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'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGGTACCCAAGGAGGTGTACAACAACTTGGACACGGGGGCTCAGGATGAGAAATGGTGGGAGgtaaatcgattcgcccccttcctgtatgactatttccctacatgctgcataaacaagggatatcaagcaacgccaatcaaatttgtttctgtttctgtttttttccttttgtaattcag

Basic information

species Oryza sativa
transcript LOC_Os02g58030.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g58030.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G015090_T01 (Zea mays), 5'ss of exon 1
------------------------------------GGAGGTACCCAAGGAGGTGTACAACAACTTGGACACGGGGGCTCAGGATGAGAAATGGTGGGAGgtaaatcgattcgcccccttcctgtatgactatttccctacatgctgcataaacaagggatatcaagcaacgccaatcaaatttgtttctgtttctgtttttttccttttgtaattcag
                                    |||| ||||||||||||| ||||||||||||||||| ||    |||||||||||||||||||||||||   |  ||    ||  ||  || ||     |    ||| ||       ||| | ||| ||||| ||    | |    | |||   | |||| |                      
TACTTCTGCCTGTTCCTTTGCCGCCTTGCTCTGCAGGGAGATACCCAAGGAGGTTTACAACAACTTGGACACTGGCAGCCAGGATGAGAAATGGTGGGAGgtaacatg-ctcattacccaccactacgagctaatatacacacgcct-----acaggtgatgtcaagtaatcagact---gtgtgtgcatttttcag----------------------
















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|88762442|gb|CI771998.1|CI771998
EST:     AGGTGTACAACAACTTGGACACGGGGGCTCAGGATGAGAAATGGTGGGAG                         GGAGTTGACCTTCANAAGCTCATATTGGCTCATAACAACCTTGAGGTGTTG
genomic: AGGTGTACAACAACTTGGACACGGGGGCTCAGGATGAGAAATGGTGGGAGgtaaatcgat ... tgtaattcagGGAGTTGACCTTCAGAAGCTCATATTGGCTCATAACAACCTTGAGGTGTTG
EST: gi|58658512|gb|CK047192.1|CK047192
EST:     AGGTGTACAACAACTTGGACACGGGGGCTCAGGATGAGAAATGGTGGGAG                         GGAGTTGACCTTCAGAAGCTCATATTGGCTCATAACAAC
genomic: AGGTGTACAACAACTTGGACACGGGGGCTCAGGATGAGAAATGGTGGGAGgtaaatcgat ... tgtaattcagGGAGTTGACCTTCAGAAGCTCATATTGGCTCATAACAAC
EST: gi|88393661|gb|CI621156.1|CI621156
EST:     AGGTGTACAACAACTTGGACACGGGGGCTCAGGATGAGAAATGGTGGGAG                         GGAGTTGACCTTCAGAAGCTCATATTGGCTCATAACAACCTTGAGGTGTTG
genomic: AGGTGTACAACAACTTGGACACGGGGGCTCAGGATGAGAAATGGTGGGAGgtaaatcgat ... tgtaattcagGGAGTTGACCTTCAGAAGCTCATATTGGCTCATAACAACCTTGAGGTGTTG
EST: gi|88589638|gb|CI708436.1|CI708436
EST:     AGGTGTACAACAACTTGGACACGGGGGCTCAGGATGAGAAATGGTGGGAG                         GGAGTTGACCTTCAGAAGCTCATATTGGCTCATAACAACCTTGAGGTGTTG
genomic: AGGTGTACAACAACTTGGACACGGGGGCTCAGGATGAGAAATGGTGGGAGgtaaatcgat ... tgtaattcagGGAGTTGACCTTCAGAAGCTCATATTGGCTCATAACAACCTTGAGGTGTTG
EST: gi|88370332|gb|CI587722.1|CI587722
EST:     AGGTGTACAACAACTTGGACACGGGGGCTCAGGATGAGAAATGGTGGGAG                         GGAGTTGACCTTCAGAAGCTCATATTGGCTCATAACAACCTTGAGGTGTTG
genomic: AGGTGTACAACAACTTGGACACGGGGGCTCAGGATGAGAAATGGTGGGAGgtaaatcgat ... tgtaattcagGGAGTTGACCTTCAGAAGCTCATATTGGCTCATAACAACCTTGAGGTGTTG
EST: gi|88372250|gb|CI619580.1|CI619580
EST:     AGGTGCACAACAACTTGGACACGGGGGCTCAGGATGAGAAATGGTGGGAG                         GGAGTTGACCTTCAGAAGCTCATATTGGCTCATAACAACCTTGAGGTGTTG
genomic: AGGTGTACAACAACTTGGACACGGGGGCTCAGGATGAGAAATGGTGGGAGgtaaatcgat ... tgtaattcagGGAGTTGACCTTCAGAAGCTCATATTGGCTCATAACAACCTTGAGGTGTTG
EST: gi|88339003|gb|CI677822.1|CI677822
EST:     AGGTGTACAACAACTTGGACACGGGGGCTCAGGATGAGAAATGGTGGGAG                         GGAGTNGACCTTCAGAAGCTCATATGGGCTCATAACAACCTTGAGGTGTTG
genomic: AGGTGTACAACAACTTGGACACGGGGGCTCAGGATGAGAAATGGTGGGAGgtaaatcgat ... tgtaattcagGGAGTTGACCTTCAGAAGCTCATATTGGCTCATAACAACCTTGAGGTGTTG
EST: gi|88739909|gb|CI761419.1|CI761419
EST:     AGGTGTACAACAACTTGGACACGGGGGCTCAGGATGAGAAATGGTGGGAG                         GGAGTTGACCTTCAGAAGCTCATATTGGCTCATAACAACCTTGAGGTGTTG
genomic: AGGTGTACAACAACTTGGACACGGGGGCTCAGGATGAGAAATGGTGGGAGgtaaatcgat ... tgtaattcagGGAGTTGACCTTCAGAAGCTCATATTGGCTCATAACAACCTTGAGGTGTTG
EST: gi|88365345|gb|CI679979.1|CI679979
EST:     AGGTGTACAACAACTTGGACACGGGGGCTCAGGATGAGAAATGGTGGGAG                         GGAGTTGACCTTCACAAGCTCATATTGGCTCATAACAACCTTGAGGTGTNG
genomic: AGGTGTACAACAACTTGGACACGGGGGCTCAGGATGAGAAATGGTGGGAGgtaaatcgat ... tgtaattcagGGAGTTGACCTTCAGAAGCTCATATTGGCTCATAACAACCTTGAGGTGTTG
EST: gi|88728403|gb|CI751913.1|CI751913
EST:     AGGTGTACAACAACTTGGACACGGGGGCTCAGGATGAGAAATGGTGGGAG                         GGAGTTGACCTTCAAAAGCTCATATTGGCTCATAACAACCTTGAGGTGTTG
genomic: AGGTGTACAACAACTTGGACACGGGGGCTCAGGATGAGAAATGGTGGGAGgtaaatcgat ... tgtaattcagGGAGTTGACCTTCAGAAGCTCATATTGGCTCATAACAACCTTGAGGTGTTG
EST: gi|88315437|gb|CI613706.1|CI613706
EST:     AGGTGTACAACAACTTGGACACGGGGGCTCAGGATGAGAAATGGTGGGAG                         GGAGTTGACCTTCAGAAGCTCATATTGGCTCATAACAACCTTGAGGTGTTG
genomic: AGGTGTACAACAACTTGGACACGGGGGCTCAGGATGAGAAATGGTGGGAGgtaaatcgat ... tgtaattcagGGAGTTGACCTTCAGAAGCTCATATTGGCTCATAACAACCTTGAGGTGTTG
EST: gi|58669154|gb|CK057840.1|CK057840
EST:     AGGTGTACAACAACTTGGACACGGGGGCTCAGGATGAGAAATGGTGGGAG                         GGAGTTGACCTTCAGAAGCTCATATTGGCTCATAACAACCTTGAGGTGTTG
genomic: AGGTGTACAACAACTTGGACACGGGGGCTCAGGATGAGAAATGGTGGGAGgtaaatcgat ... tgtaattcagGGAGTTGACCTTCAGAAGCTCATATTGGCTCATAACAACCTTGAGGTGTTG
EST: gi|88355166|gb|CI651869.1|CI651869
EST:     AGGTGTACAACAACTTGGACACGGGGGCTCAGGATGAGAAATGGTGGGAG                         GGAGTTGACCTTCAGAAGCTCATATTGGCTCATAACAACCTTGAGGTGTTG
genomic: AGGTGTACAACAACTTGGACACGGGGGCTCAGGATGAGAAATGGTGGGAGgtaaatcgat ... tgtaattcagGGAGTTGACCTTCAGAAGCTCATATTGGCTCATAACAACCTTGAGGTGTTG
EST: gi|58663247|gb|CK051933.1|CK051933
EST:     AGGTGTACAACAACTTGGACACGGGGGCTCAGGATGAGAAATGGTGGGAG                         GGAGTTGACCTTCAGAAGCTCATATTGGCTCATAACAACCTTGAGGTGTTG
genomic: AGGTGTACAACAACTTGGACACGGGGGCTCAGGATGAGAAATGGTGGGAGgtaaatcgat ... tgtaattcagGGAGTTGACCTTCAGAAGCTCATATTGGCTCATAACAACCTTGAGGTGTTG

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: 50 (upstream exon), 70 (downstream exon)
Score: 13

GGAGGTACCCAAGGAGGTGTACAACAACTTGGACACGGGGGCTCAGGATGAGAAATGGTGGGAGgtaaatcgat ... tgtaattcagGGAGTTGACCTTCAGAAGCTCATATTGGCTCATAACAACCTTGAGGTGTTGCGTGAAGACCTCAGAAATTTGTCTTCGCTCGTTGTATTAAACATTAGTC




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGGTACCCAAGGAGGTGTACAACAACTTGGACACGGGGGCTCAGGATGAGAAATGGTGGGAGgtaaatcgattcgcccccttcctgtatgactatttccctacatgctgcataaacaagggatatcaagcaacgccaatcaaatttgtttctgtttctgtttttttccttttgtaattcag

- - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG