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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgtgtactttcttaactttgtggttgctacatctggtcaactcatccatataatatgtttctggaatacaaatagctaacctttgtgttctcttgcagCATTGTGTTGTTCTTGACATTGAGGGAACAACTACTCCAATATCATTTGTGACTGATGTGATGTTTCCCTATGCCCGTGATAATGTGCGAAAGCATCTGA

Basic information

species Oryza sativa
transcript LOC_Os11g29370.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g29370.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G574782_T01 (Zea mays), 3'ss of exon 6
--------------------------------------------------------tttgtgtactttcttaactttgtggttgctacatctggtcaactcatccatataat------atgtttctggaatacaaata------gctaacctttg---------tgttctcttgcagCATTGTGTTGTTCTTGACATTGAGGGAACAACTACTCCAATATCATTTGTGACTGATGTGATGTTTCCCTATGCCCGTGATAATGTGCGAAAGCATCTGA---
                                                        |||||     | ||||    |||| |||  | | |||   ||    ||  ||   |      |||||| ||  ||     |       | ||| || ||         | ||||  ||  ||| |||||||| || ||||||||||| ||||| |||||||||||||||||||||||||| ||||| || ||||| ||||||||||| ||||| |||||||   
gttatttcaacttattattttggcaatgctttgcatgatacctgtaggatttttactttgtaactgtccttagtactgtg-ttgaaaaaactgtgtaatatttctgtagttttccttaatgtttttgtgattgctgtcttttctgttaaactctgctcgaccttttttctactgtggcagTGTGTTGTACTAGACATTGAGGGGACAACCACTCCAATATCATTTGTGACTGATGTCATGTTCCCTTATGCTCGTGATAATGTACGAAAACATCTGACTT

upper sequence: LOC_Os11g29370.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA06G36620.1 (Glycine max), 3'ss of exon 6
----tttgtgtactttcttaactttgtggttgctacatctggtcaactcatccatataatatgtttctggaatacaaatagctaacctttgtgttctcttgcagCATTGTGTTGTTCTTGACATTGAGGGAACAACTACTCCAATATCATTTGTGACTGATGTGATGTTTCCCTATGCCCGTGATAATGTGCGAAAGCATCTGA
      ||   | |||||||    | ||       |||   ||   ||  ||||| || | |     |  |   |  ||| ||  |  |    || | ||||||| |||  |||| ||||||||||| ||||| |||||||| ||||||||||| ||||| ||  | || || ||||| ||| | |||||  | | ||||||  
tgcaaatggccagtttcttagacatttgag-atatcatggagttgtctt-tccatgtagtttcaaattcaatagctgataact--ctctctctttgtattgcagCGTTGCATTGTCCTTGACATTGAAGGAACTACTACTCCCATATCATTTGTTACTGAGGTTCTCTTCCCATATGCACGTCAAAATGTTGGGAGGCATCTAT

upper sequence: LOC_Os11g29370.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA13G35120.3 (Glycine max), 3'ss of exon 6
---tttgtgtactttcttaactttgtggttgctacatctggtcaactcatccatataatatgtttctggaatacaaatagctaacctttgtg-----ttctcttgcagCATTGTGTTGTTCTTGACATTGAGGGAACAACTACTCCAATATCATTTGTGACTGATGTGATGTTTCCCTATGCCCGTGATAATGTGCGAAAGCATCTGA
   |     | | |    ||     || || | |  ||| |   | | ||   | |  | || |||   || | |||| | |    ||| |      ||   ||| ||| ||| ||||||||||||||||| ||||| |||||||| |||||||||||  | || ||  | || || |||||||||||||||||  | | ||||||  
agctcccaattcatagaaaataggatgcttcccatgtcttgc--agtgat---tttcgtgtggttc---aaaataaattgttggtttttatcactatttggtttgtagCGTTGCGTTGTTCTTGACATTGAAGGAACTACTACTCCCATATCATTTGTTTCCGAGGTTCTCTTCCCATATGCCCGTGATAATGTTGGGAGGCATCTAT

upper sequence: LOC_Os11g29370.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA12G35390.1 (Glycine max), 3'ss of exon 6
---tttgtgtactttcttaactttgtggttgctacatctggtcaactcatccatataatatgtttctggaatacaaatagctaacctttgtgttctcttg-----cagCATTGTGTTGTTCTTGACATTGAGGGAACAACTACTCCAATATCATTTGTGACTGATGTGATGTTTCCCTATGCCCGTGATAATGTGCGAAAGCATCTGA
   |     | | |    ||     || || | | |||| |   | | ||   | | || || |||   |  | |||| | | |  ||| | |    |||     |||| ||| ||||||||||||||||| ||||| |||||||| |||||||||||  |||| ||  | || || |||||||||||||| ||  | | |||| |  
agctcccaattcatagaaaataggatgcttcccatatcttgc--agtgat---tgtcatgtggttc---agaataaattgttgatttttatctctatttggtttgcagCGTTGCGTTGTTCTTGACATTGAAGGAACTACTACTCCCATATCATTTGTTTCTGAGGTTCTCTTCCCATATGCCCGTGATAACGTTGGGAGGCATTTAT

upper sequence: LOC_Os11g29370.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA13G35120.2 (Glycine max), 3'ss of exon 6
tttgtgtactttcttaactttgtggttgctacatctggtcaactcatccatataatatgtttctggaatacaaatagctaacctttgtg-----ttctcttgcagCATTGTGTTGTTCTTGACATTGAGGGAACAACTACTCCAATATCATTTGTGACTGATGTGATGTTTCCCTATGCCCGTGATAATGTGCGAAAGCATCTGA--------------------------------------------------------
                                                               |  || | |||| | |    ||| |      ||   ||| ||| ||| ||||||||||||||||| ||||| |||||||| |||||||||||  | || ||  | || || |||||||||||||||||  | | ||||||                                                          
--------------------------------------------------------------gttcaaaataaattgttggtttttatcactatttggtttgtagcgttgcgttgttcttgacattgaaggaactactactcccatatcatttgtttccgagGTTCTCTTCCCATATGCCCGTGATAATGTTGGGAGGCATCTATCTCTAACATATGATACCCCCGAGACCAAAGCTGATATCAAGTTGCTTCGTTCCCAA

upper sequence: LOC_Os11g29370.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv19s0014g02480.t01 (Vitis vinifera), 3'ss of exon 6
tttgtgtactttcttaactttgtggttgct---acatctggtcaactcatccatataatatgtttctggaatacaaatagctaacctttg---tgttctcttgcagCATTGTGTTGTTCTTGACATTGAGGGAACAACTACTCCAATATCATTTGTGACTGATGTGATGTTTCCCTATGCCCGTGATAATGTGCGAAAGCATCTGA
      ||  | ||    |  | |  | ||   || | | ||    | ||   |||  |   |  |    ||  |||  |||  || ||    |||| | || |||| |||| ||||||||||||| || || || || ||||| |||||||||||||| |||||  | ||||||| ||||||  |||||||| | | |||| || 
--cagatatatcctctggtcagagaattcttggacctttagtgcttttatttttatgcttgatccc----attaaaactgctctcccttaatttgttatgtttcagCGTTGTATTGTTCTTGACATCGAAGGGACTACCACTCCTATATCATTTGTGACCGATGTTCTCTTTCCCTTTGCCCGCAATAATGTGAGTAGGCATTTGG

upper sequence: LOC_Os11g29370.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv12s0028g03470.t01 (Vitis vinifera), 3'ss of exon 7
tttgtgtactttctta-actttgtggttgctacatctggtcaactcatccatataatatgtttctggaatacaaatagctaacctttgtgttctct--tgcagCATTGTGTTGTTCTTGACATTGAGGGAACAACTACTCCAATATCATTTGTGACTGATGTGATGTTTCCCTATGCCCGTGATAATGTGCGAAAGCATCTGA
 || | |  ||   ||  | |||  | |  ||  |||  | || |  ||    |  | | | | | ||||     |   | || ||     | | |  ||||||  ||| |  ||||||||||||| || ||||||||||| ||||||||||| || |||||  | ||||||||||||| ||  |||||| |||||||| |  
gttatattgttaaatatgccttgatggtaatatctcttttgaaattgtct---tcttttttgtttagaattgttgtttttcactttgactctttatggtgcagCGCTGTATACTTCTTGACATTGAAGGGACAACTACTCCTATATCATTTGTTACAGATGTTCTTTTTCCCTATGCCCATGCCAATGTGGGAAAGCATTTAG

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|29671699|gb|CB667974.1|CB667974
EST:     TTCTAAGCTCTAGTATTCCAAATGGATGCCCTGATTCCAAATCATCAAAG                         CATTGTGTTGTTCTTGACATTGAGGGAACAACTACTCCAATATCATTTGTG
genomic: TTCTAAGCTCTAGTATTCCAAATGGATGCCCTGATTCCAAATCATCAAAGgtctgttctt ... tctcttgcagCATTGTGTTGTTCTTGACATTGAGGGAACAACTACTCCAATATCATTTGTG
EST: gi|84117432|gb|CD151199.1|CD151199
EST:     TTCTAAGCTCTAGTATTCCAAATGGATGCCCTGATTCCAAATCATCAAAG                         CATTGTGTTGTTCTTGACATTGAGGGAACAACTACTCCAATATCATTTGTG
genomic: TTCTAAGCTCTAGTATTCCAAATGGATGCCCTGATTCCAAATCATCAAAGgtctgttctt ... tctcttgcagCATTGTGTTGTTCTTGACATTGAGGGAACAACTACTCCAATATCATTTGTG
EST: gi|33683942|gb|CF312181.1|CF312181
EST:     TTCTAAGCTCTAGTATTCCAAATGGATGCCCTGATTCCAAATCATCAAAG                         CATTGTGTTGTTCTTGACATTGAGGGAACAACTACTCCAATATCATTTGTG
genomic: TTCTAAGCTCTAGTATTCCAAATGGATGCCCTGATTCCAAATCATCAAAGgtctgttctt ... tctcttgcagCATTGTGTTGTTCTTGACATTGAGGGAACAACTACTCCAATATCATTTGTG
EST: gi|58694492|gb|CK083179.1|CK083179
EST:     TTCTAAGCTCTAGTATTCCAAATGGATGCCCTGATTCCAAATCATCAAAG                         CATTGTGTTGTTCTTGACATTGAGGGAACAACTAC
genomic: TTCTAAGCTCTAGTATTCCAAATGGATGCCCTGATTCCAAATCATCAAAGgtctgttctt ... tctcttgcagCATTGTGTTGTTCTTGACATTGAGGGAACAACTAC
EST: gi|2312274|gb|C28429.1|C28429
EST:     TTCTAAGCTCTAGTATTCCAAATGGATGCC-TGATTCCAAATCATCAAAG                         CATTGTGTTGTTCTTGACATTGNGGGA-CAACTACTCCAATATCATTTGTG
genomic: T-CTAAGCTCTAGTATTCCAAATGGATGCCCTGATTCCAAATCATCAAAGgtctgttctt ... tctcttgcagCATTGTGTTGTTCTTGACATTGAGGGAACAACTACTCCAATATCATTTGTG
EST: gi|29674778|gb|CB671053.1|CB671053
EST:     TTCTAAGCTCTAGTATTCCAAATGGATGCCCTGATTCCCAATCATCAAAG                         CATTGTGTTGTTCTTGACATTGAGGGAACAACTACTCCAATATCATTTGTG
genomic: TTCTAAGCTCTAGTATTCCAAATGGATGCCCTGATTCCAAATCATCAAAGgtctgttctt ... tctcttgcagCATTGTGTTGTTCTTGACATTGAGGGAACAACTACTCCAATATCATTTGTG
EST: gi|29686092|gb|CB682367.1|CB682367
EST:     TTCTAAGCTCTAGTATTCCAAATGGATGCCCTGATTCCAAATCATCAAAG                         CATTGTGTTGTTCTTGACATTGAGGGAACAACTACTCCAATATCATTTGTG
genomic: TTCTAAGCTCTAGTATTCCAAATGGATGCCCTGATTCCAAATCATCAAAGgtctgttctt ... tctcttgcagCATTGTGTTGTTCTTGACATTGAGGGAACAACTACTCCAATATCATTTGTG
EST: gi|58590134|gb|CF988442.1|CF988442
EST:     CCTGATTCCAAATCATCAAAG                         CATTGTGTTGTTCTTGACATTGAGGGAACAACTACTCCGAGTATCATTTGT
genomic: CCTGATTCCAAATCATCAAAGgtctgttctt ... tctcttgcagCATTGTGTTGTTCTTGACATTGAGGGAACAACTACTCC-AATATCATTTGT

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: 74 (upstream exon), 73 (downstream exon)
Score: 91

GACAACTCCTGAGCATGGTCCAATAAACAGTGCCAAAAGACCACGCAGTGTTCTAAGCTCTAGTATTCCAAATGGATGCCCTGATTCCAAATCATCAAAGgtctgttctt ... tctcttgcagCATTGTGTTGTTCTTGACATTGAGGGAACAACTACTCCAATATCATTTGTGACTGATGTGATGTTTCCCTATGCCCGTGATAATGTGCGAAAGCATCTGA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atccatataatatgtttctggaatacaaatagctaacctttgtgttctcttgcagCATTGTGTTGTTCTTGACATTGAGGGAACAACTACTCCAATATCATTTGTGACTGATGTGATGTTTCCCTATGCCCGTGATAATGTGCGAAAGCATCTGA
                              agctaac  putative branch site (score: 91)
                                    cctttgtgttctctt  CT-rich tract
     tataatatgtttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgtgtactttcttaactttgtggttgctacatctggtcaactcatccatataatatgtttctggaatacaaatagctaacctttgtgttctcttgcagCATTGTGTTGTTCTTGACATTGAGGGAACAACTACTCCAATATCATTTGTGACTGATGTGATGTTTCCCTATGCCCGTGATAATGTGCGAAAGCATCTGA

- - - - - - - - - - - - - tgctaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acaaata