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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGGGGTTGGATGCACGTCTTCGGGAGATCCGGAGTTATCTTGACCTTGTAATCGAAGGAAAGCTCCCTCTAAACCATGAGATTTTATACCATCTACAGgttagaactatatttccgtttcgtgttctgaattttacaaattatggagaaactatttgacaatgtccaaacctatgtgttttgcgctctttaaaatattctagtcactgtctctgctgttggttgatttcgtctaatgaaatatattctcgtaaaatcgacag

Basic information

species Arabidopsis thaliana
transcript AT5G05780.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G05780.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G368908_T02 (Zea mays), 5'ss of exon 7
GAAGGGGTTGGATGCACGTCTTCGGGAGATCCGGAGTTATCTTGACCTTGTAATCGAAGGAAAGCTCCCTCTAAACCATGAGATTTTATACCATCTACAGgttagaactatatttccgtttcgtgttctgaattttacaaattatggagaaactatttgacaat-gtccaaacctatgtgttttgcgctctttaaaatattctagtcactgtctctgctgttggttgatttcgtctaatgaaatatattctcgtaaaatcgacag
||||||  | |||||| | ||  |||||||||| || ||| | || |||||||| ||||| |||||||| || || ||||||||||| || ||| | ||||||||  |     || |  || ||        | ||||       | |  ||||||     ||  |   |||  ||   | ||||     |||  | || | | |                                                            
GAAGGGACTAGATGCAAGGCTCAGGGAGATCCGAAGCTATTTGGATCTTGTAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTATCATTTGCAGgttagtccctctcttgcaatttgt----caggtgttactctcgtggaatgaactatgcagtaaaagctgaaatataccagctttgt-tagtttgcagtagtattg------------------------------------------------------------

upper sequence: AT5G05780.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA11G34980.1 (Glycine max), 5'ss of exon 7
GAAGGGGTTGGATGCACGTCTTCGGGAGATCCGGAGTTATCTTGACCTTGTAATCGAAGGAAAGCTCCCTCTAAACCATGAGATTTTATACCATCTACAGgttaga--actatatttccgtttcgt--gttctgaattttacaaattatggagaaactatttgacaatgtccaaacctatgtgttttgcgctctttaaaatattctagtcactgtctctgctgttggttgatttcgtctaatgaaatatattctcgtaaaatcgacag
|||||| ||||||||| | |||   |||||| ||||||| ||||||||||| || || |||||||| ||  |||||||||||||  | |||||||| |||||| |   |  |||||   | || ||   | |||| | ||     || |    ||    ||    ||| |  |    || || ||||  |||  |  | || |                                                                 
GAAGGGTTTGGATGCAAGACTTAAAGAGATCAGGAGTTACCTTGACCTTGTTATTGATGGAAAGCTTCCATTAAACCATGAGATCCTGTACCATCTGCAGgtttgtttatcatattcttgcttagtaaatgctgattatttggctttgttatcaattggttcttgaatcttga---ttaagtattttctgctggtccacattt-----------------------------------------------------------------

upper sequence: AT5G05780.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA18G03360.1 (Glycine max), 5'ss of exon 7
GAAGGGGTTGGATGCACGTCTTCGGGAGATCCGGAGTTATCTTGACCTTGTAATCGAAGGAAAGCTCCCTCTAAACCATGAGATTTTATACCATCTACAGgttagaactatatttccgtttcgtgttctgaattttacaaattatggagaaactatttgacaatgtccaaacctatgtgttttgcgctctttaaaatattctagtcactgtctctgctgttggttgatttcgtctaatgaaatatattctcgtaaaatcgacag
|||||| ||||||||| | |||   |||||| || |||| ||||||||||| || || |||||||| ||  |||||||||||||  | |||||||| ||||||       | ||||    || | ||||    ||   ||||  ||     | |||||| |  |||    | | ||  ||| |    |||| |        ||   | |   ||||||| |   | |||                                   
GAAGGGTTTGGATGCAAGACTTAAAGAGATCAGGGGTTACCTTGACCTTGTTATTGATGGAAAGCTTCCATTAAACCATGAGATCCTGTACCATCTGCAGgtt-------tgtttc----tcatattcttg-cttagtaaatgctg-----attatttggctttgtt---atcaattggttcttgaatcttga-------ttaagtatt--ttctgctggtccataatt-----------------------------------

upper sequence: AT5G05780.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: Vv08s0007g01980.t01 (Vitis vinifera), 5'ss of exon 7
GAAGGGGTTGGATGCACGTCTTCGGGAGATCCGGAGTTATCTTGACCTTGTAATCGAAGGAAAGCTCCCTCTAAACCATGAGATTTTATACCATCTACAGgttagaactatatttccgtttcgtgt-tctgaattttacaaat--tatggagaaactatttgacaatgtccaaacctatgtgttttgcgctctttaaaatattctagtcactgtctctgctgttggttgatttcgtctaatgaaatatattctcgtaaaatcgacag
|||||| ||||||||||| ||  | || || ||  |||||||||| |||||  | || |||||||| |||||||| ||||||||| | |||||||| |||||      |   |      || ||   | ||  |  |||  ||   ||    |  ||||||   |    ||      |  | | ||||  ||| |  | |                                                                   
GAAGGGTTTGGATGCACGACTGAGAGAAATACGTGGTTATCTTGATCTTGTGGTTGATGGAAAGCTTCCTCTAAATCATGAGATTCTTTACCATCTCCAGgtagagtttgcttcatttatttgtacatttgcgtcctactgatgtcattagaatcctattttggagctaccttgatcacatatcttgctttctctgtatt-------------------------------------------------------------------

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|164186048|gb|ES012184.1|ES012184
EST:     TAATCGAAGGAAAGCTCCCTCTAAACCATGAGATTTTATACCATCTACAG                         GACGTTTTCAACTTGCTTCCTAACCTGAATGTGAACGA
genomic: TAATCGAAGGAAAGCTCCCTCTAAACCATGAGATTTTATACCATCTACAGgttagaacta ... aaatcgacagGACGTTTTCAACTTGCTTCCTAACCTGAATGTGAACGA
EST: gi|164148049|gb|ES032853.1|ES032853
EST:     TTTTATACCATCTACAG                         GACGTTTTCAACTTGCTTCCTAACCTGAATGTGAACGAGTTGGTCAAGGCC
genomic: TTTTATACCATCTACAGgttagaacta ... aaatcgacagGACGTTTTCAACTTGCTTCCTAACCTGAATGTGAACGAGTTGGTCAAGGCC
EST: gi|124977862|gb|EL051137.1|EL051137
EST:     CCCTCTAAACCATGAGATTTTATACCATCTACAG                         GACGTTTTCAACTTGCTTCCTAACCTGAATGTGAACGAGTTGGTCAAGGCC
genomic: CCCTCTAAACCATGAGATTTTATACCATCTACAGgttagaacta ... aaatcgacagGACGTTTTCAACTTGCTTCCTAACCTGAATGTGAACGAGTTGGTCAAGGCC
EST: gi|124877863|gb|EH957300.1|EH957300
EST:     TAATCGAAGGAAAGCTCCCTCTAAACCATGAGATTTTATACCATCTACAG                         GACGTTTTCAACTTGCTTCCTAACCTGAATGTGAA
genomic: TAATCGAAGGAAAGCTCCCTCTAAACCATGAGATTTTATACCATCTACAGgttagaacta ... aaatcgacagGACGTTTTCAACTTGCTTCCTAACCTGAATGTGAA
EST: gi|86079670|gb|DR375427.1|DR375427
EST:     TAATCGAAGGAAAGCTCCCTCTAAACCATGAGATTTTATACCATCTACAG                         GACGTTTTCAACTTGCTTCCTAACCTGAATGTGAACGAGTTGGTCAAGGCC
genomic: TAATCGAAGGAAAGCTCCCTCTAAACCATGAGATTTTATACCATCTACAGgttagaacta ... aaatcgacagGACGTTTTCAACTTGCTTCCTAACCTGAATGTGAACGAGTTGGTCAAGGCC
EST: gi|124983346|gb|EL056084.1|EL056084
EST:     TAATCGAAGGAAAGCTCCCTCTAAACCANGAGATTTTATACCATCTACAG                         GACGTTTTCAACTTGCTTCCTAACCTGAATGTGAACGAGTTGGTCAAGGCC
genomic: TAATCGAAGGAAAGCTCCCTCTAAACCATGAGATTTTATACCATCTACAGgttagaacta ... aaatcgacagGACGTTTTCAACTTGCTTCCTAACCTGAATGTGAACGAGTTGGTCAAGGCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGGGGTTGGATGCACGTCTTCGGGAGATCCGGAGTTATCTTGACCTTGTAATCGAAGGAAAGCTCCCTCTAAACCATGAGATTTTATACCATCTACAGgttagaactatatttccgtttcgtgttctgaattttacaaattatggagaaactatttgacaatgtccaaacctatgtgttttgcgctctttaaaatattctagtcactgtctctgctgttggttgatttcgtctaatgaaatatattctcgtaaaatcgacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA