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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccgtaccgtactcccccctccttcccctcatttccttttcatcctgtcgctattattcaaccccacgcttcgcaatcgcaacgcagGTGAAATCCTTCTACGTTGGCAAAGACCATGTCGGGGATGTGCCTCTCACCAAGAAGATCGCTGCCGGCTTCACCACTG

Basic information

species Oryza sativa
transcript LOC_Os11g48040.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g48040.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G000510_T02 (Zea mays), 3'ss of exon 2
--------------------------------------------------------gtccgtaccgtactcccccctccttcccctcatttccttttcatcctgtcgctattattcaaccccacgcttcgcaatcgcaacgcagGTGAAATCCTTCTACGTTGGCAAAGACCATGTCGGGGATGTGCCTCTCACCAAGAAGATCGCTGCCGGCTTCACCACTG
                                                         | | |   ||   | ||    ||| |  |  |     |   |   |  |  |   | || | || ||   | ||  |       ||||| |||||||||||||| ||||||||||| || |||||||| ||| |  |||||||||| || ||||||| ||| ||  
gtacggtcctcaccgcagtcaactatttactctgcatatcattaattaactttctgatgcattttgtttcctccaacacttgctgtgctactgctactaatttcccaatgccagtccaaccaaccacttgcc-tgaacttacagGTCAAATCCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAGATAGCCGCCGGCT-CACAAC--

upper sequence: LOC_Os11g48040.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G000510_T03 (Zea mays), 3'ss of exon 2
--------------------------------------------------------gtccgtaccgtactcccccctccttcccctcatttccttttcatcctgtcgctattattcaaccccacgcttcgcaatcgcaacgcagGTGAAATCCTTCTACGTTGGCAAAGACCATGTCGGGGATGTGCCTCTCACCAAGAAGATCGCTGCCGGCTTCACCACTG
                                                         | | |   ||   | ||    ||| |  |  |     |   |   |  |  |   | || | || ||   | ||  |       ||||| |||||||||||||| ||||||||||| || |||||||| ||| |  |||||                         
gtacggtcctcaccgcagtcaactatttactctgcatatcattaattaactttctgatgcattttgtttcctccaacacttgctgtgctactgctactaatttcccaatgccagtccaaccaaccacttgcc-tgaacttacagGTCAAATCCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAG-------------------------

upper sequence: LOC_Os11g48040.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G000510_T04 (Zea mays), 3'ss of exon 2
--------------------------------------------------------gtccgtaccgtactcccccctccttcccctcatttccttttcatcctgtcgctattattcaaccccacgcttcgcaatcgcaacgcagGTGAAATCCTTCTACGTTGGCAAAGACCATGTCGGGGATGTGCCTCTCACCAAGAAGATCGCTGCCGGCTTCACCACTG
                                                         | | |   ||   | ||    ||| |  |  |     |   |   |  |  |   | || | || ||   | ||  |       ||||| |||||||||||||| ||||||||||| || |||||||| ||| |  ||||||||                      
gtacggtcctcaccgcagtcaactatttactctgcatatcattaattaactttctgatgcattttgtttcctccaacacttgctgtgctactgctactaatttcccaatgccagtccaaccaaccacttgcc-tgaacttacagGTCAAATCCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAG----------------------

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|29642995|gb|CB648002.1|CB648002
EST:     TCCACCGCCAGTGCATCTACGGCGGCCTCCGCATCGGCCTCTACGAGCCC                         GTGAAATCCTTCTACGTTGGCAAAGACCATGTCGGGGATGTGCCTCTCACC
genomic: TCCACCGCCAGTGCATCTACGGCGGCCTCCGCATCGGCCTCTACGAGCCCgtccgtaccg ... cgcaacgcagGTGAAATCCTTCTACGTTGGCAAAGACCATGTCGGGGATGTGCCTCTCACC
EST: gi|88745668|gb|CI769028.1|CI769028
EST:     TCCACCGCCAGTGCATCTACGGCGGCCTCCGCATCGGCCTCTACGAGCCC                         GTGAAATCCTTCTACGTTG
genomic: TCCACCGCCAGTGCATCTACGGCGGCCTCCGCATCGGCCTCTACGAGCCCgtccgtaccg ... cgcaacgcagGTGAAATCCTTCTACGTTG
EST: gi|88296156|gb|CI667546.1|CI667546
EST:     TCCACCGCCAGTGCATCTACGGCGGCCTCCGCATCGGCCTCTACGAGCCC                         GTGAAATCCTTCTACGTTGGCAAAGACCATGTCGG
genomic: TCCACCGCCAGTGCATCTACGGCGGCCTCCGCATCGGCCTCTACGAGCCCgtccgtaccg ... cgcaacgcagGTGAAATCCTTCTACGTTGGCAAAGACCATGTCGG
EST: gi|88345333|gb|CI655991.1|CI655991
EST:     TCCACCGCCAGTGCATCTACGGGGGCCTCCGCATCGGCCTCTACGAGCCC                         GTGAAATCCTTCTACGTTGGCAAAGACCATGTCGGGG
genomic: TCCACCGCCAGTGCATCTACGGCGGCCTCCGCATCGGCCTCTACGAGCCCgtccgtaccg ... cgcaacgcagGTGAAATCCTTCTACGTTGGCAAAGACCATGTCGGGG
EST: gi|117251481|gb|CT844185.1|CT844185
EST:     TCCACCGCCAGTGCATCTACGGCGGCCTCCGCATCGGCCTCTACGAGCCC                         GTGAAATCCTTCTACGTTGGCAAAGACCATGTCGGGGATGTGCCTCTCACC
genomic: TCCACCGCCAGTGCATCTACGGCGGCCTCCGCATCGGCCTCTACGAGCCCgtccgtaccg ... cgcaacgcagGTGAAATCCTTCTACGTTGGCAAAGACCATGTCGGGGATGTGCCTCTCACC
EST: gi|88695949|gb|CI739524.1|CI739524
EST:     TCCACCGCCAGTGCATCTACGGCGGCCTCCGCATCGGCCTCTACGAGCCC                         GTGAAATCCTTCTANGTTG
genomic: TCCACCGCCAGTGCATCTACGGCGGCCTCCGCATCGGCCTCTACGAGCCCgtccgtaccg ... cgcaacgcagGTGAAATCCTTCTACGTTG
EST: gi|88345950|gb|CI632423.1|CI632423
EST:     TCCACCGCCAGTGCATCTACGGNGGCCTCCGCATCGGCCTCTACGAGCCC                         GTGAAATCCTTCTACGTTGGCAAAGACCAT
genomic: TCCACCGCCAGTGCATCTACGGCGGCCTCCGCATCGGCCTCTACGAGCCCgtccgtaccg ... cgcaacgcagGTGAAATCCTTCTACGTTGGCAAAGACCAT
EST: gi|88573462|gb|CI665033.1|CI665033
EST:     TCCACCGCCAGTGCATCTACGGCGGCCTCCGCATCGGCCTCTACGAGCCC                         GTGAAATCCTTCTACGTTGGCAAAGACCATGTCGGGGATGTGCCTCTCACC
genomic: TCCACCGCCAGTGCATCTACGGCGGCCTCCGCATCGGCCTCTACGAGCCCgtccgtaccg ... cgcaacgcagGTGAAATCCTTCTACGTTGGCAAAGACCATGTCGGGGATGTGCCTCTCACC
EST: gi|88729445|gb|CI752955.1|CI752955
EST:     TCCACCGCCAGTGCATCTACGGCGGCCTCCGCATCGGCCTCTACGAGCCC                         GTGAAATCCTTCTACGTTGGCAAAGACC
genomic: TCCACCGCCAGTGCATCTACGGCGGCCTCCGCATCGGCCTCTACGAGCCCgtccgtaccg ... cgcaacgcagGTGAAATCCTTCTACGTTGGCAAAGACC
EST: gi|88307967|gb|CI646402.1|CI646402
EST:     TCCACCGCCAGTGCATCTACGGCGGCCTCCGCATCGGCCTCTACGAGCCC                         GTGAAATCCTTCTACGTTGGCAAAGACCATGTCGG
genomic: TCCACCGCCAGTGCATCTACGGCGGCCTCCGCATCGGCCTCTACGAGCCCgtccgtaccg ... cgcaacgcagGTGAAATCCTTCTACGTTGGCAAAGACCATGTCGG
EST: gi|88332650|gb|CI660168.1|CI660168
EST:     TCCACCGCCAGTGCATCTACGGCGGCCTCCGCATCGGCCTCTACGAGCCC                         GTGAAATCCTTCTACGTTGGCAAAGACCATGTCGGGGATGTGCCTCTCACC
genomic: TCCACCGCCAGTGCATCTACGGCGGCCTCCGCATCGGCCTCTACGAGCCCgtccgtaccg ... cgcaacgcagGTGAAATCCTTCTACGTTGGCAAAGACCATGTCGGGGATGTGCCTCTCACC
EST: gi|29643037|gb|CB648044.1|CB648044
EST:     TCCACCGCCAGTGCATCTACGGCGGCCTCCGCATCGGCCTCTACGAGCCC                         GTGAAATCCTTCTACGTTGGCAAAGACCATGTCGGGGATGTGCCTCTCACC
genomic: TCCACCGCCAGTGCATCTACGGCGGCCTCCGCATCGGCCTCTACGAGCCCgtccgtaccg ... cgcaacgcagGTGAAATCCTTCTACGTTGGCAAAGACCATGTCGGGGATGTGCCTCTCACC
EST: gi|88589532|gb|CI705420.1|CI705420
EST:     TCCACCGCCAGTGCATCTACGGCGGCCTCCGCATCGGCCTCTACGAGCCC                         GTGAAATCCTTCTANGTTGGCAAAGACC
genomic: TCCACCGCCAGTGCATCTACGGCGGCCTCCGCATCGGCCTCTACGAGCCCgtccgtaccg ... cgcaacgcagGTGAAATCCTTCTACGTTGGCAAAGACC
EST: gi|88573786|gb|CI665555.1|CI665555
EST:     TCCACCGCCAGTGCATCTACGGCGGCCTCCGCATCGGCCTCTACGAGCCC                         GTGAAATCCTTCTACGTTGGCAAAGACCATGTCGGGGATGTGCCTCTCACC
genomic: TCCACCGCCAGTGCATCTACGGCGGCCTCCGCATCGGCCTCTACGAGCCCgtccgtaccg ... cgcaacgcagGTGAAATCCTTCTACGTTGGCAAAGACCATGTCGGGGATGTGCCTCTCACC
EST: gi|58661525|gb|CK050205.1|CK050205
EST:     TCCACCGCCAGTGCATCTACGGCGGCCTCCGCATCGGCCTCTACGAGCCC                         GTGAAATCCTTCTACGTTGGCAAAGACCATGTCGGGGATGTGCCTCTCACC
genomic: TCCACCGCCAGTGCATCTACGGCGGCCTCCGCATCGGCCTCTACGAGCCCgtccgtaccg ... cgcaacgcagGTGAAATCCTTCTACGTTGGCAAAGACCATGTCGGGGATGTGCCTCTCACC
EST: gi|58594298|gb|CF992606.1|CF992606
EST:     TCCACCGCCAGTGCATCTACGGCGGCCTCCGCATCGGCCTCTACTAGCCC                         GTGAAATCCTTCTACGTTGGCAAAGACCATGTCGGGGATGTGCCTCTCACC
genomic: TCCACCGCCAGTGCATCTACGGCGGCCTCCGCATCGGCCTCTACGAGCCCgtccgtaccg ... cgcaacgcagGTGAAATCCTTCTACGTTGGCAAAGACCATGTCGGGGATGTGCCTCTCACC
EST: gi|88342270|gb|CI658925.1|CI658925
EST:     TCCACCGCCAGTGCATCTACGGCGGCCTCCGCATCGGCCTCTACGAGCCC                         GTGAAATCCTTCTACGTTGGCAAAGACCATGTCGGGGATGTGCC
genomic: TCCACCGCCAGTGCATCTACGGCGGCCTCCGCATCGGCCTCTACGAGCCCgtccgtaccg ... cgcaacgcagGTGAAATCCTTCTACGTTGGCAAAGACCATGTCGGGGATGTGCC
EST: gi|88333370|gb|CI642407.1|CI642407
EST:     TCCACCGCCAGTGCATCTACGGCGGCCTCCGCATCGGCCTCTACGAGCCC                         GTGAAATCCTTCTANGTTGGCAAAG
genomic: TCCACCGCCAGTGCATCTACGGCGGCCTCCGCATCGGCCTCTACGAGCCCgtccgtaccg ... cgcaacgcagGTGAAATCCTTCTACGTTGGCAAAG

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: 45 (upstream exon), 69 (downstream exon)
Score: 15

CGCGCGCGAGGAAGGCGCCGCCGCTCTCTGGAAGGGCATCGTCCCGGGACTCCACCGCCAGTGCATCTACGGCGGCCTCCGCATCGGCCTCTACGAGCCCgtccgtaccg ... cgcaacgcagGTGAAATCCTTCTACGTTGGCAAAGACCATGTCGGGGATGTGCCTCTCACCAAGAAGATCGCTGCCGGCTTCACCACTG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccttttcatcctgtcgctattattcaaccccacgcttcgcaatcgcaacgcagGTGAAATCCTTCTACGTTGGCAAAGACCATGTCGGGGATGTGCCTCTCACCAAGAAGATCGCTGCCGGCTTCACCACTG
                   tattattcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtccgtaccgtactcccccctccttcccctcatttccttttcatcctgtcgctattattcaaccccacgcttcgcaatcgcaacgcagGTGAAATCCTTCTACGTTGGCAAAGACCATGTCGGGGATGTGCCTCTCACCAAGAAGATCGCTGCCGGCTTCACCACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG