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'   		11  
 5'  3'   		12  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTTGTGTCAAGGTTGCTGCAGTACTCGCCAAATTTGCGTTGCACAGCTgtaagactaatattggatttgagccattttaactaattattgaaccagatcggtattaggtggatcatcatgagcacaataatctaatttcctcataaga...

Basic information

species Oryza sativa
transcript LOC_Os10g37740.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g37740.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G109624_T01 (Zea mays), 5'ss of exon 11
CTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTTGTGTCAAGGTTGCTGCAGTACTCGCCAAATTTGCGTTGCACAGCTgtaagactaatattggatttgagccattttaactaattattgaaccagatcggtattaggtggatcatcatgagcacaataatctaat-ttcctcataaga---
|||||||||||||||||||||||||||||||||||||| ||||||||| | || |||||||| |||||  |||| ||||| |||||||||  ||  |||   |||   |   | ||||| | |   | ||| ||  |||| ||     ||   ||    || |   ||| || || | | | ||    
CTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCTgtaagaacaaatttgagattgtaactgatgaactagtga---atccaaattagtat-agacatgtcgctattgatactaagctcttatgtttcccttcagttaa

upper sequence: LOC_Os10g37740.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G131853_T01 (Zea mays), 5'ss of exon 11
CTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTTGTGTCAAGGTTGCTGCAGTACTCGCCAAATTTGCGTTGCACAGCTgtaaga-ctaatattggatttgagccattttaactaattattgaacc-agatcggtattaggtggatcatcatgagcacaataatctaatttcctcataaga------------------------------------------------------
||||||||||||||||||||||| || ||||| ||||| ||||||||| |||| |||||||| || ||  |||| ||||| ||||||||| |||||    ||||  | ||      || ||||| |||||| | ||  || | ||  |  |    ||   ||| |   || |  ||  || |  |                                                       
CTTTTTGGTAAGCGCATGCCACCCGAGGCTGTCGATCTCGTGTCAAGGCTGCTCCAGTACTCACCGAACCTGCGCTGCACTGCTgtaagaactaattcgagattgcaaccg-----accaattactgaacccaaattcgtgt-agacgtgttgctattgacactaagctccatatttttccttgggttaaaccagttatacggtagtttctgatcgaagatattttaattatattcccag

upper sequence: LOC_Os10g37740.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA07G08320.1 (Glycine max), 5'ss of exon 11
CTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTTGTGTCAAGGTTGCTGCAGTACTCGCCAAATTTGCGTTGCACAGCTgtaagactaatattggatttgagccattttaactaat-tattgaaccagatcggtattaggtggatca--tcatgagcacaataatctaatttcctcataaga
 |||||   ||| | ||||| |||||||| || ||||||||||||||| ||||||| || || |||||| | |||||||| ||||||||  | || |||   ||||   || ||| ||| | |||  |     |    ||     |  ||||    |         ||  |  ||   | |  ||||
GTTTTTCACAAGAGAATGCCGCCTGAAGCCGTGGATCTTGTGTCAAGGCTGCTGCAATATTCACCAAATCTACGTTGCACCGCTgtaag-ttgat-ttgctcttgaaa-atgttacctattatatctagattaaataatacatattcaatcaaactacagtttttgtatacacatactcaccaaaga

upper sequence: LOC_Os10g37740.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA03G01850.1 (Glycine max), 5'ss of exon 11
CTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTTGTGTCAAGGTTGCTGCAGTACTCGCCAAATTTGCGTTGCACAGCTgtaagactaatattggatttg--agccattttaactaattattgaaccagatcggtattaggtggatcatcatgagcacaataatctaatttcctcataaga-
 |||||   ||| | ||||||||||||||||| |||||||| |||||| |||| || || || |||||| | |||||||| ||||||||   | | ||| |  ||  | | ||| || |||   |||  |  | |    | ||      |  |   |    | |   |  || || ||  | |||| 
GTTTTTCACAAGAGAATGCCACCTGAAGCTGTGGATCTTGTATCAAGGCTGCTTCAATATTCACCAAATCTACGTTGCACTGCTgtaagttgatttttgaaaatgttacctattatatctag--attacataatacatat-ttgatcaaactacagtttttatatgcacatacttaccaaagaagaa

upper sequence: LOC_Os10g37740.1 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv15s0048g02010.t01 (Vitis vinifera), 5'ss of exon 11
CTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTTGTGTCAAGGTTGCTGCAGTACTCGCCAAATTTGCGTTGCACAGCTgtaaga----ctaatattggatttgagccattttaacta-attattgaaccagatcggtattaggtggatcatcatgagcacaataatctaatttcctcataaga
|||||   |||||| ||||| || |||||||| |||||||| |||||| |||| ||||| |||||||||||| | ||||| || ||| ||      |||  |  || | |     || |  |  ||  ||   ||| |  |  ||     | ||  |  ||       |  | |  |||  |       
CTTTTCCATAAGCGAATGCCCCCAGAAGCTGTGGATCTTGTATCAAGGCTGCTTCAGTATTCGCCAAATTTGAGATGCACCGCCgtatgaaatttgaatgctttatataaatttgttcattttcatagtttttccaaactgaaatcttccgaatgcttgtgt-tgaggtggttttgtttgatttg----

upper sequence: LOC_Os10g37740.1 (Oryza sativa), 5'ss of exon 11
lower sequence: PP1S306_43V6.2 (Physcomitrella patens), 5'ss of exon 10
CTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTTGTGTCAAGGTTGCTGCAGTACTCGCCAAATTTGCGTTGCACAGCTgtaagactaatattggatt-tgagccattttaactaat----tattgaaccagatcggtattaggtggatcatcatgagcacaataatctaatttcctcataaga
 ||||    || ||||||||||||||||| |||||  | ||||||||| | || |||||||| |||||| |||| ||||  ||||| ||  ||   |   ||| || |   ||   ||   |    | |||| |    | ||| |  | ||  || |   |  |       |   |      |||    
GTTTTCCACAAACGCATGCCACCTGAAGCAGTTGACTTGGTGTCAAGGCTCCTTCAGTACTCTCCAAATCTGCGGTGCAACGCTgtgag--tagcgtcatattctgtgttgttggtacgggtgtgatgttgagctgtgtgggtctgcgttgagtcgtggcgttctgcgaggtgccaacgaggcatt---

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|86481063|gb|CI123696.1|CI123696
EST:     ATCTTGTGTCAAGGTTGCTGCAGTACTCGCCAAATTTGCGTTGCACAGCT                         GTTGATGCTTGTGCTCATCCATTCTTTGATGAACTGCGGGATCCCAAGACC
genomic: ATCTTGTGTCAAGGTTGCTGCAGTACTCGCCAAATTTGCGTTGCACAGCTgtaagactaa ... gttcttccagGTTGATGCTTGTGCTCATCCATTCTTTGATGAACTGCGGGATCCCAAGACC
EST: gi|88361945|gb|CI682122.1|CI682122
EST:     ATCTTGTGTCAAGGTTGCTGCAGTACTCGCCAAATTTGCGTTGCACAGCT                         GTTGATGCTTGTG
genomic: ATCTTGTGTCAAGGTTGCTGCAGTACTCGCCAAATTTGCGTTGCACAGCTgtaagactaa ... gttcttccagGTTGATGCTTGTG
EST: gi|29666991|gb|CB663266.1|CB663266
EST:     ATCTTGTGTCAAGGTTGCTGCAGTACTCGCCAAATTTGCGTTGCACAGCT                         GTTGATGCTTGTGCTCATCCATTCTTTGATGAACTGCGGGATCCCAAGACC
genomic: ATCTTGTGTCAAGGTTGCTGCAGTACTCGCCAAATTTGCGTTGCACAGCTgtaagactaa ... gttcttccagGTTGATGCTTGTGCTCATCCATTCTTTGATGAACTGCGGGATCCCAAGACC
EST: gi|29680415|gb|CB676690.1|CB676690
EST:     AGTACTCGCCAAATTTGCGTGGCACAGCT                         GTTGATGCTTGTGCTCATCCATTCTTTGATGAACTGCGGGATCCCAAGACT
genomic: AGTACTCGCCAAATTTGCGTTGCACAGCTgtaagactaa ... gttcttccagGTTGATGCTTGTGCTCATCCATTCTTTGATGAACTGCGGGATCCCAAGACC
EST: gi|218488407|gb|FG957568.1|FG957568
EST:     ATCTTGTGTCAAGGTTGCTGCAGTA-TCGCCAAATTTGCATTGCACAGCT                         GTTGATGCTTGTGCTCATCCATTCTTAGATGAACTGCGGGATCCCAAGACC
genomic: ATCTTGTGTCAAGGTTGCTGCAGTACTCGCCAAATTTGCGTTGCACAGCTgtaagactaa ... gttcttccagGTTGATGCTTGTGCTCATCCATTCTTTGATGAACTGCGGGATCCCAAGACC
EST: gi|89173539|gb|CI041432.1|CI041432
EST:     GCGTTGCACAGCT                         GTTGATGCTTGTGCTCATCCATTCTTTGATGAACTGCGGGATCCCAAGACC
genomic: GCGTTGCACAGCTgtaagactaa ... gttcttccagGTTGATGCTTGTGCTCATCCATTCTTTGATGAACTGCGGGATCCCAAGACC
EST: gi|58679635|gb|CK068322.1|CK068322
EST:     ATCTTGTGTCAAGGTTGCTGCAGTACTCGCCAAATTTGCGTTGCACAGCT                         GTTGATGCTTGTGCTCATCCATTCTTTGATGAACTGCGGGATCCCAA
genomic: ATCTTGTGTCAAGGTTGCTGCAGTACTCGCCAAATTTGCGTTGCACAGCTgtaagactaa ... gttcttccagGTTGATGCTTGTGCTCATCCATTCTTTGATGAACTGCGGGATCCCAA

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

CTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTTGTGTCAAGGTTGCTGCAGTACTCGCCAAATTTGCGTTGCACAGCTgtaagactaa ... gttcttccagGTTGATGCTTGTGCTCATCCATTCTTTGATGAACTGCGGGATCCCAAGACCTGCTTGTCAAATGGACGATCATTACCACCCTTGTTCGACTTCTCAGCTG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTTGTGTCAAGGTTGCTGCAGTACTCGCCAAATTTGCGTTGCACAGCTgtaagactaatattggatttgagccattttaactaattattgaaccagatcggtattaggtggatcatcatgagcacaataatctaatttcctcataaga

- - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG