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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGTgtaagtatcaaaagttgatgcatctcactgtctctcttttggactggtagctgttatatttataaagagagggtcaaagatgataagaaaagtggtgcca...

Basic information

species Oryza sativa
transcript LOC_Os05g35140.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g35140.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G153358_T02 (Zea mays), 5'ss of exon 2
GCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGTgtaagtatcaaaagttgatgcatctcactgtctctcttttggactggtagctgttatatttataaagagagggtcaaagatgataagaaaagtggtgcca--
| ||||||||||| |||||||||||| | ||||||||||||||     | ||    ||  |||   |  |    |      ||  | | |   |     |      |   ||  ||   |||  || | || | |    
GAAATGTCATCGCTCTCTTCCTCTTCCTTTCCCCAGTgtaagtgctcgatgt-agcgcccctcctcgatttcggtaaattgtgtcaacagg-gtcggagtgtgcgcaaaatcctagcaaatataaacattgttccagta
















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|88364482|gb|CI644560.1|CI644560
EST:     GCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGT                         GCCTACTTTCTGGAGGATCATTCGGAGGAAATCAACAGAGGATTTCTCTGG
genomic: GCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGTgtaagtatca ... tttttcacagGCCTACTTTCTGGAGGATCATTCGGAGGAAATCAACAGAGGATTTCTCTGG
EST: gi|88336144|gb|CI647338.1|CI647338
EST:     GCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGT                         GCCTACTTCCTGGAGGATCATTCGGAGGAAATCAACAGAGGATTTCTCTGG
genomic: GCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGTgtaagtatca ... tttttcacagGCCTACTTTCTGGAGGATCATTCGGAGGAAATCAACAGAGGATTTCTCTGG
EST: gi|88348551|gb|CI634146.1|CI634146
EST:     GCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGT                         GCCTACTTTCTGGAGGATCATTCGGAGGAAATCAACAGAGGATTTCTCTGG
genomic: GCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGTgtaagtatca ... tttttcacagGCCTACTTTCTGGAGGATCATTCGGAGGAAATCAACAGAGGATTTCTCTGG
EST: gi|88575402|gb|CI669547.1|CI669547
EST:     GCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCACT                         GCCTACCTTTCTGGAGGATCATTCGGAGGAAATCAACAGAGGATTCCTCTG
genomic: GCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGTgtaagtatca ... tttttcacagGCCTAC-TTTCTGGAGGATCATTCGGAGGAAATCAACAGAGGATTTCTCTG
EST: gi|88573529|gb|CI665100.1|CI665100
EST:     GCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGT                         GCCTACTTTCTGGAGGATCATTCGGAGGAAATCAACAGAGGATTTCTCTGG
genomic: GCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGTgtaagtatca ... tttttcacagGCCTACTTTCTGGAGGATCATTCGGAGGAAATCAACAGAGGATTTCTCTGG
EST: gi|33799249|gb|CF325482.1|CF325482
EST:     GCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGT                         GCCTACTTTCTGGAGGATCATTCGGAGGAAATCAACAGAGGAATTTCTCTG
genomic: GCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGTgtaagtatca ... tttttcacagGCCTACTTTCTGGAGGATCATTCGGAGGAAATCAACAGAGGA-TTTCTCTG
EST: gi|29662554|gb|CB658829.1|CB658829
EST:     GCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGT                         GCCTACTTTCTGGAGGATCATTCGGAGGAAATCAACAGAGGATTTCTCTGG
genomic: GCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGTgtaagtatca ... tttttcacagGCCTACTTTCTGGAGGATCATTCGGAGGAAATCAACAGAGGATTTCTCTGG
EST: gi|88341534|gb|CI641286.1|CI641286
EST:     GCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGT                         GCCTACTTTCTGGAGGATCATTCGGAGGAAATCAACAGAGGATTCCTCTGG
genomic: GCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGTgtaagtatca ... tttttcacagGCCTACTTTCTGGAGGATCATTCGGAGGAAATCAACAGAGGATTTCTCTGG
EST: gi|29629891|gb|CB634900.1|CB634900
EST:     GCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGT                         GCCTACTTTCTGGAGGATCATTCGGAGGAAATCAACAGAGGATTTCTCTGG
genomic: GCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGTgtaagtatca ... tttttcacagGCCTACTTTCTGGAGGATCATTCGGAGGAAATCAACAGAGGATTTCTCTGG
EST: gi|88335261|gb|CI650226.1|CI650226
EST:     GCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGT                         GCCTACTTTCTGGAGGATCATTCGGAGGAAATCAACAGAGGATTTCTCTGG
genomic: GCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGTgtaagtatca ... tttttcacagGCCTACTTTCTGGAGGATCATTCGGAGGAAATCAACAGAGGATTTCTCTGG
EST: gi|88338434|gb|CI645688.1|CI645688
EST:     GCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGT                         GCCTACTTTCTGGAGGATCATTCGGAGGAAATCAACAGAGGATTTCTCTGG
genomic: GCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGTgtaagtatca ... tttttcacagGCCTACTTTCTGGAGGATCATTCGGAGGAAATCAACAGAGGATTTCTCTGG
EST: gi|86902517|gb|CI304336.1|CI304336
EST:     GCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGT                         GCCTACTTTCTGGAGGATCATTCGGAGGAAATCAACAGAGGATTTCTCTGG
genomic: GCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGTgtaagtatca ... tttttcacagGCCTACTTTCTGGAGGATCATTCGGAGGAAATCAACAGAGGATTTCTCTGG
EST: gi|29657893|gb|CB654168.1|CB654168
EST:     GCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGT                         GCCTACTTTCTGGAGGATCATTCGGAGGAAATCAACAGAGGATTTCTCTGG
genomic: GCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGTgtaagtatca ... tttttcacagGCCTACTTTCTGGAGGATCATTCGGAGGAAATCAACAGAGGATTTCTCTGG

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: 51 (upstream exon), 74 (downstream exon)
Score: 100

GCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGTgtaagtatca ... tttttcacagGCCTACTTTCTGGAGGATCATTCGGAGGAAATCAACAGAGGATTTCTCTGGGGTGCCATACAACATGACACTCATCAACTGCCTCCTCTCTGCATG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGTgtaagtatcaaaagttgatgcatctcactgtctctcttttggactggtagctgttatatttataaagagagggtcaaagatgataagaaaagtggtgcca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gagaggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagaaaa