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

AACTGTTCCTACAGATAATTCCGTCGACCTCCTCACCAATGACATTGGCGTTGTTGTTGTTTCAGATGAAAATGGGGAACCACAGGGTTTCAATATTTATgtaagttgacactcatttagcctaatgtgctattatatatatttagtgtcaggcttgtttgcccgccttttctttcagtattctttttctggatactttcttggttttaaactaatgatgataatgactcatcttgtag

Basic information

species Arabidopsis thaliana
transcript AT5G04590.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G04590.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os05g42350.1 (Oryza sativa), 5'ss of exon 2
AACTGTTCCTACAGATAATTCCGTCGACCTCCTCACCAATGACATTGGCGTTGTTGTTGTTTCAGATGAAAATGGGGAACCACAGGGTTTCAATATTTATgtaagttgacactcatttagcctaatgtgctattatatatatttagtgtcaggcttgtttgcccgccttttctttcagtattctttttctggatactttcttggttttaaactaatgatgataatgactcatcttgtag
 |||||  ||  |||||| || || ||  | || ||||||||||| || ||||||||||||||||||      || || ||    || ||||| ||||||||||           | |   | ||||  ||||| ||||| |||||   |   |||  | |      | || |||   |||      ||||    | || |  |                                   
CACTGTCGCTGGAGATAACTCTGTTGATATTCTGACCAATGACATCGGTGTTGTTGTTGTTTCAGATAGTGCAGGAGAGCCTGTTGGCTTCAACATTTATgtaa---------tgtcttaacaaatgccctatt-tatatttttagcagctttcttaatcgtagatttcttatttagttatc-----tctgacctccttttcag-----------------------------------

upper sequence: AT5G04590.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G090338_T01 (Zea mays), 5'ss of exon 2
AACTGTTCCTACAGATAATTCCGTCGACCTCCTCACCAATGACATTGGCGTTGTTGTTGTTTCAGATGAAAATGGGGAACCACAGGGTTTCAATATTTATgtaagt----tgacactcattt--agcctaatgtgctattatatatatttagt-gt-caggcttgtttgcccgccttttctttcagtattctttttctggatactttcttggttttaaactaatgatgataatgactcatcttgtag
 || |   ||   ||||| || || ||  | || ||||||||||| || ||||||||||||||||||||    || |||||    || || || || ||||||||     ||| |  ||||   | |||  | |||  ||  |||  |||  | || || | || |||   |     |  ||| | ||  || ||| |                                                 
TACCGCGGCTGGTGATAACTCTGTTGATATTCTGACCAATGACATCGGTGTTGTTGTTGTTTCAGATGATGCAGGAGAACCTATTGGCTTTAACATCTATgtaagacctatgaaaaacattctgaacctgctctgcctttgcataactttgtttgtacatgtttatttattctataatgtttttactaccctatttttcag----------------------------------------------
















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|164068474|gb|EL998050.1|EL998050
EST:     GGGTTTCAATATTTAT                         GTTGGTGGGGGTATGGGAAGAACACACAGAATGGAGTCTACTTT-GCCCGC
genomic: GGGTTTCAATATTTATgtaagttgac ... catcttgtagGTTGGTGGGGGTATGGGAAGAACACACAGAATGGAGTCTACTTTTGCCCGC
EST: gi|124947352|gb|EL023197.1|EL023197
EST:     GTTGTTGTTTCAGATGAAAATGGGGAACCACAGGGTTTCAATATTTAT                         GTTGGTGGGGGTATGGGAAGAACACACAGAATGGAGTCTA
genomic: GTTGTTGTTTCAGATGAAAATGGGGAACCACAGGGTTTCAATATTTATgtaagttgac ... catcttgtagGTTGGTGGGGGTATGGGAAGAACACACAGAATGGAGTCTA
EST: gi|125271746|gb|EL285831.1|EL285831
EST:     TTTCAATATTTAT                         GTTGGTGGGGGTATGGGAAGAACACACAGAATGGAGTCTACTTTTGCCCGC
genomic: TTTCAATATTTATgtaagttgac ... catcttgtagGTTGGTGGGGGTATGGGAAGAACACACAGAATGGAGTCTACTTTTGCCCGC
EST: gi|124866389|gb|EH950826.1|EH950826
EST:     TTGTTGTTGTTTCAGATGAAAATGGGGAACCACAGGGTTTCAATGTTTAT                         GTTGGTGGGGGTATGGGAAGAACACAACAGAATGGAGTCTACTTTTGCCCG
genomic: TTGTTGTTGTTTCAGATGAAAATGGGGAACCACAGGGTTTCAATATTTATgtaagttgac ... catcttgtagGTTGGTGGGGGTATGGGAAGAACACA-CAGAATGGAGTCTACTTTTGCCCG
EST: gi|164029821|gb|ES088571.1|ES088571
EST:     GGGTTTCAATATTTAT                         GTTGGTGGGGGTATGGGAAGAACACACAGAATGGAGTCTACTTTTGCCCGC
genomic: GGGTTTCAATATTTATgtaagttgac ... catcttgtagGTTGGTGGGGGTATGGGAAGAACACACAGAATGGAGTCTACTTTTGCCCGC
EST: gi|125187270|gb|EL202224.1|EL202224
EST:     TTGTTGTTGTTTCAGATGAAAATGGGGAACCACAGGGTTTCAATGTTTAT                         GTTGGTGGGGGTATGGGAAGAACACACAGAATGGAGTCTACTTTTGCCCGC
genomic: TTGTTGTTGTTTCAGATGAAAATGGGGAACCACAGGGTTTCAATATTTATgtaagttgac ... catcttgtagGTTGGTGGGGGTATGGGAAGAACACACAGAATGGAGTCTACTTTTGCCCGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACTGTTCCTACAGATAATTCCGTCGACCTCCTCACCAATGACATTGGCGTTGTTGTTGTTTCAGATGAAAATGGGGAACCACAGGGTTTCAATATTTATgtaagttgacactcatttagcctaatgtgctattatatatatttagtgtcaggcttgtttgcccgccttttctttcagtattctttttctggatactttcttggttttaaactaatgatgataatgactcatcttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG