Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTCTTCATTGTTGACCTGAAGGCCAGCAAGAAGCAGATCAAGGACGCCGTGTCGCGCATGTACGACGTGCAGACCAAGAAGGTCAACACCCTCATCCGgtgcgtgcgtgcgagcgggcgggcgggcgggcgggcgtggatggtggcacgcagcggcatggcgggcgggcggccggttggggcgctggccggcggctga...

Basic information

species Chlamydomonas reinhardtii
transcript EDP01709
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDP01709 (Chlamydomonas reinhardtii), 5'ss of exon 3
lower sequence: LOC_Os04g42270.1 (Oryza sativa), 5'ss of exon 3
TGGTCTTCATTGTTGACCTGAAGGCCAGCAAGAAGCAGATCAAGGACGCCGTGTCGCGCATGTACGACGTGCAGACCAAGAAGGTCAACACCCTCATCCGgtgcgtgcgtgcgagcgggcgggcgggcgggcgggcgtggatggtggcacgcagcggcatggcgggcgggcggccggttggggcgctggccggcggctga
||||||||||||||||||| |||||   ||||||| |||||||||  || ||   |   ||||||||| | ||| | ||||| || ||||| || ||| |||  |  | | |   |   |   |       ||  | ||  |  ||  | | || |   | |    | | |  ||   | |    |  |           
TGGTCTTCATTGTTGACCTTAAGGCTGACAAGAAGAAGATCAAGGCTGCTGTCAAGAAGATGTACGACATCCAGGCAAAGAAAGTGAACACTCTGATCAGgttagcactttccttcatactt-cattttatcg--cttgatt--tgctaggtagtg---tagttaactgac--cctacttgtcttccag-----------

upper sequence: EDP01709 (Chlamydomonas reinhardtii), 5'ss of exon 3
lower sequence: GRMZM2G083253_T04 (Zea mays), 5'ss of exon 3
TGGTCTTCATTGTTGACCTGAAGGCCAGCAAGAAGCAGATCAAGGACGCCGTGTCGCGCATGTACGACGTGCAGACCAAGAAGGTCAACACCCTCATCCGgtgcgtgcgtgcgagcgggcgggcgggcgggcgggcgtggatggtggcacgcagcggcatggcgggcgggcggccggttggggcgctggccggcggctga
||||||||||||||||||| |||||   ||||||| |||||||||  |||||   |   ||||| ||| | ||| | ||||||||||||||| | ||| |||  |  | |||    | |                  |  ||  ||    ||| |   |  |           |  ||  | ||                
TGGTCTTCATTGTTGACCTCAAGGCAGACAAGAAGAAGATCAAGGCTGCCGTCAAGAAGATGTATGACATCCAGGCAAAGAAGGTCAACACCTTGATCAGgttagcacttgccccagtgtaattttttcctgcacgatttattatgttgtgcaactaaagagttattct-tatcgtgtctgtgcag--------------

upper sequence: EDP01709 (Chlamydomonas reinhardtii), 5'ss of exon 3
lower sequence: PP1S47_274V6.1 (Physcomitrella patens), 5'ss of exon 1
TGGTCTTCATTGTTGACCTGAAGGCCAGCAAGAAGCAGATCAAGGACGCCGTGTCGCGCATGTACGACGTGCAGACCAAGAAGGTCAACACCCTCATCCGgtgcgtgcgtgcgagcgggcgggcgggcgggcgggcgtggatggtggcacgcagcggcatggcgggcgggcggccggttggggcgctggccggcggctga-
|||| ||||| || ||| ||   ||   ||||||| |||||||| | || |||  |   ||||||||| | ||||||||||||||||||||  | ||| ||||  ||    |      |  ||          |  |||  |   ||    | |     | |    |  |        | ||| ||  |     | |    
TGGTGTTCATCGTGGACGTGCGTGCGGACAAGAAGAAGATCAAGCAGGCTGTGAAGAAAATGTACGACATCCAGACCAAGAAGGTCAACACATTGATCAGgtgattgtcctcctctctgttgggatttccttcgaagtgccttagggttttc-gaactgttgtctccttgtaattacgtcgggtgcctgtttcagtcccgg

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|9027899|gb|BE237939.1|BE237939
EST:     GTGTCGCGCATGTACGACGTGCAGACCAAGAAGGTCAACACCCTCATCCG                         CCCCGACGGCCAGAAGAAGGCGTACGTCTGCCTCACCGCGGACTACGACGC
genomic: GTGTCGCGCATGTACGACGTGCAGACCAAGAAGGTCAACACCCTCATCCGgtgcgtgcgt ... ccgcgcgcagCCCCGACGGCCAGAAGAAGGCGTACGTCTGCCTCACCGCGGACTACGACGC
EST: gi|34983333|gb|CF557250.1|CF557250
EST:     GTGTCGCGCATGTACGACGTGCAGACCAAGAAGGTCAACACCCTCATCCG                         CCCCGACGGCCAGAAGAAGGCGTACGTCTGCCTCACCGCGGACTACGACGC
genomic: GTGTCGCGCATGTACGACGTGCAGACCAAGAAGGTCAACACCCTCATCCGgtgcgtgcgt ... ccgcgcgcagCCCCGACGGCCAGAAGAAGGCGTACGTCTGCCTCACCGCGGACTACGACGC
EST: gi|6551450|gb|AV397234.1|AV397234
EST:     GTGTCGCGCATGTACGACGTGCAGACCAAGAAGGTCAACACCCTCATCCG                         CCCCGACGGCCAGAAGAAGGCGTACGTCTGCCTCACCGCGGACTACGACGC
genomic: GTGTCGCGCATGTACGACGTGCAGACCAAGAAGGTCAACACCCTCATCCGgtgcgtgcgt ... ccgcgcgcagCCCCGACGGCCAGAAGAAGGCGTACGTCTGCCTCACCGCGGACTACGACGC
EST: gi|34992723|gb|CF566640.1|CF566640
EST:     GTGTCGCGCATGTACGACGTGCAGACCAAGAAGGTCAACACCCTCATCCG                         CCCCGACGGCCAGAAGAAGGCGTACGTCTGCCTCACCGCGGACTACGACGC
genomic: GTGTCGCGCATGTACGACGTGCAGACCAAGAAGGTCAACACCCTCATCCGgtgcgtgcgt ... ccgcgcgcagCCCCGACGGCCAGAAGAAGGCGTACGTCTGCCTCACCGCGGACTACGACGC
EST: gi|6547622|gb|AV393406.1|AV393406
EST:     GTGTCGCGCATGTACGACGTGCAGACCAAGAAGGTCAACACCCTCATCCG                         CCCCGACGGCCAGAAGAAGGCGTACGTCTGCCTCACCGCGGACTACGACGC
genomic: GTGTCGCGCATGTACGACGTGCAGACCAAGAAGGTCAACACCCTCATCCGgtgcgtgcgt ... ccgcgcgcagCCCCGACGGCCAGAAGAAGGCGTACGTCTGCCTCACCGCGGACTACGACGC
EST: gi|34987787|gb|CF561704.1|CF561704
EST:     GTGTCGCGCATGTACGACGTGCAGACCAAGAAAGTCAACACCCTCATCCG                         CCCCGACGGCCAGAAGAAGGCGTACGTCTGCCTCACCGCGGACTACGACGC
genomic: GTGTCGCGCATGTACGACGTGCAGACCAAGAAGGTCAACACCCTCATCCGgtgcgtgcgt ... ccgcgcgcagCCCCGACGGCCAGAAGAAGGCGTACGTCTGCCTCACCGCGGACTACGACGC
EST: gi|6548274|gb|AV394058.1|AV394058
EST:     GTGTCGCGCATGTACGACGTGCAGACCAAGAAGGTCAACACCCTCATCCG                         CCCCGACGGCCAGAAGAAGGCGTACGTCTGCCTCACCGCGGACTACGACGC
genomic: GTGTCGCGCATGTACGACGTGCAGACCAAGAAGGTCAACACCCTCATCCGgtgcgtgcgt ... ccgcgcgcagCCCCGACGGCCAGAAGAAGGCGTACGTCTGCCTCACCGCGGACTACGACGC
EST: gi|34982003|gb|CF555920.1|CF555920
EST:     GTGTCGCGCATGTACGACGTGCAGACCAAGAAGGTCAACACCCTCATCCG                         CCCCGACGGCCAGAAGAAGGCGTACGTCTGCCTCACCGCGGACTACGACGC
genomic: GTGTCGCGCATGTACGACGTGCAGACCAAGAAGGTCAACACCCTCATCCGgtgcgtgcgt ... ccgcgcgcagCCCCGACGGCCAGAAGAAGGCGTACGTCTGCCTCACCGCGGACTACGACGC
EST: gi|6547672|gb|AV393456.1|AV393456
EST:     GTGTCGCGCATGTACGACGTGCAGACCAAGAAGGTCAACACCCTCATCCG                         CCCCGACGGCCAGAAGAAGGCGTACGTCTGCCTCACCGCGGACTACGACGC
genomic: GTGTCGCGCATGTACGACGTGCAGACCAAGAAGGTCAACACCCTCATCCGgtgcgtgcgt ... ccgcgcgcagCCCCGACGGCCAGAAGAAGGCGTACGTCTGCCTCACCGCGGACTACGACGC
EST: gi|7427134|gb|AW661306.1|AW661306
EST:     GTGTCGCGCATGTACGACGTGCAGACCAAGAAGGTCAACACCCTCATCCG                         TCCCGACGGCCAGAAGAAGGCGTACGTCTGCCTCACC
genomic: GTGTCGCGCATGTACGACGTGCAGACCAAGAAGGTCAACACCCTCATCCGgtgcgtgcgt ... ccgcgcgcagCCCCGACGGCCAGAAGAAGGCGTACGTCTGCCTCACC
EST: gi|6549034|gb|AV394818.1|AV394818
EST:     GTGTCGCGCATGTACGACGTGCAGACCAAGAAGGTCAACACCCTCATCCG                         CCCCGACGGCCAGAAGAAGGCGTACGTCTGCCTCACCGCGGACTACGACGC
genomic: GTGTCGCGCATGTACGACGTGCAGACCAAGAAGGTCAACACCCTCATCCGgtgcgtgcgt ... ccgcgcgcagCCCCGACGGCCAGAAGAAGGCGTACGTCTGCCTCACCGCGGACTACGACGC
EST: gi|34991513|gb|CF565430.1|CF565430
EST:     GTGTCGCGCATGTACGACGTGCAGACCAAGAAGGTCAACACCCTCATCCG                         CCCCGACGGCCAGAAGAAGGCGTACGTCTGCCTCACCGCGGACTACGACGC
genomic: GTGTCGCGCATGTACGACGTGCAGACCAAGAAGGTCAACACCCTCATCCGgtgcgtgcgt ... ccgcgcgcagCCCCGACGGCCAGAAGAAGGCGTACGTCTGCCTCACCGCGGACTACGACGC
EST: gi|34991796|gb|CF565713.1|CF565713
EST:     GTGTCGCGCATGTACGACGTGCAGACCAAGAAGGTCAACACCCTCATCCG                         CCCCGACGGCCAGAAGAAGGCGTACGTCTGCCTCACCGC
genomic: GTGTCGCGCATGTACGACGTGCAGACCAAGAAGGTCAACACCCTCATCCGgtgcgtgcgt ... ccgcgcgcagCCCCGACGGCCAGAAGAAGGCGTACGTCTGCCTCACCGC
EST: gi|34985469|gb|CF559386.1|CF559386
EST:     TGTCGCGCATGTACCGACCTGCACACCAAGAAGGTCAACACCCTCATCCG                         CCCCCGACGGTCACAAGAAGGCGTACGTCTGCCTCACCGCGGACTACGACG
genomic: TGTCGCGCATGTAC-GACGTGCAGACCAAGAAGGTCAACACCCTCATCCGgtgcgtgcgt ... ccgcgcgcagCCCC-GACGGCCAGAAGAAGGCGTACGTCTGCCTCACCGCGGACTACGACG
EST: gi|6549466|gb|AV395250.1|AV395250
EST:     GTGTCGCGCATGTACGACGTGCAGACCAAGAAGGTCAACACCCTCATCCG                         CCCCGACGGCCAGAAGAAGGCGTACGTCTGCCTCACCGCGGACTACGACGC
genomic: GTGTCGCGCATGTACGACGTGCAGACCAAGAAGGTCAACACCCTCATCCGgtgcgtgcgt ... ccgcgcgcagCCCCGACGGCCAGAAGAAGGCGTACGTCTGCCTCACCGCGGACTACGACGC
EST: gi|34994536|gb|CF568453.1|CF568453
EST:     GTGTCGCGCATGTACGACGTGCAGACCAAGAAGGTCAACACCCTCATCCG                         CCCCGACGGCC
genomic: GTGTCGCGCATGTACGACGTGCAGACCAAGAAGGTCAACACCCTCATCCGgtgcgtgcgt ... ccgcgcgcagCCCCGACGGCC
EST: gi|6545394|gb|AV391178.1|AV391178
EST:     GTGTCGCGCATGTACGACGTGCAGACCAAGAAGGTCAACACCCTCATCCG                         CCCCGACGGCCAGAAGAAGGCGTACGTCTGCCTCACCGCGGACTACGACGC
genomic: GTGTCGCGCATGTACGACGTGCAGACCAAGAAGGTCAACACCCTCATCCGgtgcgtgcgt ... ccgcgcgcagCCCCGACGGCCAGAAGAAGGCGTACGTCTGCCTCACCGCGGACTACGACGC
EST: gi|10787303|gb|AV643975.1|AV643975
EST:     GTGTCGCGCATGTACGACGTGCAGACCAAGAAGGTCAACACCCTCATCCG                         CCCCGACGGCCAGAAGAAGGCGTACGTCTGCCTCACCGCGGACTACGACGC
genomic: GTGTCGCGCATGTACGACGTGCAGACCAAGAAGGTCAACACCCTCATCCGgtgcgtgcgt ... ccgcgcgcagCCCCGACGGCCAGAAGAAGGCGTACGTCTGCCTCACCGCGGACTACGACGC
EST: gi|34991855|gb|CF565772.1|CF565772
EST:     GTGTCGCGCATGTACGACGTGCAGACCAAGAAGGTCAACACCCTCATCCG                         CCCCGACGGCCAGAAGAAGGCGTACGTCTGCCTCACCGCGGACTACGACGC
genomic: GTGTCGCGCATGTACGACGTGCAGACCAAGAAGGTCAACACCCTCATCCGgtgcgtgcgt ... ccgcgcgcagCCCCGACGGCCAGAAGAAGGCGTACGTCTGCCTCACCGCGGACTACGACGC
EST: gi|49467236|gb|BP095149.1|BP095149
EST:     GTGTCGCGCATGTACGACGTGCAGACCAAGAAGGTCAACACCCTCATCCG                         CCCCGACGGCC
genomic: GTGTCGCGCATGTACGACGTGCAGACCAAGAAGGTCAACACCCTCATCCGgtgcgtgcgt ... ccgcgcgcagCCCCGACGGCC
EST: gi|6549998|gb|AV395782.1|AV395782
EST:     GTGTCGCGCATGTACGACGTGCAGACCAAGAAGGTCAACACCCTCATCCG                         CCCCGACGGCCAGAAGAAGGCGTACGTCTGCCTCACCGCGGACTACGACGC
genomic: GTGTCGCGCATGTACGACGTGCAGACCAAGAAGGTCAACACCCTCATCCGgtgcgtgcgt ... ccgcgcgcagCCCCGACGGCCAGAAGAAGGCGTACGTCTGCCTCACCGCGGACTACGACGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTCTTCATTGTTGACCTGAAGGCCAGCAAGAAGCAGATCAAGGACGCCGTGTCGCGCATGTACGACGTGCAGACCAAGAAGGTCAACACCCTCATCCGgtgcgtgcgtgcgagcgggcgggcgggcgggcgggcgtggatggtggcacgcagcggcatggcgggcgggcggccggttggggcgctggccggcggctga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcacgca