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

TTCTGCTCCAATTTATACGCAACCTAGATATTTGCCTCCTTCAAAGGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGAGAAGGGTGTGTTATTAAAgtaagaaagccttttcacatgttttctgatgtatttgtatatgttgttttcagaggctttcatatcagaatgcattttgggatcttaatttagtttgtgg...

Basic information

species Zea mays
transcript GRMZM2G106213_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G106213_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os09g12660.2 (Oryza sativa), 5'ss of exon 6
TTCTGCTCCAATTTATACGCAACCTAGATATTTGCCTCCTTCAAAGGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGAGAAGGGTGTGTTATTAAAgtaagaaagccttttcacatgttttctgat-gtatttgtatatgttgttttcagaggctttcatatcagaatgcattttgggatcttaatttagtttgtgg---------------------------------------------------------------------------------
||||||  ||||||||||||||||| |||| |||||||| ||||| ||||||||||||||||||||||||||||||||||| ||||| |||||||||| |||||| |  |||||||| |||  || | || |   ||   | | |  | |   ||   | | | |||| ||  ||| || ||| ||| | ||| |   ||                                                                                  
TTCTGCCGCAATTTATACGCAACCTCGATACTTGCCTCCATCAAAAGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGTTGTGTTATTAGAgtaagtat-ccttttcagatgaattatcatagcgcttccttctatgatctgtggatagtattagatcataa--catattaggaccttgagttattacttgttagtcgaacatttctttttcattgcttcaaaacagagaccctaaatttgttgacatgcctttccccctttattttggctag

upper sequence: GRMZM2G106213_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA02G47460.1 (Glycine max), 5'ss of exon 6
TTCTGCTCCAATTTATACGCAACCTAGATATTTGCCTCCTTCAAAGGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGAGAAGGGTGTGTTATTAAAgtaagaa----agccttttcacatgttttctgatgtatt-tgtatatgttgttttcagaggctttcatatcagaatgcattttgg-gatcttaatttagtttgtgg-----------------------------------
|||  ||||||| || || |||||  ||||||||||||| || ||| | |||||||||||||| || || ||||||||||| ||||| ||||| ||||| ||||| |    ||    ||||||| | | ||||| |  | | || |||   |||  | |    || | |      |  | | |   ||  || ||||| ||| | |                                   
TTCATCTCCAATCTACACCCAACCACGATATTTGCCTCCCTCTAAGATGCTTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAGgtaagtatttcagaaccttcacat-tctactgatctgctctataaatgagatttatacaattcttaacaaagatgtcaaatataatgagattgattta-tttataggaaactaactttgtattccatattttgttccatag

upper sequence: GRMZM2G106213_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA14G01290.1 (Glycine max), 5'ss of exon 6
TTCTGCTCCAATTTATACGCAACCTAGATATTTGCCTCCTTCAAAGGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGAGAAGGGTGTGTTATTAAAgtaagaa----agccttttcacatgttttctgatgtatt-tgtatatgttgttttcagaggctttcatatcagaatgcattttgg-gatcttaatttagtttgtgg-----------------------------------
|||  ||||||| || || |||||  ||||||||||||| || ||| | |||||||||||||| || || ||||||||||| ||||| ||||| ||||| ||||| |    ||    ||||||| | | ||||| |  | |||| |||   |||  | |    || | |      |  | | |   ||  |||||||| ||| | |                                   
TTCATCTCCAATCTACACCCAACCACGATATTTGCCTCCCTCTAAGATGCTTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAGgtaagcatttcagaaccttcacat-tctactgatctgctctgtacatgagatttatacaattcttaacaaagatgtcaaatataatgagattaattta-tttataggaaactaaccttgtattccatactttgtgccatag

upper sequence: GRMZM2G106213_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv12s0057g01480.t01 (Vitis vinifera), 5'ss of exon 6
TTCTGCTCCAATTTATACGCAACCTAGATATTTGCCTCCTTCAAAGGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGAGAAGGGTGTGTTATTAAAgtaagaaagccttttc----acatgttttctgatgtattt----gtatatgt----tgttttcagaggctttcatatcagaatgcattttgggatcttaatttagtttgtgg-----------------------
|||  ||||||| || || |||||| |||||||||| || || ||| | |||||||||||||| || || ||||||||||| || || ||||| ||||| |||||  |  | |       ||| || |  || ||| |||    ||   |||    || ||    |||||||  ||| |   |  ||| ||     |||| | ||||  | |                       
TTCCTCTCCAATCTACACCCAACCTCGATATTTGCCCCCATCTAAGATGCTTGATGCTGATGTAACCGATAGTGTTATTGGTGAGGGCTGTGTGATTAAGgtaagttacacatgggcaagacaggtctcttgctgtgtttcatagttggtgtcacatgcttatgaaggctttt-tataattgttgattatgcag--ttaagtaagttccttgttcacccttttctgtgcatgcag

upper sequence: GRMZM2G106213_T01 (Zea mays), 5'ss of exon 6
lower sequence: PP1S76_105V6.1 (Physcomitrella patens), 5'ss of exon 6
TTCTGCTCCAATTTATACGCAACCTAGATATTTGCCTCCTTCAAAGGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGAGAAGGGTGTGTTATTAAAgtaag-------aaagccttttcacatgt--tttctgat----gtatttgtatatgttgttttcagaggctttcata----tcagaatgcattttggga------tcttaatttagtttgtgg----------------------------------
 ||  |||| ||||| || ||  || |||   | ||||| |||||  |  | || ||||||||||| |||||||||||||||||||| || ||||| || ||| |       | | || |||    ||   |||  |||    | | |     || |    |  |    | || ||     ||    |||    || ||       ||| ||  | ||||||                                   
GTCGTCTCCTATTTACACACAGGCTCGATTCCTTCCTCCATCAAAAATGTTGGACGCTGATGTGACTGACAGTGTTATTGGAGAAGGTTGCGTTATCAAGgtaggttctgcaagaaccctttggtctgaagttttggatcaaggcaatgaataatctcacctcaatgtacatttattcctctctctctgcgccatgcgaagtattccttgatacaatttgtgcttactgattgaaaatatatatctatgatgtacag

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|60337923|gb|DN204896.1|DN204896
EST:     TTGATGCTGATGTGACAGACAGTGTTATTGGAGAAGGGTGTGTTATTAAA                         CATTGCACAATCAATCATTCCGTAGTTGGACTCCGTTCCTGCATTTCTGAA
genomic: TTGATGCTGATGTGACAGACAGTGTTATTGGAGAAGGGTGTGTTATTAAAgtaagaaagc ... ctttcgctagCATTGCACAATCAATCATTCCGTAGTTGGACTCCGTTCCTGCATTTCTGAA
EST: gi|31356186|gb|CD440543.1|CD440543
EST:     TTGATGCTGATGTGACAGACAGTGTTATTGGAGAAGGGTGTGTTATTAAA                         CATTGCACAATCAATCATTCCGTAGTTGGACTCCGTTCCTGCATTTCTGAA
genomic: TTGATGCTGATGTGACAGACAGTGTTATTGGAGAAGGGTGTGTTATTAAAgtaagaaagc ... ctttcgctagCATTGCACAATCAATCATTCCGTAGTTGGACTCCGTTCCTGCATTTCTGAA
EST: gi|31357016|gb|CD441373.1|CD441373
EST:     TTGATGCTGATGTGACAGACAGTGTTATTGGAGAAGGGTGTGTTATTAAA                         CATTGCACAATCAATCATTCCGTAGTTGGACTCCGTTCCTGCATTTCTGAA
genomic: TTGATGCTGATGTGACAGACAGTGTTATTGGAGAAGGGTGTGTTATTAAAgtaagaaagc ... ctttcgctagCATTGCACAATCAATCATTCCGTAGTTGGACTCCGTTCCTGCATTTCTGAA
EST: gi|32929383|gb|CF034195.1|CF034195
EST:     TTGATGCTGATGTGACAGACAGTGTTATTGGAGAAGGGTGTGTTATTAAA                         CATTGCACAATCAATCATTCCGTAGTTGGACTCCGTTCCTGCATTTCTGAA
genomic: TTGATGCTGATGTGACAGACAGTGTTATTGGAGAAGGGTGTGTTATTAAAgtaagaaagc ... ctttcgctagCATTGCACAATCAATCATTCCGTAGTTGGACTCCGTTCCTGCATTTCTGAA
EST: gi|463337|gb|T18304.1|T18304
EST:     TTGATGCTGATGTGACAGACAGTGTTATTGGAGAAGGGTGTGTTATTAAA                         CATTGCACAATCAATCATTCCGTAGTTGGACTCCGTTCCTGCATTTCTGAA
genomic: TTGATGCTGATGTGACAGACAGTGTTATTGGAGAAGGGTGTGTTATTAAAgtaagaaagc ... ctttcgctagCATTGCACAATCAATCATTCCGTAGTTGGACTCCGTTCCTGCATTTCTGAA
EST: gi|32934685|gb|CF039497.1|CF039497
EST:     TTATTGGAGAAGGGTGTGTTATTAAA                         CATTGCACAATCAATCATTCCGTAGTTGGACTCCGTTCCTGCATTTCTGAA
genomic: TTATTGGAGAAGGGTGTGTTATTAAAgtaagaaagc ... ctttcgctagCATTGCACAATCAATCATTCCGTAGTTGGACTCCGTTCCTGCATTTCTGAA
EST: gi|67042108|gb|CO468363.1|CO468363
EST:     TTGATGCTGATGTGACAGACAGTGTTATTGGAGAAGGGTGTGTTATTAAA                         CATTGCACAATCAATCATTCCGTAGTTGGACTCCGTTCCTGCATTTCTGAA
genomic: TTGATGCTGATGTGACAGACAGTGTTATTGGAGAAGGGTGTGTTATTAAAgtaagaaagc ... ctttcgctagCATTGCACAATCAATCATTCCGTAGTTGGACTCCGTTCCTGCATTTCTGAA
EST: gi|211441725|gb|FL406263.1|FL406263
EST:     TTGATGCTGATGTGACAGACAGTGTTATTGGAGAAGGGTGTGTTATTAAA                         CATTGCACAATCAATCATTCCGTAGTTGGACTCCGTTCCTGCATTTCTGAA
genomic: TTGATGCTGATGTGACAGACAGTGTTATTGGAGAAGGGTGTGTTATTAAAgtaagaaagc ... ctttcgctagCATTGCACAATCAATCATTCCGTAGTTGGACTCCGTTCCTGCATTTCTGAA
EST: gi|71301127|gb|DR786596.1|DR786596
EST:     TTGATGCTGATGTGACAGACAGTGTTATTGGAGAAGGGTGTGTTATTAAA                         CATTGCACAATCAATCATTCCGTAGTTGGACTCCGTTCCTGCATTTCTGAA
genomic: TTGATGCTGATGTGACAGACAGTGTTATTGGAGAAGGGTGTGTTATTAAAgtaagaaagc ... ctttcgctagCATTGCACAATCAATCATTCCGTAGTTGGACTCCGTTCCTGCATTTCTGAA
EST: gi|32846616|gb|CD986297.1|CD986297
EST:     ATGCTGATGTGACAGACAGTGTTATTGGAGAAGGGTGTGTTATTAAA                         CATTGCACAATCAATCATTCCGTAGTTGGACTCCGTTCCTGCATTTCTGAA
genomic: ATGCTGATGTGACAGACAGTGTTATTGGAGAAGGGTGTGTTATTAAAgtaagaaagc ... ctttcgctagCATTGCACAATCAATCATTCCGTAGTTGGACTCCGTTCCTGCATTTCTGAA
EST: gi|148950460|gb|EC896030.2|EC896030
EST:     TTGATGCTGATGTGACAGACAGTGTTATTGGAGAAGGGTGTGTTATTAAA                         CATTGCACAATCAATCATTCCGTAGTTGGACTCCGTTCCTGCATTTCTGAA
genomic: TTGATGCTGATGTGACAGACAGTGTTATTGGAGAAGGGTGTGTTATTAAAgtaagaaagc ... ctttcgctagCATTGCACAATCAATCATTCCGTAGTTGGACTCCGTTCCTGCATTTCTGAA
EST: gi|60352415|gb|DN219388.1|DN219388
EST:     GAGAAGGGTGTGTTATTAAA                         CATTGCACAATCAATCATTCCGTAGTTGGACTCCGTTCCTGCATTTCTGAA
genomic: GAGAAGGGTGTGTTATTAAAgtaagaaagc ... ctttcgctagCATTGCACAATCAATCATTCCGTAGTTGGACTCCGTTCCTGCATTTCTGAA
EST: gi|37381963|gb|CF627890.1|CF627890
EST:     GATGCTGATGTGACAGACAGTGTTATTGGAGAAGGGTGTGTTATTAAA                         CATTGCACAATCAATCATTCCGTAGTTGGACTCCGTTCCTGCATTTCTGAA
genomic: GATGCTGATGTGACAGACAGTGTTATTGGAGAAGGGTGTGTTATTAAAgtaagaaagc ... ctttcgctagCATTGCACAATCAATCATTCCGTAGTTGGACTCCGTTCCTGCATTTCTGAA
EST: gi|32856251|gb|CD995932.1|CD995932
EST:     TTGATGCTGATGTGACAGACAGTGTTATTGGAGAAGGGTGTGTTATTAAA                         CATTGCACAATCAATCATTCCGTAGTTGGACTCCGTTCCTGCATTTCTGAA
genomic: TTGATGCTGATGTGACAGACAGTGTTATTGGAGAAGGGTGTGTTATTAAAgtaagaaagc ... ctttcgctagCATTGCACAATCAATCATTCCGTAGTTGGACTCCGTTCCTGCATTTCTGAA
EST: gi|32929486|gb|CF034298.1|CF034298
EST:     TTGATGCTGATGTGACAGACAGTGTTATTGGAGAAGGGTGTGTTATTAAA                         CATTGCACAATCAATCATTCCGTAGTTGGACTCCGTTCCTGCATTTCTGAA
genomic: TTGATGCTGATGTGACAGACAGTGTTATTGGAGAAGGGTGTGTTATTAAAgtaagaaagc ... ctttcgctagCATTGCACAATCAATCATTCCGTAGTTGGACTCCGTTCCTGCATTTCTGAA
EST: gi|211186265|gb|FL114940.1|FL114940
EST:     TTGATGCTGATGTGACAGACAGTGTTATTGGAGAAGGGTGTGTTATTAAA                         CATTGCACAATCAATCATTCCGTAGTTGGACTCCGTTCCTGCATTTCTGAA
genomic: TTGATGCTGATGTGACAGACAGTGTTATTGGAGAAGGGTGTGTTATTAAAgtaagaaagc ... ctttcgctagCATTGCACAATCAATCATTCCGTAGTTGGACTCCGTTCCTGCATTTCTGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCTGCTCCAATTTATACGCAACCTAGATATTTGCCTCCTTCAAAGGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGAGAAGGGTGTGTTATTAAAgtaagaaagccttttcacatgttttctgatgtatttgtatatgttgttttcagaggctttcatatcagaatgcattttgggatcttaatttagtttgtgg

- - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA