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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGCGCCCCCCGCCGGCGACGGCGACGGCGAGAGATGCGGGCCCGAGCCGCCGACCACCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCAGAAGgttatatcctgccccttcctctccgcattccggttcctgcccccccccccccccccccctcatcgtctcgttctttcattgatttccgggagggttgggt...

Basic information

species Oryza sativa
transcript LOC_Os01g05830.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g05830.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM5G871336_T01 (Zea mays), 5'ss of exon 1
GAGCGCCCCCCGCCGGCGACGGCGACGGCGAGAGATGCGGGCCCGAGCCGCC---GACCACCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCAGAAGgttatatcctgccccttcctct-ccgcattccggttcctgcccccccccccccccccccctcatcgtctcgt---tctttcattgatttccgggagggttgggt
  |||||  |   |  |   ||||   ||| || ||| ||  ||| | | ||   |||| ||||||||||||||||||||||||||||||||||||||| |||||   | ||  || ||||| || |||    |||| |   ||||  |    |     |  | |      |||     |  ||  ||     ||   | | |    
--GCGCCGACGATCACCTCAGGCGTGCGCG-GATATGGGGCGCCGCGGCTCCTACGACCGCCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCACAAGgt---aacccaccgcttcccctaccgtgcgccggctggcgcccgtcaattcgtgttcgtcgcgcttaatcgaggaccaatctctgtcgcgcgcacgcgctcac-
















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|86850164|gb|CI305403.1|CI305403
EST:     CCGACCACCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCAGAAG                         GCTCTCAACTCCAATTCGCAACGTCTTCAGCTGCTGCAGCAGTTGTTTGCT
genomic: CCGACCACCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCAGAAGgttatatcct ... ttgcgtgtagGCTCTCAACTCCAATTCGCAACGTCTTCAGCTGCTGCAGCAGTTGTTTGCT
EST: gi|88583291|gb|CI700762.1|CI700762
EST:     CCGACCACCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCAGAAG                         GCTCTCAACTCCAATTCGCAACGTCTTCAGCTGCTGCAGCAGTTGTTTGCT
genomic: CCGACCACCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCAGAAGgttatatcct ... ttgcgtgtagGCTCTCAACTCCAATTCGCAACGTCTTCAGCTGCTGCAGCAGTTGTTTGCT
EST: gi|88727199|gb|CI750854.1|CI750854
EST:     CCGACCACCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCAGAAG                         GCTCTCAACTCCAATTCGCAACGTCTTCAGCTGCTGCAGCAGTTGTTTGCT
genomic: CCGACCACCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCAGAAGgttatatcct ... ttgcgtgtagGCTCTCAACTCCAATTCGCAACGTCTTCAGCTGCTGCAGCAGTTGTTTGCT
EST: gi|88345521|gb|CI629782.1|CI629782
EST:     CCGACCACCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCAGAAG                         GCTCTCAACTCCAATTCGCCACGTCTTCAGCTGCTGCAGCAGTTGTTTGCT
genomic: CCGACCACCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCAGAAGgttatatcct ... ttgcgtgtagGCTCTCAACTCCAATTCGCAACGTCTTCAGCTGCTGCAGCAGTTGTTTGCT
EST: gi|86888521|gb|CI303803.1|CI303803
EST:     CCGACCACCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCAGAAG                         GCTCTCAACTCCAATTCGCAACGTCTTCAGCTGCTGCAGCAGTTGTTTGCT
genomic: CCGACCACCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCAGAAGgttatatcct ... ttgcgtgtagGCTCTCAACTCCAATTCGCAACGTCTTCAGCTGCTGCAGCAGTTGTTTGCT
EST: gi|33655950|gb|CF278564.1|CF278564
EST:     CCGACCACCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCAGAAG                         GCTCTCAACTCCAATTCGCAACGTCTTCAGCTGCTGCAGCAGTTGTTTGCT
genomic: CCGACCACCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCAGAAGgttatatcct ... ttgcgtgtagGCTCTCAACTCCAATTCGCAACGTCTTCAGCTGCTGCAGCAGTTGTTTGCT
EST: gi|88727073|gb|CI750728.1|CI750728
EST:     CCGACCACCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCAGAAG                         GCTCTCAACTCCAATTCGCAACGTCTTCAGCTGCTGCAGCAGTTGTTTGCT
genomic: CCGACCACCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCAGAAGgttatatcct ... ttgcgtgtagGCTCTCAACTCCAATTCGCAACGTCTTCAGCTGCTGCAGCAGTTGTTTGCT
EST: gi|117251249|gb|CT844083.1|CT844083
EST:     CCGACCACCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCAGAAG                         GCTCTCAACTCCAATTCGCAACGTCTTCAGCTGCTGCAGCAGTTGTTTGCT
genomic: CCGACCACCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCAGAAGgttatatcct ... ttgcgtgtagGCTCTCAACTCCAATTCGCAACGTCTTCAGCTGCTGCAGCAGTTGTTTGCT
EST: gi|88333764|gb|CI643796.1|CI643796
EST:     CCGACCACCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCAGAAG                         GCTCTCAACTCCAATTCGCAACGTCTTCAGCTGCTGCAGCAGTTGTTTGCT
genomic: CCGACCACCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCAGAAGgttatatcct ... ttgcgtgtagGCTCTCAACTCCAATTCGCAACGTCTTCAGCTGCTGCAGCAGTTGTTTGCT
EST: gi|88720488|gb|CI743787.1|CI743787
EST:     CCGACCACCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCAGAAG                         GCTCTCAACTCCAATTCGCAACGTCTTCAGCTGCTGCAGCAGTTGTTTGCT
genomic: CCGACCACCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCAGAAGgttatatcct ... ttgcgtgtagGCTCTCAACTCCAATTCGCAACGTCTTCAGCTGCTGCAGCAGTTGTTTGCT
EST: gi|86908885|gb|CI302621.1|CI302621
EST:     CCGACCACCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCAGAAG                         GCTCTCAACTCCAATTCGCAACGTCTTCAGCTGCTGCAGCAGTTGTTTGCT
genomic: CCGACCACCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCAGAAGgttatatcct ... ttgcgtgtagGCTCTCAACTCCAATTCGCAACGTCTTCAGCTGCTGCAGCAGTTGTTTGCT
EST: gi|88350625|gb|CI631348.1|CI631348
EST:     CCGACCACCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCAGAAG                         GCTCTCAACTCCAATTCGCCACGCTCTTCAGCCTGCTGGCAGCAGTTGTTT
genomic: CCGACCACCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCAGAAGgttatatcct ... ttgcgtgtagGCTCTCAACTCCAATTCGCAACG-TCTTCAG-CTGCT-GCAGCAGTTGTTT
EST: gi|29616435|gb|CB621447.1|CB621447
EST:     CCGACCACCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCAGAAG                         GCTCTCAACTCCAATTCGCAACGTCTTCAGCTGCTGCAGCAGTTGTTTGCT
genomic: CCGACCACCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCAGAAGgttatatcct ... ttgcgtgtagGCTCTCAACTCCAATTCGCAACGTCTTCAGCTGCTGCAGCAGTTGTTTGCT

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: 28 (upstream exon), 73 (downstream exon)
Score: 4

GAGCGCCCCCCGCCGGCGACGGCGACGGCGAGAGATGCGGGCCCGAGCCGCCGACCACCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCAGAAGgttatatcct ... ttgcgtgtagGCTCTCAACTCCAATTCGCAACGTCTTCAGCTGCTGCAGCAGTTGTTTGCTGACATCGCATTGAAGGTGGATGACCGCGCTCGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGCGCCCCCCGCCGGCGACGGCGACGGCGAGAGATGCGGGCCCGAGCCGCCGACCACCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCAGAAGgttatatcctgccccttcctctccgcattccggttcctgcccccccccccccccccccctcatcgtctcgttctttcattgatttccgggagggttgggt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgcccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcccccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccccccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cgggagg