Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagattctttatttagctttcccttgatgtcatcatggagtcatcttcacaaatggcaggctttcttatagcatttgatcttgaaatttcaagtgccaaaacatgttctcataaacaaattttttttcatgtgcagGCTTATGCCAGAGTCAGCTCTTACAGCTCCGAAGGAAAAGAAACTCTCAGGAAGACAGTATTTTGAAAGTGGAAGGCATACAATG

Basic information

species Oryza sativa
transcript LOC_Os01g37770.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g37770.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G015364_T02 (Zea mays), 3'ss of exon 8
gtaagattc----tttatttagctttc---ccttgatgtcatca--tggagtcatct--tcacaaatggcaggctt--tcttatagcatttgatcttgaaatttca--agtgccaaaacatgttctca--taaacaaattttttttc---atgtgcagGCTTATGCCAGAGTCAGCTCTTACAGCTCCGAAGGAAAAGAAACTCTCAGGAAGACAGTATTTTGAAAGTGGAAGGCATACAATG
|||| |||     ||| ||||  | |      ||  | | ||||  |||| ||   |  | ||   ||  |   |   ||| || |  ||||||    | |||  |  ||| || |||  |||  | |  | | |   |   |||||        ||| ||||||||||| ||||||||||||||  | ||||||||||||||| | ||| | |||||||||||||||||||||||| || ||
gtaaaatttgtattttgtttacatattaagtttttttatgatcagatggaatctcttgtttacttgtgatatcttccatctaatggtgtttgattcccatattatataagtacccaaatctgtgtttagatgatcttttgcattttctgggcacacagACTTATGCCAGATTCAGCTCTTACAGCCACAAAGGAAAAGAAACTCACGGGACGGCAGTATTTTGAAAGTGGAAGGCATGCAGTG

upper sequence: LOC_Os01g37770.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G094595_T01 (Zea mays), 3'ss of exon 8
--------gtaagattctttat---ttagctttcccttgatgtcatcatggag---tcatcttcacaaatggcaggctt--tcttatagcatttgatcttgaaatttca--agtgccaaaacatgttctcataaa------caaattttttttcatgtgcagGCTTATGCCAGAGTCAGCTCTTACAGCTCCGAAGGAAAAGAAACTCTCAGGAAGACAGTATTTTGAAAGTGGAAGGCATACAATG---------------
           |  || ||||    |||  |||  || ||||    |||||     |  | || ||   ||  |   |   ||| || |  |||| |    | |||  |  ||| || |||  |||  | | |           ||||| ||     ||||| ||||||||||| |||||||||||| |  | ||||||||||||||| ||||| | |||||||||||||||||||||||| || ||               
gtaaactttctattttgtttacatattaagtttttctcgatgatcacatgggaatcttttgtttacttgtgatatcttcaatctaatggtgtttgtttcccatattatataagtacccaaatgtgtgtttagattatcttttgcattttgttgggcatgcagACTTATGCCAGATTCAGCTCTTACATCCTCAAAGGAAAAGAAACTCACAGGACGGCAGTATTTTGAAAGTGGAAGGCATGCAGTGGTTCGTTATCCCAGA

upper sequence: LOC_Os01g37770.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G094595_T02 (Zea mays), 3'ss of exon 8
--------gtaagattctttat---ttagctttcccttgatgtcatcatggag---tcatcttcacaaatggcaggctt--tcttatagcatttgatcttgaaatttca--agtgccaaaacatgttctcataaa------caaattttttttcatgtgcagGCTTATGCCAGAGTCAGCTCTTACAGCTCCGAAGGAAAAGAAACTCTCAGGAAGACAGTATTTTGAAAGTGGAAGGCATACAATG
           |  || ||||    |||  |||  || ||||    |||||     |  | || ||   ||  |   |   ||| || |  |||| |    | |||  |  ||| || |||  |||  | | |           ||||| ||     ||||| ||||||||||| |||||||||||| |  | ||||||||||||||| ||||| | |||||||||||||||||||||||| || ||
gtaaactttctattttgtttacatattaagtttttctcgatgatcacatgggaatcttttgtttacttgtgatatcttcaatctaatggtgtttgtttcccatattatataagtacccaaatgtgtgtttagattatcttttgcattttgttgggcatgcagACTTATGCCAGATTCAGCTCTTACATCCTCAAAGGAAAAGAAACTCACAGGACGGCAGTATTTTGAAAGTGGAAGGCATGCAGTG

upper sequence: LOC_Os01g37770.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA07G01520.1 (Glycine max), 3'ss of exon 8
gtaagattctttatttagctttcccttgatgtcatcatggagtcatcttcacaaatggcaggctttcttatagcatttgatcttgaaatttcaagtgccaaaacatgttctcataaacaaattttttttcatgtgcagGCTTATGCCAGAGTCAGCTCTTACAGCTCCGAAGGAAAAGAAACTCTCAGGAAGACAGTATTTTGAAAGTGGAAGGCATACAATG
                            ||| ||| || |||| |     | || | |  |   |  |   |     || | ||| || ||            | | |  |   |||  ||||| || |  | |||||||| ||||||||||| |  || |||||||| ||||||||||| |||   || |||||||  ||||||||||||||   |      
----------------------taacaaatgacataatagagtaa-----ataattagtcgatctattctaaatgcctgctgttgcaactttt----------cttttgatgccaaaacaatttgttctggt-tgcagGCTAATGCCAGAGTCTGTGCTCACAGCTCCTAAGGAAAAGAAGCTCAGTGGTAGACAGTGGTTTGAAAGTGGAAGA-GTG-----

upper sequence: LOC_Os01g37770.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv09s0002g02540.t01 (Vitis vinifera), 3'ss of exon 8
gtaagattctttatttagctttcccttgatgtcatcatggagtcatcttcacaaatggcaggctttcttatagcatttgatcttgaaatttcaagtgccaaaacatgttctcat---aaacaaattttttttc--atgtgcagGCTTATGCCAGAGTCAGCTCTTACAGCTCCGAAGGAAAAGAAACTCTCAGGAAGACAGTATTTTGAAAGTGGAAGGCATACAATG
                                          | |   | |  | | |      |   ||| | ||   |  |     |||    |  | ||  || |  ||||   ||  || |   |  ||  || | |||||| ||||| ||||| || ||||||||||| ||||||||||| |||||||| |||||||  ||||||||||||||   |  |  |
------------------------------------------taacgattaagattagtgtctatatctat-gtatcatagatgattgtttattctttcgaactatatcttcatgacaattaactccatcctccaattttcagGCTAATGCCCGAGTCTGCACTTACAGCTCCCAAGGAAAAGAAGCTCTCAGGCAGACAGTGGTTTGAAAGTGGAAGAGCTGTAGCG

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|55410164|gb|CV722540.1|CV722540
EST:     CTGGCTTGGAGAGATCGTTTTGAAGCTGAATTGGCGCTACAGCGTGCCAA                         GCTTATGCCAGAGTCAGCTCTTACAGCTCCGAAGGAAAAGAAACTCTCAGG
genomic: CTGGCTTGGAGAGATCGTTTTGAAGCTGAATTGGCGCTACAGCGTGCCAAgtaagattct ... tcatgtgcagGCTTATGCCAGAGTCAGCTCTTACAGCTCCGAAGGAAAAGAAACTCTCAGG
EST: gi|88353314|gb|CI654580.1|CI654580
EST:     GTTTTGAAGCTGAATTGGCGCTACAGCGTGCCAA                         GCTTATGCCAGAGTCAGCTCTTACAGCTCCGAAGGAAAAGAAACTCTCAGG
genomic: GTTTTGAAGCTGAATTGGCGCTACAGCGTGCCAAgtaagattct ... tcatgtgcagGCTTATGCCAGAGTCAGCTCTTACAGCTCCGAAGGAAAAGAAACTCTCAGG
EST: gi|29670377|gb|CB666652.1|CB666652
EST:     CTGGCTTGGAGAGATCGTTTTGAAGCTGAATTGGCGCTACAGCGTGCCAA                         GCTTATGCCAGAGTCAGCTCTTACAGCTCCGAAGGAAAAGAAACTCTCAGG
genomic: CTGGCTTGGAGAGATCGTTTTGAAGCTGAATTGGCGCTACAGCGTGCCAAgtaagattct ... tcatgtgcagGCTTATGCCAGAGTCAGCTCTTACAGCTCCGAAGGAAAAGAAACTCTCAGG
EST: gi|29670376|gb|CB666651.1|CB666651
EST:     CTGGCTTGGAGAGATCGTTTTGAAGCTGAATTGGCGCTACAGCGTGCCAA                         GCTTATGCCAGAGTCAGCTCTTACAGCTCCGAAGGAAAAGAAACTCTCAGG
genomic: CTGGCTTGGAGAGATCGTTTTGAAGCTGAATTGGCGCTACAGCGTGCCAAgtaagattct ... tcatgtgcagGCTTATGCCAGAGTCAGCTCTTACAGCTCCGAAGGAAAAGAAACTCTCAGG
EST: gi|86880817|gb|CI339152.1|CI339152
EST:     TTGGCGC-ACAGCGTGCCAA                         GCTTATGCCAGAGTCAGCTCTTACAGCTCCGAA-GAAAAGAAACTCTCAGG
genomic: TTGGCGCTACAGCGTGCCAAgtaagattct ... tcatgtgcagGCTTATGCCAGAGTCAGCTCTTACAGCTCCGAAGGAAAAGAAACTCTCAGG
EST: gi|33665592|gb|CF296559.1|CF296559
EST:     CTGGCTTGGAGAGATCGTTTTGAAGCTGAATTGGCGCTACAGCGTGCCAA                         GCTTATGCCAGAGTCAGCTCTTACAGCTCCGAAGGAAAAGAAACTCTCAGG
genomic: CTGGCTTGGAGAGATCGTTTTGAAGCTGAATTGGCGCTACAGCGTGCCAAgtaagattct ... tcatgtgcagGCTTATGCCAGAGTCAGCTCTTACAGCTCCGAAGGAAAAGAAACTCTCAGG
EST: gi|218496890|gb|FG962706.1|FG962706
EST:     CTGGCTTGGAGAGATCGTTTTGAAGCTGAATTGGCGCTACAGCGTGCCAA                         GCTTATGCCAGAGTCAGCTCTTACAGCTCCGAAGGAAAAGAAACTCTCAGC
genomic: CTGGCTTGGAGAGATCGTTTTGAAGCTGAATTGGCGCTACAGCGTGCCAAgtaagattct ... tcatgtgcagGCTTATGCCAGAGTCAGCTCTTACAGCTCCGAAGGAAAAGAAACTCTCAGG
EST: gi|88250975|gb|CI349205.1|CI349205
EST:     GATCGTTTTGAAGCTGAATTGGCGCTACAGCGTGCCAA                         GCTTATGCCAGAGTCAGCTCTTACAGCTCCGAAGGAAAAGAAACTCTCAGG
genomic: GATCGTTTTGAAGCTGAATTGGCGCTACAGCGTGCCAAgtaagattct ... tcatgtgcagGCTTATGCCAGAGTCAGCTCTTACAGCTCCGAAGGAAAAGAAACTCTCAGG
EST: gi|87010761|gb|CI312453.1|CI312453
EST:     CTGGCTTGGAGAGATCGTTTTGAAGCTGAATTGGCGCTACAGCGTGCCAA                         GCTTATGCCAGAGTCAGCTCTTACAGCTCCGAAGGAAAAGAAACTCTCAGG
genomic: CTGGCTTGGAGAGATCGTTTTGAAGCTGAATTGGCGCTACAGCGTGCCAAgtaagattct ... tcatgtgcagGCTTATGCCAGAGTCAGCTCTTACAGCTCCGAAGGAAAAGAAACTCTCAGG

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: 34 (upstream exon), 63 (downstream exon)
Score: 16

GTCATTGTGCCCCATGGTGAAGCTGTTACTGTAGAGAGCTTTCTGGCTTGGAGAGATCGTTTTGAAGCTGAATTGGCGCTACAGCGTGCCAAgtaagattct ... tcatgtgcagGCTTATGCCAGAGTCAGCTCTTACAGCTCCGAAGGAAAAGAAACTCTCAGGAAGACAGTATTTTGAAAGTGGAAGGCATACAATG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaatttcaagtgccaaaacatgttctcataaacaaattttttttcatgtgcagGCTTATGCCAGAGTCAGCTCTTACAGCTCCGAAGGAAAAGAAACTCTCAGGAAGACAGTATTTTGAAAGTGGAAGGCATACAATG
                                      ttttttttcat  CT-rich tract
                        ttctcataaacaaatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagattctttatttagctttcccttgatgtcatcatggagtcatcttcacaaatggcaggctttcttatagcatttgatcttgaaatttcaagtgccaaaacatgttctcataaacaaattttttttcatgtgcagGCTTATGCCAGAGTCAGCTCTTACAGCTCCGAAGGAAAAGAAACTCTCAGGAAGACAGTATTTTGAAAGTGGAAGGCATACAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG