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

gtactcctttcttcttcttcatgtttcgttttgtaatacatttttcttatgattttctgcaattttctttcaatctgtgtcttgttctgggcttttagGTATTTCAACTTCGTATGAACTTCGTCAAGGATGTTAATAAGCACGAGGAGATGTGGGAGAGACAACATGAACTTGCTGCTCATAAAGTTTATTCTATGT

Basic information

species Arabidopsis thaliana
transcript AT4G24810.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G24810.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv17s0000g10260.t01 (Vitis vinifera), 3'ss of exon 1
gtactcctttcttcttcttcatgtttcgttt-tgtaatacatttttcttatgattttctgcaattttctttcaatc-tgtgtcttgttctgggctttt----------agGTATTTCAACTTCGTATGAACTTCGTCAAGGATGTTAATAAGCACGAGGAGATGTGGGAGAGACAACATGAACTTGCTGCTCATAAAGTTTATTCTATGT
    ||||||  | | |   |    || ||| | | ||   | | ||| | ||||   |    | ||  || | |  |   | |  || |||| ||||          |||| |||||||||||  |||  ||||| |||||||| || ||||| ||||| |||||||||   ||||| |||||||| ||| | ||  | ||| ||| ||
---gtccttttctgtgcaaaacaactcttttatctgatttgtctctctgaggattgcattggttatttatttatttatacatgtatttttgggttttttttttggattagGTGTTTCAACTTCGGGTGAGTTTCGTGAAGGATGTGAAGAAGCAGGAGGAAATGTGGGAGGTGCAACACGAACTTGCAGCTGAGAAGATATATGCTACGT
















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|86071123|gb|DR366880.1|DR366880
EST:     TCGTGCCACTGATATCTACACCGGATACAAGGTTTCTCTTTGATTGATGG                         GTATTTCAACTTCGTATGAACTTCGTCAAGGATGNTAATAAGCACGAGGAG
genomic: TCGTGCCACTGATATCTACACCGGATACAAGGTTTCTCTTTGATTGATGGgtactccttt ... gggcttttagGTATTTCAACTTCGTATGAACTTCGTCAAGGATGTTAATAAGCACGAGGAG
EST: gi|86071117|gb|DR366874.1|DR366874
EST:     TCGTGCCACTGATATCTACACCGGATNCAAGGTTTCTCTTTGATTGATGG                         GTATTTCAACTTCGTATGANCTTCGTCAGGGATGTTAATAAGCACGAGGAG
genomic: TCGTGCCACTGATATCTACACCGGATACAAGGTTTCTCTTTGATTGATGGgtactccttt ... gggcttttagGTATTTCAACTTCGTATGAACTTCGTCAAGGATGTTAATAAGCACGAGGAG
EST: gi|86071119|gb|DR366876.1|DR366876
EST:     CGTGCCACTGATATCTACACCGGGATACAAGGGTTCTCTTTGATTGATGG                         GNATTTCAACTTCGTATGAACTTCGTCAAGGATGTTAATAAGCACGAGGAG
genomic: CGTGCCACTGATATCTACACCGG-ATACAAGGTTTCTCTTTGATTGATGGgtactccttt ... gggcttttagGTATTTCAACTTCGTATGAACTTCGTCAAGGATGTTAATAAGCACGAGGAG
EST: gi|86071124|gb|DR366881.1|DR366881
EST:     TCGTGCCACTGATATCTACACCGGATACAAGGTTTCTCTTTGATTGATGG                         GNATTTCAACTTCGTATGAACTTCGTCAAGGATGTTAATAAGCACGAGGAG
genomic: TCGTGCCACTGATATCTACACCGGATACAAGGTTTCTCTTTGATTGATGGgtactccttt ... gggcttttagGTATTTCAACTTCGTATGAACTTCGTCAAGGATGTTAATAAGCACGAGGAG
EST: gi|86071121|gb|DR366878.1|DR366878
EST:     TCGTGCCACTGATATCTACACCGGATACAAGGTTTCTCTTTGATTGATGG                         GTATTTCAACTTCGT-TGAACTTCGTCAAGGATGTTAATAAGCACGAGGAG
genomic: TCGTGCCACTGATATCTACACCGGATACAAGGTTTCTCTTTGATTGATGGgtactccttt ... gggcttttagGTATTTCAACTTCGTATGAACTTCGTCAAGGATGTTAATAAGCACGAGGAG
EST: gi|86071120|gb|DR366877.1|DR366877
EST:     TCGTGCCACTGATATCTACACCGGATACAAGGTTTCTCTTTGATTGATGG                         GTATTTCAACTTCGTATGAACTTCGTCAAGGATGTTAATAAGCACGAGGAG
genomic: TCGTGCCACTGATATCTACACCGGATACAAGGTTTCTCTTTGATTGATGGgtactccttt ... gggcttttagGTATTTCAACTTCGTATGAACTTCGTCAAGGATGTTAATAAGCACGAGGAG
EST: gi|86071122|gb|DR366879.1|DR366879
EST:     TCGTGCCACTGATATCTACACCGGATACAAGGTTTCTCTTTGATTGATGG                         GTATTTCAACTTCGNATGAACTTCNTCNAGGATGTTAATAAGCACGAGGAG
genomic: TCGTGCCACTGATATCTACACCGGATACAAGGTTTCTCTTTGATTGATGGgtactccttt ... gggcttttagGTATTTCAACTTCGTATGAACTTCGTCAAGGATGTTAATAAGCACGAGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttatgattttctgcaattttctttcaatctgtgtcttgttctgggcttttagGTATTTCAACTTCGTATGAACTTCGTCAAGGATGTTAATAAGCACGAGGAGATGTGGGAGAGACAACATGAACTTGCTGCTCATAAAGTTTATTCTATGT
                                                ctttt  CT-rich tract
                 aattttctttcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactcctttcttcttcttcatgtttcgttttgtaatacatttttcttatgattttctgcaattttctttcaatctgtgtcttgttctgggcttttagGTATTTCAACTTCGTATGAACTTCGTCAAGGATGTTAATAAGCACGAGGAGATGTGGGAGAGACAACATGAACTTGCTGCTCATAAAGTTTATTCTATGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT