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

gtgggtcttttttattttgctttcattgtgtgcatcatgatttggtttatttttagtagaccaaaggagatatgatggtttttcattctctacagAGGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGTCTTTTGAATGCCCTGTGTGTACACAGTACTTCAAG

Basic information

species Arabidopsis thaliana
transcript AT1G80230.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G80230.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os06g05080.1 (Oryza sativa), 3'ss of exon 4
--------------------------------------------------------gtgggtcttttttattttgctttcattgtgtgcat-catgatttggtt--tatttttagtagaccaaaggagatatgatggtttttcattctctacagAGGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGTCTTTTGAATGCCCTGTGTGTACACAGTACTTCAAG
                                                        |  |   | || |  |     |||  | |    || |||    |       | |   | ||    |||    | ||     |  || ||  | | ||||||| ||||||||||| || ||||||||| |||||||||||||| |   |||||||||||| || || ||||| |||  |
gtatagtacctgtgcatgctaatttccttgtttttgacctataaagaagcttctaggatgaaatcttctcctgcatcttctctataaatattcatcgactaaccaccaatggaattaacttaaactgcaaattgcaatgattgatatttt-cagAGGACGAGCATGATGTCGTGTGGTTTTGGTTGGAGAAAGGCAAGCCACATGAATGCCCTGTCTGCACTCAGTATTTCTCG

upper sequence: AT1G80230.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os01g42650.1 (Oryza sativa), 3'ss of exon 4
gtgggtcttttttattttgctttcattgtgtgcatcatgatttggtttatttttagtag-accaaaggagatatgatggtttttcattc-tctacagAGGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGTCTTTTGAATGCCCTGTGTGTACACAGTACTTCAAG
||  |||  | ||   |||  |     | |   |   | |  ||    || ||  | |  ||        | ||  |     ||| ||| | |||||||||||||||||||||||| ||||| ||| || | ||||   |  |   ||| ||||| || ||| |||| || ||   |
gtcagtcagtgttgacttggctca---gcgaaaactctaaactgccaaatattatgcaatactggtatcaacattttttcacttctttcatttacagAGGATGAGCATGATGTTGTATGGTTCTGGTTGAAAAAAGATGAACCGCATGAGTGCCCAGTCTGTTCACAATATTTTGTG
















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|86037662|gb|DR333417.1|DR333417
EST:     CAAATCCTACTACGACATGAGAATAGTTGGTTGCCCTGGAGGTGAAGGAG                         AGGATGAGCATGATGTTGTC
genomic: CAAATCCTACTACGACATGAGAATAGTTGGTTGCCCTGGAGGTGAAGGAGgtgggtcttt ... ttctctacagAGGATGAGCATGATGTTGTC
EST: gi|86037651|gb|DR333406.1|DR333406
EST:     CAAATCCTACTACGACATGAGAATAGTTGGTTGCCCTGGAGGTGAAGGAG                         AGGATGAGCATGATGTTGTCTGGTTTTGGCT
genomic: CAAATCCTACTACGACATGAGAATAGTTGGTTGCCCTGGAGGTGAAGGAGgtgggtcttt ... ttctctacagAGGATGAGCATGATGTTGTCTGGTTTTGGCT
EST: gi|164109389|gb|ES189813.1|ES189813
EST:     GCCCTGGAGGTGAAGGAG                         AGGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGTCTTTTG
genomic: GCCCTGGAGGTGAAGGAGgtgggtcttt ... ttctctacagAGGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGTCTTTTG
EST: gi|86037669|gb|DR333424.1|DR333424
EST:     CAAATCCTACTACGACATGAGAATAGTTGGTTGCCCTGGAGGTGAAGGAG                         AGGATGAGCATGATGTTGTCTGGT
genomic: CAAATCCTACTACGACATGAGAATAGTTGGTTGCCCTGGAGGTGAAGGAGgtgggtcttt ... ttctctacagAGGATGAGCATGATGTTGTCTGGT
EST: gi|86037675|gb|DR333430.1|DR333430
EST:     CAAATCCTACTACGACATGAGAATAGTTGGTTGCCCTGGAGGTGAAGGAG                         AGGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGTCTT
genomic: CAAATCCTACTACGACATGAGAATAGTTGGTTGCCCTGGAGGTGAAGGAGgtgggtcttt ... ttctctacagAGGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGTCTT
EST: gi|86037647|gb|DR333402.1|DR333402
EST:     CAAATCCTACTACGACATGAGAATAGTTGGTTGCCCTGGAGGTGAAGGAG                         AGGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAA-GGCAAGTCTTTT
genomic: CAAATCCTACTACGACATGAGAATAGTTGGTTGCCCTGGAGGTGAAGGAGgtgggtcttt ... ttctctacagAGGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGTCTTTT
EST: gi|86037656|gb|DR333411.1|DR333411
EST:     CAAATCCTACTACGACATGAGAATAGTTGGTTGCCCTGGAGGTGA-GGAG                         AGGATGAGCATGATGTTGTCTGGTTTT
genomic: CAAATCCTACTACGACATGAGAATAGTTGGTTGCCCTGGAGGTGAAGGAGgtgggtcttt ... ttctctacagAGGATGAGCATGATGTTGTCTGGTTTT
EST: gi|86037646|gb|DR333401.1|DR333401
EST:     CAAATCCTACTACGACATGAGAATAGTTGGTTGCCCTGGAGGTGAAGGAG                         AGGATGAGCATGATGTTGTCTGG
genomic: CAAATCCTACTACGACATGAGAATAGTTGGTTGCCCTGGAGGTGAAGGAGgtgggtcttt ... ttctctacagAGGATGAGCATGATGTTGTCTGG
EST: gi|86037648|gb|DR333403.1|DR333403
EST:     CAAATCCTACTACGACATGAGAATAGTTGGTTGCCCTGGAGGTGAAGGAG                         AGGATGAGCATGATGTTGTC
genomic: CAAATCCTACTACGACATGAGAATAGTTGGTTGCCCTGGAGGTGAAGGAGgtgggtcttt ... ttctctacagAGGATGAGCATGATGTTGTC
EST: gi|86037661|gb|DR333416.1|DR333416
EST:     CAAATCCTACTACGACATGAGAATAGTTGGTTGCCCTGGAGGTGAAGGAG                         AGGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAAGCAAG
genomic: CAAATCCTACTACGACATGAGAATAGTTGGTTGCCCTGGAGGTGAAGGAGgtgggtcttt ... ttctctacagAGGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAG
EST: gi|86037654|gb|DR333409.1|DR333409
EST:     CAAATCCTACTACGACATGAGAATAGTTGGTTGCCCTGGAGGTGAAGGAG                         AGGATGAGCATGATGTTGTCTGGTTTTG
genomic: CAAATCCTACTACGACATGAGAATAGTTGGTTGCCCTGGAGGTGAAGGAGgtgggtcttt ... ttctctacagAGGATGAGCATGATGTTGTCTGGTTTTG
EST: gi|86037660|gb|DR333415.1|DR333415
EST:     CAAATCCTACTACGACATGAGAATAGTTGGTTGCCCTGGAGGTGA-GGAG                         AGGATGAGCATGATGTTGTCT
genomic: CAAATCCTACTACGACATGAGAATAGTTGGTTGCCCTGGAGGTGAAGGAGgtgggtcttt ... ttctctacagAGGATGAGCATGATGTTGTCT
EST: gi|86037664|gb|DR333419.1|DR333419
EST:     CAAATCCTACTACGACATGAGAATAGTTGGTTGCCCTGGAGGTGAAGGAG                         AGGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGTCTTTTT
genomic: CAAATCCTACTACGACATGAGAATAGTTGGTTGCCCTGGAGGTGAAGGAGgtgggtcttt ... ttctctacagAGGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGTCTTTT-
EST: gi|86037670|gb|DR333425.1|DR333425
EST:     CAAATCCTACTACGACATGAGAATAGTTGGTTGCCCTGGAGGTGAAGGAG                         AGGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAA-GGCAAGTCTTTT
genomic: CAAATCCTACTACGACATGAGAATAGTTGGTTGCCCTGGAGGTGAAGGAGgtgggtcttt ... ttctctacagAGGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGTCTTTT
EST: gi|86037672|gb|DR333427.1|DR333427
EST:     CAAATCCTACTACGACATGAGAATAGTTGGTTGCCCTGGAGGTGAAGGAG                         AGGATGAGCATGATG
genomic: CAAATCCTACTACGACATGAGAATAGTTGGTTGCCCTGGAGGTGAAGGAGgtgggtcttt ... ttctctacagAGGATGAGCATGATG
EST: gi|164022632|gb|ES131657.1|ES131657
EST:     CCTACTACGACATGAGAATAGTTGGTTGCCCTGGAGGTGAAGGAG                         AGGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGTCTTTTG
genomic: CCTACTACGACATGAGAATAGTTGGTTGCCCTGGAGGTGAAGGAGgtgggtcttt ... ttctctacagAGGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGTCTTTTG
EST: gi|86037645|gb|DR333400.1|DR333400
EST:     CAAATCCTACTACGACATGAGAATAGTTGGTTGCCCTGGAGGTGAAGGAG                         AGGATGAGCATGATGTTGTCTG
genomic: CAAATCCTACTACGACATGAGAATAGTTGGTTGCCCTGGAGGTGAAGGAGgtgggtcttt ... ttctctacagAGGATGAGCATGATGTTGTCTG
EST: gi|86037676|gb|DR333431.1|DR333431
EST:     AAATCCTACTACGACATGAGAATAGTTGGTTTGCCCTGGAGGTGAAGGAG                         AGGATGAGCATGATG
genomic: AAATCCTACTACGACATGAGAATAGTTGGTT-GCCCTGGAGGTGAAGGAGgtgggtcttt ... ttctctacagAGGATGAGCATGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttggtttatttttagtagaccaaaggagatatgatggtttttcattctctacagAGGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGTCTTTTGAATGCCCTGTGTGTACACAGTACTTCAAG
                                      tttttcattctctac  CT-rich tract
     tttatttttagtaga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggtcttttttattttgctttcattgtgtgcatcatgatttggtttatttttagtagaccaaaggagatatgatggtttttcattctctacagAGGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGTCTTTTGAATGCCCTGTGTGTACACAGTACTTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA