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

TAAAGGAATTAAAGGCCATGGTTACCGTGACGAATTGGTGGTTCCTATAATTGAGAACACTCCTTATGAGTATGAGCTCACTGACTCACTGGCTGAGGCGgtatgttactattgtccttctttggagtttcagtttctcaatcttcgcaaaaaaacaaatattatatttgtagtctgttgttctcataacttcgtgtgga...

Basic information

species Oryza sativa
transcript LOC_Os11g29370.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g29370.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G574782_T01 (Zea mays), 5'ss of exon 4
TAAAGGAATTAAAGGCCATGGTTACCGTGACGAATTGGTGGTTCCTATAATTGAGAACACTCCTTATGAGTATGAGCTCACTGACTCACTGGCTGAGGCGgtatgttactattgtccttctttggagtttcagtttctcaatcttcgcaaaaaaacaaatattatatttgtagtctgttgttctcataacttcgtgtgga---
 |||||||| ||||| ||||| |||| ||| ||||||||  ||||||| |||||||| || |||||||||||||||||||||||||| ||   |||||||||||| ||  |   ||||   ||  | |     | | |   ||||| |  |    |||    |||     |  |    |        |  || ||    |   
CAAAGGAATCAAAGGTCATGGCTACCATGATGAATTGGTCATTCCTATTATTGAGAATACCCCTTATGAGTATGAGCTCACTGACTCCCTAAGTGAGGCGgtatgctatcaaactcctatctttcaatc---atctttttttcttctcggacgcgcaagagatatgcacatcattaaattaagaagaagtttggtccaaaata
















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|157650028|gb|EX449662.1|EX449662
EST:     TTGAGAACACTCCTTATGAGTATGAGCTCACTGACTCACTGGCTGAGGCG                         ATTGCAGCATACCCTAAGGCAACTGCAGTCCTTGTAC
genomic: TTGAGAACACTCCTTATGAGTATGAGCTCACTGACTCACTGGCTGAGGCGgtatgttact ... tatataacagATTGCAGCATACCCTAAGGCAACTGCAGTCCTTGTAC
EST: gi|29671699|gb|CB667974.1|CB667974
EST:     TTGAGAACACTCCTTATGAGTATGAGCTCACTGACTCACTGGCTGAGGCG                         ATTGCAGCATACCCTAAGGCAACTGCAGTCCTTGTACGGAACCATGGAATT
genomic: TTGAGAACACTCCTTATGAGTATGAGCTCACTGACTCACTGGCTGAGGCGgtatgttact ... tatataacagATTGCAGCATACCCTAAGGCAACTGCAGTCCTTGTACGGAACCATGGAATT
EST: gi|218485973|gb|FG956977.1|FG956977
EST:     TTGAGAACACTCCTTATGAGTATGAGCTCACTGACTCACTGGCTGAGGCG                         ATTGCAGCATACCCTAAGGCAACTGCAGTCCTTGTACGGAACCATGGAATT
genomic: TTGAGAACACTCCTTATGAGTATGAGCTCACTGACTCACTGGCTGAGGCGgtatgttact ... tatataacagATTGCAGCATACCCTAAGGCAACTGCAGTCCTTGTACGGAACCATGGAATT
EST: gi|29634818|gb|CB639827.1|CB639827
EST:     TTGAGAACACTCCTTATGAGTATGAGCTCACTGACTCACTGGCTGAGGCG                         ATTGCAGCATACCCTAAGGCAACTGCAGTCCTTGTACGGAACCATGGAATT
genomic: TTGAGAACACTCCTTATGAGTATGAGCTCACTGACTCACTGGCTGAGGCGgtatgttact ... tatataacagATTGCAGCATACCCTAAGGCAACTGCAGTCCTTGTACGGAACCATGGAATT
EST: gi|428336|gb|D24484.1|D24484
EST:     TTGAGAACACTCCTTATGAGTATGAGCTCACTGACTCACTNNCTGAGGCG                         ATTGCAGCATACCCTAAGGCAACTGCAGTCCTTGTACGGAACCATGGAATT
genomic: TTGAGAACACTCCTTATGAGTATGAGCTCACTGACTCACTGGCTGAGGCGgtatgttact ... tatataacagATTGCAGCATACCCTAAGGCAACTGCAGTCCTTGTACGGAACCATGGAATT
EST: gi|58696100|gb|CK084787.1|CK084787
EST:     TTGAGAACACTCCTTATGAGTATGAGCTCACTGACTCACTGGCTGAGGCG                         ATTGCAGCATACCCTAAGGCAACTGCAGTCCTTGTACGGAACCATGGAATT
genomic: TTGAGAACACTCCTTATGAGTATGAGCTCACTGACTCACTGGCTGAGGCGgtatgttact ... tatataacagATTGCAGCATACCCTAAGGCAACTGCAGTCCTTGTACGGAACCATGGAATT
EST: gi|29634836|gb|CB639845.1|CB639845
EST:     TTGAGAACACTCCTTATGAGTATGAGCTCACTGACTCACTGGCTGAGGCG                         ATTGCAGCATACCCTAAGGCAACTGCAGTCCTTGTACGGAACCATGGAATT
genomic: TTGAGAACACTCCTTATGAGTATGAGCTCACTGACTCACTGGCTGAGGCGgtatgttact ... tatataacagATTGCAGCATACCCTAAGGCAACTGCAGTCCTTGTACGGAACCATGGAATT
EST: gi|29631427|gb|CB636436.1|CB636436
EST:     TTGAGAACACTCCTTATGAGTATGAGCTCACTGACTCACTGGCTGAGGCG                         ATTGCAGCATACCCTAAGGCAACTGCAGTCCTTGTACGGAACCATGGAATT
genomic: TTGAGAACACTCCTTATGAGTATGAGCTCACTGACTCACTGGCTGAGGCGgtatgttact ... tatataacagATTGCAGCATACCCTAAGGCAACTGCAGTCCTTGTACGGAACCATGGAATT
EST: gi|58694492|gb|CK083179.1|CK083179
EST:     TTGAGAACACTCCTTATGAGTATGAGCTCACTGACTCACTGGCTGAGGCG                         ATTGCAGCATACCCTAAGGCAACTGCAGTCCTTGTACGGAACCATGGAATT
genomic: TTGAGAACACTCCTTATGAGTATGAGCTCACTGACTCACTGGCTGAGGCGgtatgttact ... tatataacagATTGCAGCATACCCTAAGGCAACTGCAGTCCTTGTACGGAACCATGGAATT
EST: gi|2312274|gb|C28429.1|C28429
EST:     TTGAGAACACTCCTTATGAGTATGAGCTCACTGACTCACTGGCTGAGGCG                         ATTGCAGCATACCCTAAGGCAACTGCAGTCCTTGTACGGAACCATGGAATT
genomic: TTGAGAACACTCCTTATGAGTATGAGCTCACTGACTCACTGGCTGAGGCGgtatgttact ... tatataacagATTGCAGCATACCCTAAGGCAACTGCAGTCCTTGTACGGAACCATGGAATT
EST: gi|13807201|gb|AU181860.1|AU181860
EST:     TTGAGAACACTCCTTATGAGTATGAGCTCACTGACTCACTGGCTGAGGCG                         ATTGCAGCATACCCTAAGGCAACTGCAGTCCTTGTACGGAACCATGGAATT
genomic: TTGAGAACACTCCTTATGAGTATGAGCTCACTGACTCACTGGCTGAGGCGgtatgttact ... tatataacagATTGCAGCATACCCTAAGGCAACTGCAGTCCTTGTACGGAACCATGGAATT
EST: gi|29674778|gb|CB671053.1|CB671053
EST:     TTGAGAACACTCCTTATGAGTATGAGCTCACTGACTCACTGGCTGAGGCG                         ATTGCAGCATACCCTAAGGCAACTGCAGTCCTTGTACGGAACCATGGAATT
genomic: TTGAGAACACTCCTTATGAGTATGAGCTCACTGACTCACTGGCTGAGGCGgtatgttact ... tatataacagATTGCAGCATACCCTAAGGCAACTGCAGTCCTTGTACGGAACCATGGAATT
EST: gi|29686092|gb|CB682367.1|CB682367
EST:     TTGAGAACACTCCTTATGAGTATGAGCTCACTGACTCACTGGCTGAGGCG                         ATTGCAGCATACCCTAAGGCAACTGCAGTCCTTGTACGGAACCATGGAATT
genomic: TTGAGAACACTCCTTATGAGTATGAGCTCACTGACTCACTGGCTGAGGCGgtatgttact ... tatataacagATTGCAGCATACCCTAAGGCAACTGCAGTCCTTGTACGGAACCATGGAATT

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: 75 (upstream exon), 75 (downstream exon)
Score: 105

TAAAGGAATTAAAGGCCATGGTTACCGTGACGAATTGGTGGTTCCTATAATTGAGAACACTCCTTATGAGTATGAGCTCACTGACTCACTGGCTGAGGCGgtatgttact ... tatataacagATTGCAGCATACCCTAAGGCAACTGCAGTCCTTGTACGGAACCATGGAATTTATGTATGGGGTGATTCCTGGATCAATGCCAAGACACAG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAAAGGAATTAAAGGCCATGGTTACCGTGACGAATTGGTGGTTCCTATAATTGAGAACACTCCTTATGAGTATGAGCTCACTGACTCACTGGCTGAGGCGgtatgttactattgtccttctttggagtttcagtttctcaatcttcgcaaaaaaacaaatattatatttgtagtctgttgttctcataacttcgtgtgga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa