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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGAGCATATACGTGCCACAGAGAGAGAGAGGGAGGGAGAGATGGCGTAGGACAGCATGTGTTCTTGACGAGAGTTCTTCTTGGCTGGGTCCAATCCCAAGgtgagtggtggatggattgtttgttgattcttgtttgagagtgaggatgattggaattgtttctaggggggtgattgtaggattggggttagggtggtgg...

Basic information

species Oryza sativa
transcript LOC_Os07g07080.1
intron # 1
splice site 5'
intron type U2

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|88391866|gb|CI603385.1|CI603385
EST:     ACAGCATGTGTTCTTGACGAGAGTTCTTCTTGGCTGGGTCCAATCCCAAG                         ATTGATCTATATTATATAGATGGCTCTTTATATAGAATCTTATCTTGAGAT
genomic: ACAGCATGTGTTCTTGACGAGAGTTCTTCTTGGCTGGGTCCAATCCCAAGgtgagtggtg ... cattgtgcagATTGATCTATATTATATAGATGGCTCTTTATATAGAATCTTATCTTGAGAT
EST: gi|88371246|gb|CI597723.1|CI597723
EST:     ACAGCATGTGTTCTTGACGAGAGTTCTTCTTGGCTGGGTCCAATCCCAAG                         ATTGATCTATATTATATAGATGGCTCTTTATATAGAATCTTATCTTGAGAT
genomic: ACAGCATGTGTTCTTGACGAGAGTTCTTCTTGGCTGGGTCCAATCCCAAGgtgagtggtg ... cattgtgcagATTGATCTATATTATATAGATGGCTCTTTATATAGAATCTTATCTTGAGAT
EST: gi|88370871|gb|CI594983.1|CI594983
EST:     ACAGCATGTGTTCTTGACGAGAGTTCTTCTTGGCTGGGTCCAATCCCAAG                         ATTGATCTATATTATATAGATGGCTCTTTATATAGAATCTTATCTTGAGAT
genomic: ACAGCATGTGTTCTTGACGAGAGTTCTTCTTGGCTGGGTCCAATCCCAAGgtgagtggtg ... cattgtgcagATTGATCTATATTATATAGATGGCTCTTTATATAGAATCTTATCTTGAGAT
EST: gi|88453742|gb|CI684465.1|CI684465
EST:     ACAGCATGTGTTCTTGACGAGAGTTCTTCTTGGCTGGGTCCAATCCCAAG                         ATTGATCTATATTATATAGATGGCTCTTTATATAGAATCTTATCTTGAGAT
genomic: ACAGCATGTGTTCTTGACGAGAGTTCTTCTTGGCTGGGTCCAATCCCAAGgtgagtggtg ... cattgtgcagATTGATCTATATTATATAGATGGCTCTTTATATAGAATCTTATCTTGAGAT
EST: gi|88302199|gb|CI668045.1|CI668045
EST:     ACAGCATGTGTTCTTGACGAGAGTTCTTCTTGGCTGGGTCCAATCCCAAG                         ATTGATCTATATTATATAGATGGCTCTTTATATAGAATCTTATCTTGAGAT
genomic: ACAGCATGTGTTCTTGACGAGAGTTCTTCTTGGCTGGGTCCAATCCCAAGgtgagtggtg ... cattgtgcagATTGATCTATATTATATAGATGGCTCTTTATATAGAATCTTATCTTGAGAT
EST: gi|88415660|gb|CI591440.1|CI591440
EST:     ACAGCATGTGTTCTTGACGAGAGTTCTTCTTGGCTGGGTCCAATCCCAAG                         ATTGATCTATATTATATAGATGGCTCTTTATATAGAATCTTATCTTGAGAT
genomic: ACAGCATGTGTTCTTGACGAGAGTTCTTCTTGGCTGGGTCCAATCCCAAGgtgagtggtg ... cattgtgcagATTGATCTATATTATATAGATGGCTCTTTATATAGAATCTTATCTTGAGAT
EST: gi|88351713|gb|CI617438.1|CI617438
EST:     ACAGCATGTGTTCTTGACGAGAGTTCTTCTTGGCTGGGTCCAATCCCAAG                         ATTGATCTATATTATATAGATGGCTCTTTATATAGAATCTTATCTTGAGAT
genomic: ACAGCATGTGTTCTTGACGAGAGTTCTTCTTGGCTGGGTCCAATCCCAAGgtgagtggtg ... cattgtgcagATTGATCTATATTATATAGATGGCTCTTTATATAGAATCTTATCTTGAGAT
EST: gi|88370844|gb|CI592610.1|CI592610
EST:     ACAGCATGTGTTCTTGACGAGAGTTCTTCTTGGCTGGGTCCAATCCCAAG                         ATTGATCTATATTATATAGATGGCTCTTTATATAGAATCTTATCTTGAGAT
genomic: ACAGCATGTGTTCTTGACGAGAGTTCTTCTTGGCTGGGTCCAATCCCAAGgtgagtggtg ... cattgtgcagATTGATCTATATTATATAGATGGCTCTTTATATAGAATCTTATCTTGAGAT
EST: gi|88453994|gb|CI690086.1|CI690086
EST:     ACAGCATGTGTTCTTGACGAGAGTTCTTCTTGGCTGGGTCCAATCCCAAG                         ATTGATCTATATTATATAGATGGCTCTTTATATAGAATCTTATCTTGAGAT
genomic: ACAGCATGTGTTCTTGACGAGAGTTCTTCTTGGCTGGGTCCAATCCCAAGgtgagtggtg ... cattgtgcagATTGATCTATATTATATAGATGGCTCTTTATATAGAATCTTATCTTGAGAT
EST: gi|88398439|gb|CI595840.1|CI595840
EST:     ACAGCATGTGTTCTTGACGAGAGTTCTTCTTGGCTGGGTCCAATCCCAAG                         ATTGATCTATATTATATAGATGGCTCTTTATATAGAATCTTATCTTGAGAT
genomic: ACAGCATGTGTTCTTGACGAGAGTTCTTCTTGGCTGGGTCCAATCCCAAGgtgagtggtg ... cattgtgcagATTGATCTATATTATATAGATGGCTCTTTATATAGAATCTTATCTTGAGAT
EST: gi|88403916|gb|CI601326.1|CI601326
EST:     ACAGCATGTGTTCTTGACGAGAGTTCTTCTTGGCTGGGTCCAATCCCAAG                         ATTGATCTATATTATATAGATGGCTCTTTATATAGAATCTTATCTTGAGAT
genomic: ACAGCATGTGTTCTTGACGAGAGTTCTTCTTGGCTGGGTCCAATCCCAAGgtgagtggtg ... cattgtgcagATTGATCTATATTATATAGATGGCTCTTTATATAGAATCTTATCTTGAGAT
EST: gi|88346292|gb|CI635770.1|CI635770
EST:     ACAGCATGTGTTCTTGACGAGAGTTCTTCTTGGCTGGGTCCAATCCCAAG                         ATTGATCTATATTATATAGATGGCTCTTTATATAGAATCTTATCTTGAGAT
genomic: ACAGCATGTGTTCTTGACGAGAGTTCTTCTTGGCTGGGTCCAATCCCAAGgtgagtggtg ... cattgtgcagATTGATCTATATTATATAGATGGCTCTTTATATAGAATCTTATCTTGAGAT
EST: gi|88433496|gb|CI594310.1|CI594310
EST:     AAAGCATGTGTTCTTGACGAGAG-TCTTCTTGGCTGGGTCCAATCCCAAG                         ATTGATCTATATTATATAGATGGGTCTTTATATAGAATCTTATCTTGAGAT
genomic: ACAGCATGTGTTCTTGACGAGAGTTCTTCTTGGCTGGGTCCAATCCCAAGgtgagtggtg ... cattgtgcagATTGATCTATATTATATAGATGGCTCTTTATATAGAATCTTATCTTGAGAT
EST: gi|88425650|gb|CI689297.1|CI689297
EST:     ACAGCATGTGTTCTTGACGAGAGTTCTTCTTGGCTGGGTCCAATCCCAAG                         ATTGATCTATATTATATAGATGGCTCTTTATATAGAATCTTATCTTGAGAT
genomic: ACAGCATGTGTTCTTGACGAGAGTTCTTCTTGGCTGGGTCCAATCCCAAGgtgagtggtg ... cattgtgcagATTGATCTATATTATATAGATGGCTCTTTATATAGAATCTTATCTTGAGAT

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: 56 (upstream exon), 74 (downstream exon)
Score: 21

CGAGCATATACGTGCCACAGAGAGAGAGAGGGAGGGAGAGATGGCGTAGGACAGCATGTGTTCTTGACGAGAGTTCTTCTTGGCTGGGTCCAATCCCAAGgtgagtggtg ... cattgtgcagATTGATCTATATTATATAGATGGCTCTTTATATAGAATCTTATCTTGAGATGGAATTGTCATCCTAGCTTCATGGAACTCTAACAAGAACAATTTATTAC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGAGCATATACGTGCCACAGAGAGAGAGAGGGAGGGAGAGATGGCGTAGGACAGCATGTGTTCTTGACGAGAGTTCTTCTTGGCTGGGTCCAATCCCAAGgtgagtggtggatggattgtttgttgattcttgtttgagagtgaggatgattggaattgtttctaggggggtgattgtaggattggggttagggtggtgg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gggggtg