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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatgcagtgccccaatactagctaacatattctaaactgaattgcttttgatgtatttagtgcaccgacatgtgaatgaattctgtatttcttctttcagGGGGAGCCATGATGGTGATTTCTGTGCTGTGGATGTAAAGAAGATGGATGTTTCTCACTGGAGCAAGAAGGTCCATCTTGGTTCTCCGGTTTCCTCAATT

Basic information

species Oryza sativa
transcript LOC_Os07g09000.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g09000.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G158489_T02 (Zea mays), 3'ss of exon 5
--tatgcagt-gccccaatactagctaacatattctaaactgaattgcttttgatgtatttagtgcaccgacatgtgaatg-aattctgtatttcttctttcagGGGGAGCCATGATGGTGATTTCTGTGCTGTGGATGTAAAGAAGATGGATGTTTCTCACTGGAGCAAGAAGGTCCATCTTGGTTCTCCGGTTTCCTCAATT
     ||| | ||    ||  | |||     | | |   ||| |     || |   ||  | |        ||||   |      ||||| ||||||   |||| || ||||| |||||||| ||||||||||| ||||| ||||| ||||| ||||| |||||||||||||||||||||||||| || || ||  |||| |||
aagtcgcactagctatgattatcgctctataactatgtgctgcacaatcttcggactaactcgc-ttttagcatgctcacatggatctgtgtttctt---tcagAGGAAGCCACGATGGTGACTTCTGTGCTGTTGATGTGAAGAAAATGGAAGTTTCCCACTGGAGCAAGAAGGTCCATCTTGGCTCCCCAGTCACCTCCATT
















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|24208350|gb|AU225377.1|AU225377
EST:     AAACCTATCTCCACACTTTCAGTTAGCATGGATGGGAAGTATCTGGCTTT                         GGGGAGCCATGATGGTGATTTCTGTGCTGTGGATGTAAAGAAGATGGATGT
genomic: AAACCTATCTCCACACTTTCAGTTAGCATGGATGGGAAGTATCTGGCTTTgtaagtacat ... cttctttcagGGGGAGCCATGATGGTGATTTCTGTGCTGTGGATGTAAAGAAGATGGATGT
EST: gi|58603054|gb|CK013582.1|CK013582
EST:     AAACCTATCTCCACACTTTCAGTTAGCATGGATGGGAAGTATCTGGCTTT                         GGGGAGCCATGATGGTGATTTCTGTGCTGTGGATGTAAAGAAGATGGATGT
genomic: AAACCTATCTCCACACTTTCAGTTAGCATGGATGGGAAGTATCTGGCTTTgtaagtacat ... cttctttcagGGGGAGCCATGATGGTGATTTCTGTGCTGTGGATGTAAAGAAGATGGATGT
EST: gi|117233168|gb|CT848021.1|CT848021
EST:     AAACCTATCTCCACACTTTCAGTTAGCATGGATGGGAAGTATCTGGCTTT                         GGGGAGCCATGATGGTGATTTCTGTGCTGTGGATGTAAAGAAGATGGATGT
genomic: AAACCTATCTCCACACTTTCAGTTAGCATGGATGGGAAGTATCTGGCTTTgtaagtacat ... cttctttcagGGGGAGCCATGATGGTGATTTCTGTGCTGTGGATGTAAAGAAGATGGATGT
EST: gi|58687497|gb|CK076184.1|CK076184
EST:     AAACCTATCTCCACACTTTCAGTTAGCATGGATGGGAAGTATCTGGCTTT                         GGGGAGCCATGATGGTGATTTCTGTGCTGTGGATGTAAAGAAGATGGATGT
genomic: AAACCTATCTCCACACTTTCAGTTAGCATGGATGGGAAGTATCTGGCTTTgtaagtacat ... cttctttcagGGGGAGCCATGATGGTGATTTCTGTGCTGTGGATGTAAAGAAGATGGATGT
EST: gi|163918152|gb|EG714798.1|EG714798
EST:     AAACCTATCTCCACACTTTCAGTTAGCATGGATGGGAAGTATCTGGCTTT                         GGGGAGCCATGATGGTGATTTCTGTGCTGTGGATGTAAAGAAGATGGATGT
genomic: AAACCTATCTCCACACTTTCAGTTAGCATGGATGGGAAGTATCTGGCTTTgtaagtacat ... cttctttcagGGGGAGCCATGATGGTGATTTCTGTGCTGTGGATGTAAAGAAGATGGATGT
EST: gi|29627838|gb|CB632849.1|CB632849
EST:     AACCTATCTCCACACTTTCAGTTAGCATGGGATGGGAAGTATCTGGCTTT                         GGGGAGCCATGATGGTGATTTCT
genomic: AACCTATCTCCACACTTTCAGTTAGCATGG-ATGGGAAGTATCTGGCTTTgtaagtacat ... cttctttcagGGGGAGCCATGATGGTGATTTCT
EST: gi|88395653|gb|CI590668.1|CI590668
EST:     AAACCTATCTCCACACTTTCAGTTAGCATGGATGGGAAGTATCTGGCTTT                         GGGGAGCCATG
genomic: AAACCTATCTCCACACTTTCAGTTAGCATGGATGGGAAGTATCTGGCTTTgtaagtacat ... cttctttcagGGGGAGCCATG
EST: gi|38480849|gb|CF964938.1|CF964938
EST:     AAACCTATCTCCACACTTTCAGTTAGCATGGATGGGAAGTATCTGGCTTT                         GGGGAGCCATGATGGTGATTTCTGTGCTGTGGATGTAAAGAAGATGGATGT
genomic: AAACCTATCTCCACACTTTCAGTTAGCATGGATGGGAAGTATCTGGCTTTgtaagtacat ... cttctttcagGGGGAGCCATGATGGTGATTTCTGTGCTGTGGATGTAAAGAAGATGGATGT
EST: gi|27410230|gb|CA923300.1|CA923300
EST:     AAACCCATCTCCACACTTTCAGTTAGCATGGATGGGAAGTATCTGGCTTT                         GGGGAGCCATGATGGTGATTTCTGTGCTGTGGATGTAAAGAAGATGGATGT
genomic: AAACCTATCTCCACACTTTCAGTTAGCATGGATGGGAAGTATCTGGCTTTgtaagtacat ... cttctttcagGGGGAGCCATGATGGTGATTTCTGTGCTGTGGATGTAAAGAAGATGGATGT
EST: gi|29674146|gb|CB670421.1|CB670421
EST:     AAACCTATCTCCACACTTTCAGTTAGCATGGATGGGAAGTATCTGGCTTT                         GGGGAGCCATGATGGTGATTTCTGTGCTGTGGATGTAAAGAAGATGGATGT
genomic: AAACCTATCTCCACACTTTCAGTTAGCATGGATGGGAAGTATCTGGCTTTgtaagtacat ... cttctttcagGGGGAGCCATGATGGTGATTTCTGTGCTGTGGATGTAAAGAAGATGGATGT

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: 48 (upstream exon), 69 (downstream exon)
Score: 6

TCTGGAACATAAGTGACTGGAGTCGAATTGGATACAAGAGACTTCTGGGAAAACCTATCTCCACACTTTCAGTTAGCATGGATGGGAAGTATCTGGCTTTgtaagtacat ... cttctttcagGGGGAGCCATGATGGTGATTTCTGTGCTGTGGATGTAAAGAAGATGGATGTTTCTCACTGGAGCAAGAAGGTCCATCTTGGTTCTCCGGTTTCCTCAATT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgatgtatttagtgcaccgacatgtgaatgaattctgtatttcttctttcagGGGGAGCCATGATGGTGATTTCTGTGCTGTGGATGTAAAGAAGATGGATGTTTCTCACTGGAGCAAGAAGGTCCATCTTGGTTCTCCGGTTTCCTCAATT
 ttttgat  putative branch site (score: 6)
                                   ttctgtatttcttctt  putative PPT
     atgtattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatgcagtgccccaatactagctaacatattctaaactgaattgcttttgatgtatttagtgcaccgacatgtgaatgaattctgtatttcttctttcagGGGGAGCCATGATGGTGATTTCTGTGCTGTGGATGTAAAGAAGATGGATGTTTCTCACTGGAGCAAGAAGGTCCATCTTGGTTCTCCGGTTTCCTCAATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
tatgcag
- - - -tgcccca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgcacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttctgta