         GTGCTGGATGGAGGGTTGAGGGATAAGCCTGGGAAGAACAGAGATCACTAC
genomic: CACTGTTCCACAACATCGCGCTGCAGCAATACATCCTGCTTTGCGCACAGgtaataaaag ... aatcacgcagGTGCTGGATGGAGGGTTGAGGGATAAGCCTGGGAAGAACAGAGATCACTAC
EST: gi|88547667|gb|CI477979.1|CI477979
EST:     CCCTGTTCCACAACATCGCGCTGCATCAATACATCCTGCTTTGCGCACAG                         GTGCTGGATGGAGGGTTGAGGGATAAGCCTGGGAAGAACAGANATCAGTAC
genomic: CACTGTTCCACAACATCGCGCTGCAGCAATACATCCTGCTTTGCGCACAGgtaataaaag ... aatcacgcagGTGCTGGATGGAGGGTTGAGGGATAAGCCTGGGAAGAACAGAGATCACTAC
EST: gi|88546759|gb|CI474429.1|CI474429
EST:     CAACATCGCGCTNCAGCAATACATCCTGCTTTGCGCACAG                         GTGCTGGATGGAGGGTTGAGGGATAAGCCTGGGAAGAACAGAGATCACTAC
genomic: CAACATCGCGCTGCAGCAATACATCCTGCTTTGCGCACAGgtaataaaag ... aatcacgcagGTGCTGGATGGAGGGTTGAGGGATAAGCCTGGGAAGAACAGAGATCACTAC
EST: gi|22306108|gb|BQ907330.1|BQ907330
EST:     CACTGTTCCACAACATCGCGCTGCAGCAATACATCCTGCTTTGCGCACAG                         GTGCTGGATGGAGGGTTGAGGGATAAGCCTGGGAAGAACAGAGATCACTAC
genomic: CACTGTTCCACAACATCGCGCTGCAGCAATACATCCTGCTTTGCGCACAGgtaataaaag ... aatcacgcagGTGCTGGATGGAGGGTTGAGGGATAAGCCTGGGAAGAACAGAGATCACTAC
EST: gi|88539269|gb|CI466369.1|CI466369
EST:     CACTGTTCCACAACATCGCGCTGCAGCAATACATCCTGCTTTGCGCACAG                         GTGCTGGATGGAGGGTTGAGGGATAAGCCTGGGAAGAACAGAGATCACTAC
genomic: CACTGTTCCACAACATCGCGCTGCAGCAATACATCCTGCTTTGCGCACAGgtaataaaag ... aatcacgcagGTGCTGGATGGAGGGTTGAGGGATAAGCCTGGGAAGAACAGAGATCACTAC
EST: gi|29645257|gb|CB650264.1|CB650264
EST:     CACTGTTCCACAACATCGCGCTGCAGCAATACATCCTGCTTTGCGCACAG                         GTGCTGGATGGAGGGTTGAGGGATAAGCCTGGGAAGAACAGAGATCACTAC
genomic: CACTGTTCCACAACATCGCGCTGCAGCAATACATCCTGCTTTGCGCACAGgtaataaaag ... aatcacgcagGTGCTGGATGGAGGGTTGAGGGATAAGCCTGGGAAGAACAGAGATCACTAC
EST: gi|88487889|gb|CI425160.1|CI425160
EST:     CACTGTTCCACAACATCGCGCTGCAGCAATACATCCTGCTTTGCGCACAG                         GTGCTGGATGGAGGGTTGAGGGATAAGCCTGGGAAGAACAGAGATCACTAC
genomic: CACTGTTCCACAACATCGCGCTGCAGCAATACATCCTGCTTTGCGCACAGgtaataaaag ... aatcacgcagGTGCTGGATGGAGGGTTGAGGGATAAGCCTGGGAAGAACAGAGATCACTAC
EST: gi|29674661|gb|CB670936.1|CB670936
EST:     CACTGTTCCACAACATCGCGCTGCAGCAATACATCCTGCTTTGCGCACAG                         GTGCTGGATGGAGGGTTGAGGGATAAGCCTGGGAAGAACAGAGATCACTAC
genomic: CACTGTTCCACAACATCGCGCTGCAGCAATACATCCTGCTTTGCGCACAGgtaataaaag ... aatcacgcagGTGCTGGATGGAGGGTTGAGGGATAAGCCTGGGAAGAACAGAGATCACTAC
EST: gi|86489887|gb|CI132520.1|CI132520
EST:     CACTGTTCCACAACATCGCGCTGCAGCAATACATCCTGCTTTGCGCACAG                         GTGCTGGATGGAGGGTTGAGGGATAAGCCTGGGAAGAACAGAGATCACTAC
genomic: CACTGTTCCACAACATCGCGCTGCAGCAATACATCCTGCTTTGCGCACAGgtaataaaag ... aatcacgcagGTGCTGGATGGAGGGTTGAGGGATAAGCCTGGGAAGAACAGAGATCACTAC
EST: gi|29674620|gb|CB670895.1|CB670895
EST:     CACTGTTCCACAACATCGCGCTGCAGCAATACATCCTGCTTTGCGCACAG                         GTGCTGGATGGAGGGTTGAGGGATAAGCCTGGGAAGAACAGAGATCACTAC
genomic: CACTGTTCCACAACATCGCGCTGCAGCAATACATCCTGCTTTGCGCACAGgtaataaaag ... aatcacgcagGTGCTGGATGGAGGGTTGAGGGATAAGCCTGGGAAGAACAGAGATCACTAC
EST: gi|29645420|gb|CB650427.1|CB650427
EST:     CACTGTTCCACAACATCGCGCTGCAGCAATACATCCTGCTTTGCGCACAG                         GTGCTGGATGGAGGGTTGAGGGATAAGCCTGGGAAGAACAGAGATCACTAC
genomic: CACTGTTCCACAACATCGCGCTGCAGCAATACATCCTGCTTTGCGCACAGgtaataaaag ... aatcacgcagGTGCTGGATGGAGGGTTGAGGGATAAGCCTGGGAAGAACAGAGATCACTAC
EST: gi|29640149|gb|CB645158.1|CB645158
EST:     CACTGTTCCACAACATCGCGCTGCAGCAATACATCCTGCTTTGCGCACAG                         GTGCTGGATGGAGGGTTGAGGGATAAGCCTGGGAAGAACAGAGATCACTAC
genomic: CACTGTTCCACAACATCGCGCTGCAGCAATACATCCTGCTTTGCGCACAGgtaataaaag ... aatcacgcagGTGCTGGATGGAGGGTTGAGGGATAAGCCTGGGAAGAACAGAGATCACTAC
EST: gi|29661886|gb|CB658161.1|CB658161
EST:     CACTGTTCCACAACATCGCGCTGCAGCAATACATCCTGCTTTGCGCACAG                         GTGCTGGATGGAGGGTTGAGGGATAAGCCTGGGAAGAACAGAGATCACTAC
genomic: CACTGTTCCACAACATCGCGCTGCAGCAATACATCCTGCTTTGCGCACAGgtaataaaag ... aatcacgcagGTGCTGGATGGAGGGTTGAGGGATAAGCCTGGGAAGAACAGAGATCACTAC

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: 60 (upstream exon), 40 (downstream exon)
Score: 9

TTATGCTAAGTTTGGATTTGATTTTATAGAGAAGAGCAACCAAATAGGCCCACTGTTCCACAACATCGCGCTGCAGCAATACATCCTGCTTTGCGCACAGgtaataaaag ... aatcacgcagGTGCTGGATGGAGGGTTGAGGGATAAGCCTGGGAAGAACAGAGATCACTACCACTCGTGCTACTGCCTGAGTGGTCTGTCAGTTAGCCAGTACAGCGCCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTATGCTAAGTTTGGATTTGATTTTATAGAGAAGAGCAACCAAATAGGCCCACTGTTCCACAACATCGCGCTGCAGCAATACATCCTGCTTTGCGCACAGgtaataaaagaacatctaatttcatgcttagctggatttgtagaaaatttcttgctgtaacttggaaattctctagtgtttacttgacacttgaatggtaaatctgattcgtgttccaaatcacgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG