Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCTGCTTTACAGGGACTACGGGACGCACCACAAGTTCACCCTCACCACCTGCACCCCCGAGGGCGTCgtgagtatcctcccctccctctctctctctctctcccactcggatccgtcacccaccatttcttgtctggcacgatttgtattctcgtgtcggtgtgaat...

Basic information

species Oryza sativa
transcript LOC_Os01g40570.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g40570.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G155021_T01 (Zea mays), 5'ss of exon 2
ATCTGCTTTACAGGGACTACGGGACGCACCACAAGTTCACCCTCACCACCTGCACCCCCGAGGGCGTCgtgagtatcctcccctccctc-tctctctctctctcccactcggatccgtcacccaccatttcttgtctggcacgatttgtattctcgtgtcggtgtgaat
||||||| |||| |||||||   |||||||| |||||| |||||||||||||| ||||| | ||||||||||||  || | ||  |||  ||  || |  | |||  ||         | | | |        |     | |  ||| | | |      |   ||| | 
ATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTCgtgagtgccccctccctcctaatcaatcaccatttcctcctttacctgagcgcgc-ctccccagaggacaccgcactttatttgcgtagtccttagtggag
















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|88720969|gb|CI744268.1|CI744268
EST:     ACGGGACGCACCACAAGTTCACCCTCACCACCTGCACCCCCGAGGGCGTC                         ACTATCACAGCTGCAGGAACAAGGAAAAATGAGTCTGTCTTTGGTGAGCTC
genomic: ACGGGACGCACCACAAGTTCACCCTCACCACCTGCACCCCCGAGGGCGTCgtgagtatcc ... tgtactgcagACTATCACAGCTGCAGGAACAAGGAAAAATGAGTCTGTCTTTGGTGAGCTC
EST: gi|88333135|gb|CI640978.1|CI640978
EST:     ACGGGACGCACCACAAGTTCACCCTCACCACCTGCACCCCCGAGGGCGTC                         ACTATCACAGCTGCAGGAACAAGGAAAAATGAGTCTGTCTTTGGTGAGCTC
genomic: ACGGGACGCACCACAAGTTCACCCTCACCACCTGCACCCCCGAGGGCGTCgtgagtatcc ... tgtactgcagACTATCACAGCTGCAGGAACAAGGAAAAATGAGTCTGTCTTTGGTGAGCTC
EST: gi|84117319|gb|CD151086.1|CD151086
EST:     ACGGGACGCACCACAAGTTCACCCTCACCACCTGCACCCCCGAGGGCGTC                         ACTATCACAGCTGCAGGAACAAGGAAAAATGAGTCTGTCTTTGGTGAGCTC
genomic: ACGGGACGCACCACAAGTTCACCCTCACCACCTGCACCCCCGAGGGCGTCgtgagtatcc ... tgtactgcagACTATCACAGCTGCAGGAACAAGGAAAAATGAGTCTGTCTTTGGTGAGCTC
EST: gi|88736441|gb|CI759949.1|CI759949
EST:     ACGGGACGCACCACAAGTTCACCCTCACCACCTGCACCCCCGAGGGCGTC                         ACTATCACAGCTGCAGGAACAAGGAAAAATGAGTCTGTCTTTGGTGAGCTC
genomic: ACGGGACGCACCACAAGTTCACCCTCACCACCTGCACCCCCGAGGGCGTCgtgagtatcc ... tgtactgcagACTATCACAGCTGCAGGAACAAGGAAAAATGAGTCTGTCTTTGGTGAGCTC
EST: gi|8857889|gb|AU095207.1|AU095207
EST:     ACGGGACGCACCACAAGTTCACCCTCACCACCTGCACCCCCGAGGGCGTC                         ACTATCACAGCTGCAGGAACAAGGAAAAATGAGTCTGTCTTTGGTGAGCTC
genomic: ACGGGACGCACCACAAGTTCACCCTCACCACCTGCACCCCCGAGGGCGTCgtgagtatcc ... tgtactgcagACTATCACAGCTGCAGGAACAAGGAAAAATGAGTCTGTCTTTGGTGAGCTC
EST: gi|88720087|gb|CI745177.1|CI745177
EST:     ACGGGACGCACCACAAGTTCACCCTCACCACCTGCACCCCCGAGGGCGTC                         ACTATCACAGCTGCAGGAACAAGGAAAAATGAGTCTGTCTTTGGTGAGCTC
genomic: ACGGGACGCACCACAAGTTCACCCTCACCACCTGCACCCCCGAGGGCGTCgtgagtatcc ... tgtactgcagACTATCACAGCTGCAGGAACAAGGAAAAATGAGTCTGTCTTTGGTGAGCTC
EST: gi|88294738|gb|CI604610.1|CI604610
EST:     ACGGGACGCACCACAAGTTCACCCTCACCACCTGCACCCCCGAGGGCGTC                         ACTATCACAGCTGCAGGAACAAGGAAAAATGAGTCTGTCTTTGGTGAGCTC
genomic: ACGGGACGCACCACAAGTTCACCCTCACCACCTGCACCCCCGAGGGCGTCgtgagtatcc ... tgtactgcagACTATCACAGCTGCAGGAACAAGGAAAAATGAGTCTGTCTTTGGTGAGCTC
EST: gi|11565269|gb|AU165905.1|AU165905
EST:     ACGGGACGCACCACAAGTTCACCCTCACCACCTGCACCCCCGAGGGCGTC                         ACTATCACAGCTTGCAGGAACAAGGAAAAATGAGTCTGTCTTTGGTGAGCT
genomic: ACGGGACGCACCACAAGTTCACCCTCACCACCTGCACCCCCGAGGGCGTCgtgagtatcc ... tgtactgcagACTATCACAGCT-GCAGGAACAAGGAAAAATGAGTCTGTCTTTGGTGAGCT
EST: gi|88416058|gb|CI594170.1|CI594170
EST:     ACGGGACGCACCACAAGTTCACCCTCACCACCTGCACCCCCGAGGGCGTC                         ACTATCACAGCTGCAGGAACAAGGAAAAATGAGTCTGTCTTTGGTGAGCTC
genomic: ACGGGACGCACCACAAGTTCACCCTCACCACCTGCACCCCCGAGGGCGTCgtgagtatcc ... tgtactgcagACTATCACAGCTGCAGGAACAAGGAAAAATGAGTCTGTCTTTGGTGAGCTC
EST: gi|88734309|gb|CI757817.1|CI757817
EST:     ACGGGACGCACCACAAGTTCACCCTCACCACCTGCACCCCCGAGGGCGTC                         ACTATCACAGCTGCAGGAACAAGGAAAAATGAGTCTGTCTTTGGTGAGCTC
genomic: ACGGGACGCACCACAAGTTCACCCTCACCACCTGCACCCCCGAGGGCGTCgtgagtatcc ... tgtactgcagACTATCACAGCTGCAGGAACAAGGAAAAATGAGTCTGTCTTTGGTGAGCTC
EST: gi|88720970|gb|CI744269.1|CI744269
EST:     ACGGGACGCACCACAAGTTCACCCTCACCACCTGCACCCCCGAGGGCGTC                         ACTATCACAGCTGCAGGAACAAGGAAAAATGAGTCTGTCTTTGGTGAGCTC
genomic: ACGGGACGCACCACAAGTTCACCCTCACCACCTGCACCCCCGAGGGCGTCgtgagtatcc ... tgtactgcagACTATCACAGCTGCAGGAACAAGGAAAAATGAGTCTGTCTTTGGTGAGCTC
EST: gi|33684445|gb|CF312684.1|CF312684
EST:     ACGGGACGCACCACAAGTTCACCCTCACCACCTGCACCCCCTAGGGCGTC                         ACTATCACAGCTGCAGGAACAAGGAAAAATGAGTCTGTCTTTGGTGAGCTC
genomic: ACGGGACGCACCACAAGTTCACCCTCACCACCTGCACCCCCGAGGGCGTCgtgagtatcc ... tgtactgcagACTATCACAGCTGCAGGAACAAGGAAAAATGAGTCTGTCTTTGGTGAGCTC
EST: gi|88760947|gb|CI770503.1|CI770503
EST:     ACGGGACGCACCACAAGTTCACCCTCACCACCTGCACCCCCGAGGGCGTC                         ACTATCACAGCTGCAGGAACAAGGAAAAATGAGTCTGTCTTTGGTGAGCTC
genomic: ACGGGACGCACCACAAGTTCACCCTCACCACCTGCACCCCCGAGGGCGTCgtgagtatcc ... tgtactgcagACTATCACAGCTGCAGGAACAAGGAAAAATGAGTCTGTCTTTGGTGAGCTC
EST: gi|33797333|gb|CF324529.1|CF324529
EST:     ACGGGACGCACCACAAGTTCACCCTCACCACCTGCACCCCCGAGGGCGTC                         ACTATCACAGCTGCAGGAACAAGGAAAAATGAGTCTGTCTTTGGTGAGCTC
genomic: ACGGGACGCACCACAAGTTCACCCTCACCACCTGCACCCCCGAGGGCGTCgtgagtatcc ... tgtactgcagACTATCACAGCTGCAGGAACAAGGAAAAATGAGTCTGTCTTTGGTGAGCTC
EST: gi|117243612|gb|CT843146.1|CT843146
EST:     ACGGGACGCACCACAAGTTCACCCTCACCACCTGCACCCCCGAGGGCGTC                         ACTATCACAGCTGCAGGAACAAGGAAAAATGAGTCTGTCTTTGGTGAGCTC
genomic: ACGGGACGCACCACAAGTTCACCCTCACCACCTGCACCCCCGAGGGCGTCgtgagtatcc ... tgtactgcagACTATCACAGCTGCAGGAACAAGGAAAAATGAGTCTGTCTTTGGTGAGCTC
EST: gi|86905077|gb|CI289224.1|CI289224
EST:     ACGGGACGCACCACAAGTTCACCCTCACCACCTGCACCCCCGAGGGCGTC                         ACTATCACAGCTGCAGGAACAAGGAAAAATGAGTCTGTCTTTGGTGAGCTC
genomic: ACGGGACGCACCACAAGTTCACCCTCACCACCTGCACCCCCGAGGGCGTCgtgagtatcc ... tgtactgcagACTATCACAGCTGCAGGAACAAGGAAAAATGAGTCTGTCTTTGGTGAGCTC
EST: gi|58661680|gb|CK050360.1|CK050360
EST:     ACGGGACGCACCACAAGTTCACCCTCACCACCTGCACGCCCGAGGGCGTC                         ACTATCACAGCTGCAGGAACAAGGAAAAATGAGTCTGTCTTTGGTGAGCTC
genomic: ACGGGACGCACCACAAGTTCACCCTCACCACCTGCACCCCCGAGGGCGTCgtgagtatcc ... tgtactgcagACTATCACAGCTGCAGGAACAAGGAAAAATGAGTCTGTCTTTGGTGAGCTC

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: 66 (upstream exon), 69 (downstream exon)
Score: 37

ATCTGCTTTACAGGGACTACGGGACGCACCACAAGTTCACCCTCACCACCTGCACCCCCGAGGGCGTCgtgagtatcc ... tgtactgcagACTATCACAGCTGCAGGAACAAGGAAAAATGAGTCTGTCTTTGGTGAGCTCCAAACCCAGCTTAAGAACAAGAAATTGACTGTTGATGTCAAAGCAAACT




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCTGCTTTACAGGGACTACGGGACGCACCACAAGTTCACCCTCACCACCTGCACCCCCGAGGGCGTCgtgagtatcctcccctccctctctctctctctctcccactcggatccgtcacccaccatttcttgtctggcacgatttgtattctcgtgtcggtgtgaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctctct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccactc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacccac