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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgatgttcttgatattttggcatttaaaacctgcttgcaataattcaatagatctcttcatgattcttatgaattagcatttgcaattgaaattttcagGTCTTCCTTTGCTTCGGAAACTCTGTGGCCTCTACCCGCTTTCTTCTGCAGGATGAATTCAACATCCAGACAACACAATGCGACAATTGCATAATT

Basic information

species Arabidopsis thaliana
transcript AT1G63830.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G63830.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G065696_T01 (Zea mays), 3'ss of exon 5
gtgatgttcttgatattttggcatttaaa-acctgcttgcaataattcaatagatctcttcatgattcttatgaattagcatttgcaattgaaattttcagGTCTTCCTTTGCTTCGGAAACTCTGTGGCCTCTACCCGCTTTCTTCTGCAGGATGAATTCAACATCCAGACAACACAATGCGACAATTGCATAATT
|||| |     |  |      ||  ||   | | ||||    |   ||||| |     | |   ||||   ||  | | ||    |  ||     | |||||| |||   |||||||| ||||| || || || ||||| || || |||||||| || ||||||||||||||||| || |||||||| ||||| || 
gtgacgcctgcgcgacacacacacatagccatcagctttgtctg--tcaatcggataatccgcaattcggttgc-tgaccacgctcccttct--ctctcagGTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCAACCCGGTTCCTGCTGCAGGACGAGTTCAACATCCAGACAACGCAGTGCGACAACTGCATCATC

upper sequence: AT1G63830.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G065696_T02 (Zea mays), 3'ss of exon 5
gtgatgttcttgatattttggcatttaaa-acctgcttgcaataattcaatagatctcttcatgattcttatgaattagcatttgcaattgaaattttcagGTCTTCCTTTGCTTCGGAAACTCTGTGGCCTCTACCCGCTTTCTTCTGCAGGATGAATTCAACATCCAGACAACACAATGCGACAATTGCATAATT----
|||| |     |  |      ||  ||   | | ||||    |   ||||| |     | |   ||||   ||  | | ||    |  ||     | |||||| |||   |||||||| ||||| || || || ||||| || || |||||||| || ||||||||||||||||| || |||||||| ||||| ||     
gtgacgcctgcgcgacacacacacatagccatcagctttgtctg--tcaatcggataatccgcaattcggttgc-tgaccacgctcccttct--ctctcagGTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCAACCCGGTTCCTGCTGCAGGACGAGTTCAACATCCAGACAACGCAGTGCGACAACTGCATCATCGTGC
















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|124748849|gb|EH838979.1|EH838979
EST:     GTGGAAGGTGTGGAGAAAGCAAATGTCCTCAACTTTGCCTTGCCACTGAG                         GTCTTCCTTTGCTTCGGAAACT
genomic: GTGGAAGGTGTGGAGAAAGCAAATGTCCTCAACTTTGCCTTGCCACTGAGgtgagacttc ... aaattttcagGTCTTCCTTTGCTTCGGAAACT
EST: gi|124850068|gb|EH934505.1|EH934505
EST:     CAACTTTGCCTTGCCACTGAG                         GTCTTCCTTTGCTTCGGAAACTCTGTGGCCTCTACCCGCTTTCTTCTGCAG
genomic: CAACTTTGCCTTGCCACTGAGgtgagacttc ... aaattttcagGTCTTCCTTTGCTTCGGAAACTCTGTGGCCTCTACCCGCTTTCTTCTGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaatagatctcttcatgattcttatgaattagcatttgcaattgaaattttcagGTCTTCCTTTGCTTCGGAAACTCTGTGGCCTCTACCCGCTTTCTTCTGCAGGATGAATTCAACATCCAGACAACACAATGCGACAATTGCATAATT
                                                ttttc  CT-rich tract
                  attcttatgaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatgttcttgatattttggcatttaaaacctgcttgcaataattcaatagatctcttcatgattcttatgaattagcatttgcaattgaaattttcagGTCTTCCTTTGCTTCGGAAACTCTGTGGCCTCTACCCGCTTTCTTCTGCAGGATGAATTCAACATCCAGACAACACAATGCGACAATTGCATAATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG