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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCCATCTCGGGGATACACCACACAACTTAAATGAAAGTGATTTTGAGAACTTGGCTCGTCGAACAGACGGGTTTTCTGGTTCGGATATTGCTGTTTGTgtaagttgttttctgcaacattctcatgtatccatgctctgttagcatatactgaaatctcgttgctcttttttctttcaacag

Basic information

species Oryza sativa
transcript LOC_Os01g04814.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g04814.3 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G088834_T01 (Zea mays), 5'ss of exon 6
GTCCATCTCGGGGATACACCACACAACTTAAATGAAAGTGATTTTGAGAACTTGGCTCGTCGAACAGACGGGTTTTCTGGTTCGGATATTGCTGTTTGTgtaagttgttttc-------tgcaac----attctcatgtatccatgctctgt---------tagcatatactgaaatctcgttgctcttttttctttcaacag-
|||||||||||||||||||||||||  |||| |||||||||||| |||| |||||| ||||| |||||||||||||||||||| ||  ||||||| |||||||||  |||         |||| |    ||    |||  ||  ||||| ||         ||  |   | ||||||||  |   | |||||||  || ||   
GTCCATCTCGGGGATACACCACACAGTTTAACTGAAAGTGATTTCGAGAGCTTGGCCCGTCGGACAGACGGGTTTTCTGGTTCTGACGTTGCTGTCTGTgtaagtaatttctgaacttgtgcatctgtcatcactatgcttcactgctcagtctcacattgtactaagcaatgaaatctgatacattttttttccctcgaccag

upper sequence: LOC_Os01g04814.3 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G126860_T01 (Zea mays), 5'ss of exon 6
GTCCATCTCGGGGATACACCACACAACTTAAATGAAAGTGATTTTGAGAACTTGGCTCGTCGAACAGACGGGTTTTCTGGTTCGGATATTGCTGTTTGTgtaagttgtttt-----ctgcaa-----cattctcatgt------atccatgctctgttagcatatactgaaatctcgt-tgctcttttttctttcaacag
|||||||||||||||||||||||||  |||| |||||| ||||| |||| |||||| ||||||||||| || ||||||||||| ||| ||||||||||||||||   ||||     ||  ||     ||||   |||        | ||  |||   || | ||   || ||| |  | || |  || ||  ||||||||
GTCCATCTCGGGGATACACCACACAGTTTAACTGAAAGCGATTTCGAGAGCTTGGCCCGTCGAACAGATGGATTTTCTGGTTCTGATGTTGCTGTTTGTgtaagcaattttggactcttgaatctgtcattactatgctccacagttcagtctcatctatcttactatgcaatttaatctgatacttgtttcttcaacag

upper sequence: LOC_Os01g04814.3 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA13G39410.1 (Glycine max), 5'ss of exon 7
GTCCATCTCGGGGATACACCACACAACTTAAATGAAAGTGATTTTGAGAACTTGGCTCGTCGAACAGACGGGTTTTCTGGTTCGGATATTGCTGTTTGTgtaagtt-----gttttctgcaacattctcatgtatccatgctctg-ttagcatatactgaaatctcgttgctcttttttctttcaacag
|| ||||| || ||||| || || ||||| | |||||||||||||||  |||||||| |  | ||||| || ||||||||||| |||||  |||| ||||||||||     | | | || ||        |  ||  ||  | |  ||     ||  | || |        | |        ||  |||
GTGCATCTAGGAGATACTCCCCATAACTTGACTGAAAGTGATTTTGAATACTTGGCTAGCAGGACAGAGGGTTTTTCTGGTTCAGATATATCTGTCTGTgtaagttttactgctatatgaaatgactggtttcattaatcttatacttgatgaatttttaagtaaaaagtttttggacctcctcttcag

upper sequence: LOC_Os01g04814.3 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv06s0080g00160.t01 (Vitis vinifera), 5'ss of exon 6
GTCCATCTCGGGGATACACCACACAACTTAAATGAAAGTGATTTTGAGAACTTGGCTCGTCGAACAGACGGGTTTTCTGGTTCGGATATTGCTGTTTGTgtaagt-tgttttctgcaacattctcatgtatccatgctctgttagcatatactgaaatctcgttgctcttttttctttc-aacag----------------------------------------------
|| ||||| || ||||| || |||||||| | ||||||||||||||| | ||| ||||     ||||| |||||||||||||| |||||||||||||||||||||  |  | ||  | ||    |     |  || |||  || |    | |   | |    | | |     |       || ||                                              
GTGCATCTTGGAGATACTCCTCACAACTTGACTGAAAGTGATTTTGAAAGCTTAGCTCAGAAGACAGAAGGGTTTTCTGGTTCAGATATTGCTGTTTGTgtaagtgcgagtgctatatcagatgctcaactaaattctccctttgagctttcctcagtagtatggtttaaggtgggacagaatagtagaaaatagcttatcatcttgctttttttggtgtaccctttgcag

upper sequence: LOC_Os01g04814.3 (Oryza sativa), 5'ss of exon 6
lower sequence: PP1S76_197V6.1 (Physcomitrella patens), 5'ss of exon 6
GTCCATCTCGGGGATACACCACACAACTTAAATGAAAGTGATTTTGAGAACTTGGCTCGTCGAACAGACGGGTTTTCTGGTTCGGATATTGCTGTTTGTgtaagttgttttctgcaacattc-tcatgtatc---catgctctgttagcatatactgaaatctcgttgctcttttttctttcaacag------------
|| ||| | || ||||| ||| ||||| | | |||| |||||| |||| |  ||||| |    || || |||||||| || ||||||||||| ||||||||||||||||  |||   | ||  |||  |  |   |||  || | |  || | ||   ||     || | |     |    ||  ||            
GTGCATTTGGGAGATACGCCAAACAACCTGACTGAACGTGATTATGAGGATCTGGCTAGGAAGACTGATGGGTTTTCAGGCTCGGATATTGCAGTTTGTgtaagttgttacctgtctctttaatcacatcactatcatcatcggctctcagaaacatgaagtgttttacacgaagataacacagtagaaactgttcggt

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|58588483|gb|CF986791.1|CF986791
EST:     GCTTGGGTCGTCGAACAGACGGGTTTTCTGGTTCGGATATTGCTGTTTGT                         GTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTC
genomic: ACTTGGCTCGTCGAACAGACGGGTTTTCTGGTTCGGATATTGCTGTTTGTgtaagttgtt ... ctttcaacagGTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTC
EST: gi|58687600|gb|CK076287.1|CK076287
EST:     GCTTGGCTCGTCGAACAGACGGGTTTTCTGGTTCGGATATTGCTGTTTGT                         GTAAAGGATGTGTTATTTGAACCTGTCCGCCAAACACAGGATGCCATGTTC
genomic: ACTTGGCTCGTCGAACAGACGGGTTTTCTGGTTCGGATATTGCTGTTTGTgtaagttgtt ... ctttcaacagGTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTC
EST: gi|9865194|gb|AU100944.1|AU100944
EST:     NCTTGGCTCGTCGAACAGACGGGTTTTCTGGTTCGGATATTGCTGTTTGT                         GTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTC
genomic: ACTTGGCTCGTCGAACAGACGGGTTTTCTGGTTCGGATATTGCTGTTTGTgtaagttgtt ... ctttcaacagGTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTC
EST: gi|29642909|gb|CB647916.1|CB647916
EST:     ACTTGGCTCGTCGAACAGACGGGTTTTCTGGTTCGGATATTGCTGTTTGT                         GTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTC
genomic: ACTTGGCTCGTCGAACAGACGGGTTTTCTGGTTCGGATATTGCTGTTTGTgtaagttgtt ... ctttcaacagGTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTC
EST: gi|29660448|gb|CB656723.1|CB656723
EST:     ACTTGGCTCGTCGAACAGACGGGTTTTCTGGTTCGGATATTGCTGTTTGT                         GTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTC
genomic: ACTTGGCTCGTCGAACAGACGGGTTTTCTGGTTCGGATATTGCTGTTTGTgtaagttgtt ... ctttcaacagGTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTC
EST: gi|29619358|gb|CB624370.1|CB624370
EST:     GCTTGGCTCGTCGAACAGACGGGTTTTCTGGTTCGGATATTGCTGTTTGT                         GTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTC
genomic: ACTTGGCTCGTCGAACAGACGGGTTTTCTGGTTCGGATATTGCTGTTTGTgtaagttgtt ... ctttcaacagGTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTC
EST: gi|29619357|gb|CB624369.1|CB624369
EST:     GCTTGGCTCGTCGAACAGACGGGTTTTCTGGTTCGGATATTGCTGTTTGT                         GTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTC
genomic: ACTTGGCTCGTCGAACAGACGGGTTTTCTGGTTCGGATATTGCTGTTTGTgtaagttgtt ... ctttcaacagGTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTC
EST: gi|300215967|gb|HO088593.1|HO088593
EST:     GCTTGGCTCGTCGAACAGACGGGTTTTCTGGTTCGGATATTGCTGTTTGT                         GTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTC
genomic: ACTTGGCTCGTCGAACAGACGGGTTTTCTGGTTCGGATATTGCTGTTTGTgtaagttgtt ... ctttcaacagGTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTC
EST: gi|29625991|gb|CB631002.1|CB631002
EST:     GCTTGGCTCGTCGAACAGACGGGTTTTCTGGTTCGGATATTGCTGTTTGT                         GTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTC
genomic: ACTTGGCTCGTCGAACAGACGGGTTTTCTGGTTCGGATATTGCTGTTTGTgtaagttgtt ... ctttcaacagGTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTC
EST: gi|58600304|gb|CK010832.1|CK010832
EST:     GCTTGGCTCGTCGAACAGACGGGTTTTCTGGTTCGGATATTGCTGTTTGT                         GTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTC
genomic: ACTTGGCTCGTCGAACAGACGGGTTTTCTGGTTCGGATATTGCTGTTTGTgtaagttgtt ... ctttcaacagGTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTC
EST: gi|29627907|gb|CB632918.1|CB632918
EST:     GCTTGGCTCGTCGAACAGACGGGTTTTCTGGTTCGGATATTGCTGTTTGT                         GTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTC
genomic: ACTTGGCTCGTCGAACAGACGGGTTTTCTGGTTCGGATATTGCTGTTTGTgtaagttgtt ... ctttcaacagGTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTC
EST: gi|88844615|gb|CI021190.1|CI021190
EST:     ACTTGGCTCGTCGAACAGACGGGTTTTCTGGTTCGGATATTGCTGTTTGT                         GTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTC
genomic: ACTTGGCTCGTCGAACAGACGGGTTTTCTGGTTCGGATATTGCTGTTTGTgtaagttgtt ... ctttcaacagGTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTC
EST: gi|29640679|gb|CB645688.1|CB645688
EST:     ACTTGGCTCGTCGAACAGACGGGTTTTCTGGTTCGGATATTGCTGTTTGT                         GTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTC
genomic: ACTTGGCTCGTCGAACAGACGGGTTTTCTGGTTCGGATATTGCTGTTTGTgtaagttgtt ... ctttcaacagGTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTC
EST: gi|29643243|gb|CB648250.1|CB648250
EST:     ACTTGGCTCGTCGAACAGACGGGTTTTCTGGTTCGGATATTGCTGTTTGT                         GTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTC
genomic: ACTTGGCTCGTCGAACAGACGGGTTTTCTGGTTCGGATATTGCTGTTTGTgtaagttgtt ... ctttcaacagGTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTC
EST: gi|29676832|gb|CB673107.1|CB673107
EST:     ACTTGGCTCGTCGAACAGACGGGTTTTCTGGTTCGGATATTGCTGTTTGT                         GTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTC
genomic: ACTTGGCTCGTCGAACAGACGGGTTTTCTGGTTCGGATATTGCTGTTTGTgtaagttgtt ... ctttcaacagGTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTC
EST: gi|396941489|gb|HO188698.1|HO188698
EST:     ACTTGGCTCGTCGAACAGACGGGTTTTCTGGTTCGGATATTGCTGTTTGT                         GTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTC
genomic: ACTTGGCTCGTCGAACAGACGGGTTTTCTGGTTCGGATATTGCTGTTTGTgtaagttgtt ... ctttcaacagGTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTC
EST: gi|58588110|gb|CF986418.1|CF986418
EST:     CTTGGCTCGTCGAACAGACGGGTTTTCTGGTGGCGGATATTGCTGTTTGT                         GTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTC
genomic: CTTGGCTCGTCGAACAGACGGGTTTTCTGGTT-CGGATATTGCTGTTTGTgtaagttgtt ... ctttcaacagGTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTC
EST: gi|313080751|gb|HO213548.1|HO213548
EST:     GCTTGGCTCGTCGAACAGACGGGTTTTCTGGTTCGGATATTGCTGTTTGT                         GTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTC
genomic: ACTTGGCTCGTCGAACAGACGGGTTTTCTGGTTCGGATATTGCTGTTTGTgtaagttgtt ... ctttcaacagGTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTC

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), 66 (downstream exon)
Score: 55

GTCCATCTCGGGGATACACCACACAACTTAAATGAAAGTGATTTTGAGAACTTGGCTCGTCGAACAGACGGGTTTTCTGGTTCGGATATTGCTGTTTGTgtaagttgtt ... ctttcaacagGTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTCTTCTTTAAGGCTGATGGTGATATGTGGATGCCTTGTGGACCAAAGCAAT




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCCATCTCGGGGATACACCACACAACTTAAATGAAAGTGATTTTGAGAACTTGGCTCGTCGAACAGACGGGTTTTCTGGTTCGGATATTGCTGTTTGTgtaagttgttttctgcaacattctcatgtatccatgctctgttagcatatactgaaatctcgttgctcttttttctttcaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT