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

gtgacttatcgcactattgtctcagtaaaacatttagatgcatcattgttgatgctgcaggtccatttttctttcagATGTTCATTGAGACAACCAGGGAACCGAGCCTTACTTTCATCATCGGGAAGTTTGATGGAATTCTTGGACTTGGATTTCCGGAGATCTCTGTGGGAGGAG

Basic information

species Oryza sativa
transcript LOC_Os01g18630.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g18630.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G077233_T04 (Zea mays), 3'ss of exon 4
gtgactta-tcgcactattgtctcagtaaaacatttagatgcatcattgttgatgctgcaggt-ccatttttctttcagATGTTCATTGAGACAACCAGGGAACCGAGCCTTACTTTCATCATCGGGAAGTTTGATGGAATTCTTGGACTTGGATTTCCGGAGATCTCTGTGGGAGGAG
|| |  |  || ||  |||  |||| | |||  ||   || ||||||||||  || |    || |   ||||  ||||||  || |||||||||||  | ||| | |||| |||||||||||| ||||||||||||||||||||||| || |||||||| || || ||||| |||||||
gtaaactgctcacagaatt-cctcaattaaatgttcctatccatcattgttagtgataatagtactgctttttgttcagAAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAGTTTGATGGAATTCTTGGTCTCGGATTTCCTGAAATTTCTGTAGGAGGAG

upper sequence: LOC_Os01g18630.1 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ34432 (Selaginella moellendorffii), 3'ss of exon 3
gtgacttatcgcactattgtctcagtaaaacatttagatgcatcattgttg-atgctgcaggtccatttttctttcagATGTTCATTGAGACAACCAGGGAACCGAGCCTTACTTTCATCATCGGGAAGTTTGATGGAATTCTTGGACTTGGATTTCCGGAGATCTCTGTGGGAGGAG
                     |  | |||    |       ||  | | |  || |     | | ||   | ||  |||  ||    ||  |||| || || ||  | |||  |||| || | |  ||||||||||| |||||||||||||||||    | ||| ||  |||||   |
--------------------gtttgcaaagttatcgatcttatggtcgctatataccttttg-ctatgcctgttgtagACATTTGCGGAATCAACAAGTGAGCCTGGGCTTGTTTTCCTCTTTGCCAAGTTTGATGGCATTCTTGGACTTGGATTCAAAGCGATTTCCATGGGACAGG

upper sequence: LOC_Os01g18630.1 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ06917 (Selaginella moellendorffii), 3'ss of exon 3
gtgacttatcgcactattgtctcagtaaaacatttagatgcatcattgttg-atgctgcaggtccatttttctttcagATGTTCATTGAGACAACCAGGGAACCGAGCCTTACTTTCATCATCGGGAAGTTTGATGGAATTCTTGGACTTGGATTTCCGGAGATCTCTGTGGGAGGAG
                     |  | |||    |       |  || | |  || |     | | ||   | ||  |||  ||    ||  |||| || || ||  | |||  |||| || | |  ||||||||||| |||||||||||||||||    | ||| ||  |||||   |
--------------------gtttgcaaagttatcgatcttacgatcgctatataccttttg-ctatgcctgttgtagACATTTGCGGAATCAACAAGTGAGCCTGGGCTTGTTTTCCTCTTTGCCAAGTTTGATGGCATTCTTGGACTTGGATTCAAAGCGATTTCCATGGGACAGG

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|29645987|gb|CB650994.1|CB650994
EST:     TCTTCAGTGAGGATAGCGTGCTAGTTGGGGATCTTGCTGTGAAAAATCAG                         ATGTTCATTGAGACAACCAGGGAACCGAGCCTTACTTTCATCATCGGGAAG
genomic: TCTTCAGTGAGGATAGCGTGCTAGTTGGGGATCTTGCTGTGAAAAATCAGgtgacttatc ... tttctttcagATGTTCATTGAGACAACCAGGGAACCGAGCCTTACTTTCATCATCGGGAAG
EST: gi|300216028|gb|HO088654.1|HO088654
EST:     TCTTCAGTGAGGATAGCGTGCTAGTTGGGGATCTTGCTGTGAAAAATCAG                         ATGTTCATTGAGACAACCAGGGAACCGAGCCTTACTTTCATCATCGGGAAG
genomic: TCTTCAGTGAGGATAGCGTGCTAGTTGGGGATCTTGCTGTGAAAAATCAGgtgacttatc ... tttctttcagATGTTCATTGAGACAACCAGGGAACCGAGCCTTACTTTCATCATCGGGAAG
EST: gi|117226899|gb|CT848683.1|CT848683
EST:     TCTTCAGTGAGGATAGCGTGCTAGTTGGGGATCTTGCTGTGAAAAATCAG                         ATGTTCATTGAGACAACCAGGGAACCGAGCCTTACTTTCATCATCGGGAAG
genomic: TCTTCAGTGAGGATAGCGTGCTAGTTGGGGATCTTGCTGTGAAAAATCAGgtgacttatc ... tttctttcagATGTTCATTGAGACAACCAGGGAACCGAGCCTTACTTTCATCATCGGGAAG
EST: gi|29639114|gb|CB644123.1|CB644123
EST:     TCTTCAGTGAGGATAGCGTGCTAGTTGGGGATCTTGCTGTGAAAAATCAG                         ATGTTCATTGAGACAACCAGGGAACCGAGCCTTACTTTCATCATCGGGAAG
genomic: TCTTCAGTGAGGATAGCGTGCTAGTTGGGGATCTTGCTGTGAAAAATCAGgtgacttatc ... tttctttcagATGTTCATTGAGACAACCAGGGAACCGAGCCTTACTTTCATCATCGGGAAG
EST: gi|29643123|gb|CB648130.1|CB648130
EST:     TCTTCAGTGAGGATAGCGTGCTAGTTGGGGATCTTGCTGTGAAAAATCAG                         ATGTTCATTGAGACAACCAGGGAACCGAGCCTTACTTTCATCATCGGGAAG
genomic: TCTTCAGTGAGGATAGCGTGCTAGTTGGGGATCTTGCTGTGAAAAATCAGgtgacttatc ... tttctttcagATGTTCATTGAGACAACCAGGGAACCGAGCCTTACTTTCATCATCGGGAAG
EST: gi|29662753|gb|CB659028.1|CB659028
EST:     TCTTCAGTGAGGATAGCGTGCTAGTTGGGGATCTTGCTGTGAAAAATCAG                         ATGTTCATTGAGACAACCAGGGAACCGAGCCTTACTTTCATCATCGGGAAG
genomic: TCTTCAGTGAGGATAGCGTGCTAGTTGGGGATCTTGCTGTGAAAAATCAGgtgacttatc ... tttctttcagATGTTCATTGAGACAACCAGGGAACCGAGCCTTACTTTCATCATCGGGAAG
EST: gi|29665539|gb|CB661814.1|CB661814
EST:     TCTTCAGTGAGGATAGCGTGCTAGTTGGGGATCTTGCTGTGAAAAATCAG                         ATGTTCATTGAGACAACCAGGGAACCGAGCCTTACTTTCATCATCGGGAAG
genomic: TCTTCAGTGAGGATAGCGTGCTAGTTGGGGATCTTGCTGTGAAAAATCAGgtgacttatc ... tttctttcagATGTTCATTGAGACAACCAGGGAACCGAGCCTTACTTTCATCATCGGGAAG
EST: gi|33664969|gb|CF295936.1|CF295936
EST:     TCTTCAGTGAGGATAGCGTGCTAGTTGGGGATCTTGCTGTGAAAAATCAG                         ATGTTCATTGAGACAACCAGGGAACCGAGCCTTACTTTCATCATCGGGAAG
genomic: TCTTCAGTGAGGATAGCGTGCTAGTTGGGGATCTTGCTGTGAAAAATCAGgtgacttatc ... tttctttcagATGTTCATTGAGACAACCAGGGAACCGAGCCTTACTTTCATCATCGGGAAG
EST: gi|29664681|gb|CB660956.1|CB660956
EST:     TCTTCAGTGAGGATAGCGTGCTAGTTGGGGATCTTGCTGTGAAAAATCAG                         ATGTTCATTGAGACAACCAGGGAACCGAGCCTTACTTTCATCATCGGGAAG
genomic: TCTTCAGTGAGGATAGCGTGCTAGTTGGGGATCTTGCTGTGAAAAATCAGgtgacttatc ... tttctttcagATGTTCATTGAGACAACCAGGGAACCGAGCCTTACTTTCATCATCGGGAAG
EST: gi|300215808|gb|HO088434.1|HO088434
EST:     TCTTCAGTGAGGATAGCGTGCTAGTTGGGGATCTTGCTGTGAAAAATCAG                         ATGTTCATTGAGACAACCAGGGAACCGAGCCTTACTTTCATCATCGGGAAG
genomic: TCTTCAGTGAGGATAGCGTGCTAGTTGGGGATCTTGCTGTGAAAAATCAGgtgacttatc ... tttctttcagATGTTCATTGAGACAACCAGGGAACCGAGCCTTACTTTCATCATCGGGAAG
EST: gi|88304198|gb|CI599886.1|CI599886
EST:     CTTCAGTGAGGATAGCGTGCTAGTTGGG-ATTTTGGCTGTGAAAAATTAG                         ATTTTCATTGAGAAAACCAGGGAAACCGA-CCTTACTTTCATCATCGGGA-
genomic: CTTCAGTGAGGATAGCGTGCTAGTTGGGGATCTTG-CTGTGAAAAATCAGgtgacttatc ... tttctttcagATGTTCATTGAGACAACCAGGGAA-CCGAGCCTTACTTTCATCATCGGGAA
EST: gi|218504625|gb|FG968741.1|FG968741
EST:     TCTTCAGTGAGGATAGCGTGCTAGTTGGGGATCTTGCTGTGAAAAATCAG                         ATGTTCATTGAGACAACCAGGGAACCGAGCCTTACTTTCATCATCGGGAAG
genomic: TCTTCAGTGAGGATAGCGTGCTAGTTGGGGATCTTGCTGTGAAAAATCAGgtgacttatc ... tttctttcagATGTTCATTGAGACAACCAGGGAACCGAGCCTTACTTTCATCATCGGGAAG
EST: gi|38471583|gb|CF955714.1|CF955714
EST:     TCTTCAGTGAGGATAGCGTGCTAGTTGGGGATCTTGCTGTGAAAAATCAG                         ATGTTCATTGAGACAACCAGGGAACCGAGCCTTACTTTCATCATCGGGAAG
genomic: TCTTCAGTGAGGATAGCGTGCTAGTTGGGGATCTTGCTGTGAAAAATCAGgtgacttatc ... tttctttcagATGTTCATTGAGACAACCAGGGAACCGAGCCTTACTTTCATCATCGGGAAG

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), 65 (downstream exon)
Score: 38

GAGAATCTTGCAGCATTTCCTATGGGTCTGGATCAATTGCTGGTTTCTTCAGTGAGGATAGCGTGCTAGTTGGGGATCTTGCTGTGAAAAATCAGgtgacttatc ... tttctttcagATGTTCATTGAGACAACCAGGGAACCGAGCCTTACTTTCATCATCGGGAAGTTTGATGGAATTCTTGGACTTGGATTTCCGGAGATCTCTGTGGGAGGAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtaaaacatttagatgcatcattgttgatgctgcaggtccatttttctttcagATGTTCATTGAGACAACCAGGGAACCGAGCCTTACTTTCATCATCGGGAAGTTTGATGGAATTCTTGGACTTGGATTTCCGGAGATCTCTGTGGGAGGAG
                        tgttgat  putative branch site (score: 38)
                                       tccatttttctttc  putative PPT
                                          atttttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgacttatcgcactattgtctcagtaaaacatttagatgcatcattgttgatgctgcaggtccatttttctttcagATGTTCATTGAGACAACCAGGGAACCGAGCCTTACTTTCATCATCGGGAAGTTTGATGGAATTCTTGGACTTGGATTTCCGGAGATCTCTGTGGGAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG