Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGAAAATGACGCAGATTATGTTTGAAACCTTCGAATGCCCAGCAATGTATGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTGgtaagatggctgtcgcctcagatatatatagtgatatgcactacaaagatcatacatacatacggcaatcctgacacggtctctttgtcaaatatctctgtgtgcag

Basic information

species Zea mays
transcript GRMZM2G126010_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G126010_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os05g36290.2 (Oryza sativa), 5'ss of exon 3
GAGAAAATGACGCAGATTATGTTTGAAACCTTCGAATGCCCAGCAATGTATGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTGgtaagatggctgtcgcctcagatatatatagtgatatgcactacaaagatcatacatacatacggcaatcctgacacggtctctttgtcaaatatctctgtgtgcag
||||| ||||| ||||| |||||||| |||||| | ||||||||||||||||| || |||||||||||||| || ||||| ||||| || ||||||||||||| |||   | |  |||  |  ||| || ||| ||         ||  |||   ||   |  ||      ||||||    | | | |  |                
GAGAAGATGACACAGATCATGTTTGAGACCTTCAATTGCCCAGCAATGTATGTCGCAATCCAGGCTGTTCTATCCTTGTATGCTAGCGGTCGAACAACTGgtatgat---tattacctttgcaatagatcgtgtta---------aaattca---atgtgttggggggcagtgacacttcttttatctgcag---------------

upper sequence: GRMZM2G126010_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA05G32220.1 (Glycine max), 5'ss of exon 2
GAGAAAATGACGCAGATTATGTTTGAAACCTTCGAATGCCCAGCAATGTATGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTGgtaagatggctgtcgcctcagatatatatagtgatatgcactacaaagatcatacatacatacggcaatcctgacacggtctctttgtcaaatatctctgtgtgcag
|| || ||||| || || |||||||| |||||| |    || || |||||||| || |||||||||||||| || ||||| || ||||| || |||||||||    ||  | |  ||      || | |  ||||     ||   |  |||| |    ||| |      |||||  |  |  ||||   ||| |             
GAAAAGATGACCCAAATCATGTTTGAGACCTTCAATGTGCCTGCCATGTATGTGGCCATCCAGGCTGTTCTCTCCTTGTATGCCAGTGGTCGCACAACTGgtt---tgtatattacc------atctgtcttgattcattcttttataatcacat---cattcttt--ccctgaatcaattccttt-caaaacag------------

upper sequence: GRMZM2G126010_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA08G15480.1 (Glycine max), 5'ss of exon 3
GAGAAAATGACGCAGATTATGTTTGAAACCTTCGAATGCCCAGCAATGTATGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTGgtaagatggctgtcgcctcagatatatatagtgatatgcactacaaagatcatacatacatacggcaatcctgacacggtctctttgtcaaatatctctgtgtgcag
|| || ||||| || || |||||||| |||||| |    || || |||||||| || |||||||||||||| || ||||| || ||||| || |||||||||    ||  | || ||      || | |  ||||     ||   |  |||| |      |        |||||  |  |  |||| | ||| |             
GAAAAGATGACCCAAATCATGTTTGAGACCTTCAATGTGCCTGCCATGTATGTGGCCATCCAGGCTGTTCTCTCCTTGTATGCAAGTGGTCGCACAACTGgtt---tgtatatcacc------atctgtcttgattcattcttttataatcacat-----tgttctttccctgaatcaattccttt-taaaacag------------

upper sequence: GRMZM2G126010_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv04s0044g00580.t01 (Vitis vinifera), 5'ss of exon 4
GAGAAAATGACGCAGATTATGTTTGAAACCTTCGAATGCCCAGCAATGTATGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTGgtaag-atggctgtcgcctcagatatatatagtgatatgcactacaaagatcatacatacatacggcaatcctgacacggtctctttgtcaaatatctctgtgtgcag
|| || ||||| || || |||||||| || ||  |    || || ||||||||||| || ||||||||||||||  | || || |||||||| |||||||||  | ||     ||   |  |||    ||  | || |    |       |  |   |  |  | | | | || ||  | ||  ||    |                 
GAAAAGATGACTCAAATCATGTTTGAGACTTTTAATGTGCCTGCCATGTATGTTGCCATTCAGGCTGTTCTTTCTCTATATGCCAGTGGGCGTACAACTGgttcgtattaaaatctttttggattggaattttcatttttcttttct--gttgttagtgtagcctg-agttctaacttgctcctttgactag----------------

upper sequence: GRMZM2G126010_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv12s0178g00200.t01 (Vitis vinifera), 5'ss of exon 2
GAGAAAATGACGCAGATTATGTTTGAAACCTTCGAATGCCCAGCAATGTATGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTGgtaagatggctgtcgcctcagatatatatagtgatatgcactacaaagat-catacatacatacggcaatcctgacacggtctctttgtcaaatatctctgtgtgcag
||||||||||| |||||||||||||| |||||| |    || || ||||||||||||||||| ||||| || ||  |||| || ||||| || ||||| |||  |        | |  ||  |      ||  | || ||  ||     |   |   |   |  | || |  | | |   | ||||   |   || |  |        
GAGAAAATGACCCAGATTATGTTTGAGACCTTCAACGTACCTGCCATGTATGTTGCTATCCAAGCTGTGCTGTCTCTGTATGCCAGTGGTCGTACAACAGgtttgtgtcaaagcactgcaagttgtagaagcaaaatacaagacctttttgtgtgtgtgtgtgtgtcattgttcatattat-tcttgaaccgttagccatt-------

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|44681926|gb|CK786974.1|CK786974
EST:     TGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTG                         GTATTGTGATGGAATTCCGGTGATGGGGTGAGCCACACGG
genomic: TGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTGgtaagatggc ... ctgtgtgcagGTATTGTGATGGA-TTCCGGTGATGGTGTGAGCCACACGG
EST: gi|13178444|gb|BG349702.1|BG349702
EST:     TGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTG                         GTATTGTGATGGATTCCGGTGATGGTGTGAGCCACACGGTTCCAATCTATG
genomic: TGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTGgtaagatggc ... ctgtgtgcagGTATTGTGATGGATTCCGGTGATGGTGTGAGCCACACGGTTCCAATCTATG
EST: gi|67040133|gb|CO466388.1|CO466388
EST:     TGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTG                         GTATTGTGATGGATTCCGGTGATGGTGTGAGCCACACGGTTCCAATCTATG
genomic: TGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTGgtaagatggc ... ctgtgtgcagGTATTGTGATGGATTCCGGTGATGGTGTGAGCCACACGGTTCCAATCTATG
EST: gi|32928430|gb|CF033242.1|CF033242
EST:     TGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTG                         GTATTGTGATGGATTCCGGTGATGGTGTGAGCCACACGGTTCCAATCTATG
genomic: TGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTGgtaagatggc ... ctgtgtgcagGTATTGTGATGGATTCCGGTGATGGTGTGAGCCACACGGTTCCAATCTATG
EST: gi|211510973|gb|FL146258.1|FL146258
EST:     TGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTG                         GTATTGTGATGGATTCCGGTGATGGTGTGAGCCACACGGTTCCAATCTATG
genomic: TGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTGgtaagatggc ... ctgtgtgcagGTATTGTGATGGATTCCGGTGATGGTGTGAGCCACACGGTTCCAATCTATG
EST: gi|31349223|gb|CD433580.1|CD433580
EST:     TGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTG                         GTATTGTGATGGATTCCGGTGATGGTGTGAGCCACACGGTTCCAATCTATG
genomic: TGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTGgtaagatggc ... ctgtgtgcagGTATTGTGATGGATTCCGGTGATGGTGTGAGCCACACGGTTCCAATCTATG
EST: gi|116814875|gb|EC857503.1|EC857503
EST:     TGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTG                         GTATTGTGATGGATTCCGGTGATGGTGTGAGCCACACGGTTCCAATCTATG
genomic: TGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTGgtaagatggc ... ctgtgtgcagGTATTGTGATGGATTCCGGTGATGGTGTGAGCCACACGGTTCCAATCTATG
EST: gi|211510971|gb|FL146256.1|FL146256
EST:     TGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTG                         GTATTGTGATGGATTCCGGTGATGGTGTGAGCCACACGGTTCCAATCTATG
genomic: TGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTGgtaagatggc ... ctgtgtgcagGTATTGTGATGGATTCCGGTGATGGTGTGAGCCACACGGTTCCAATCTATG
EST: gi|67032946|gb|CO461695.1|CO461695
EST:     TGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTG                         GTATTGTGATGGATTCCGGTGATGGTGTGAGCCACACGGTTCCAATCTATG
genomic: TGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTGgtaagatggc ... ctgtgtgcagGTATTGTGATGGATTCCGGTGATGGTGTGAGCCACACGGTTCCAATCTATG
EST: gi|31356169|gb|CD440526.1|CD440526
EST:     TGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTG                         GTATTGTGATGGATTCCGGTGATGGTGTGAGCCACACGGTTCCAATCTATG
genomic: TGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTGgtaagatggc ... ctgtgtgcagGTATTGTGATGGATTCCGGTGATGGTGTGAGCCACACGGTTCCAATCTATG
EST: gi|31356251|gb|CD440608.1|CD440608
EST:     TGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTG                         GTATTGTGATGGATTCCGGTGATGGTGTGAGCCACACGGTTCCAATCTATG
genomic: TGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTGgtaagatggc ... ctgtgtgcagGTATTGTGATGGATTCCGGTGATGGTGTGAGCCACACGGTTCCAATCTATG
EST: gi|31354227|gb|CD438584.1|CD438584
EST:     TGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTG                         GTATTGTGATGGATTCCGGTGATGGTGTGAGCCACACGGTTCCAATCTATG
genomic: TGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTGgtaagatggc ... ctgtgtgcagGTATTGTGATGGATTCCGGTGATGGTGTGAGCCACACGGTTCCAATCTATG
EST: gi|87298742|gb|DY470745.1|DY470745
EST:     TGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTG                         GTATTGTGATGGATTCCGGTGATGGTGTGAGCCACACGGTTCCAATCTATG
genomic: TGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTGgtaagatggc ... ctgtgtgcagGTATTGTGATGGATTCCGGTGATGGTGTGAGCCACACGGTTCCAATCTATG
EST: gi|213170101|gb|FM191920.1|FM191920
EST:     TGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTG                         GTATTGTGATGGATTCCGGTGATGGTGTGAGCCACACGGTTCCAATCTATG
genomic: TGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTGgtaagatggc ... ctgtgtgcagGTATTGTGATGGATTCCGGTGATGGTGTGAGCCACACGGTTCCAATCTATG
EST: gi|31348973|gb|CD433330.1|CD433330
EST:     TGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTG                         GTATTGTGATGGATTCCGGTGATGGTGTGAGCCACACGGTTCCAATCTATG
genomic: TGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTGgtaagatggc ... ctgtgtgcagGTATTGTGATGGATTCCGGTGATGGTGTGAGCCACACGGTTCCAATCTATG
EST: gi|67040134|gb|CO466389.1|CO466389
EST:     TGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTG                         GTATTGTGATGGATTCCGGTGATGGTGTGAGCCACACGGTTCCAATCTATG
genomic: TGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTGgtaagatggc ... ctgtgtgcagGTATTGTGATGGATTCCGGTGATGGTGTGAGCCACACGGTTCCAATCTATG
EST: gi|31354413|gb|CD438770.1|CD438770
EST:     TGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTG                         GTATTGTGATGGATTCCGGTGATGGTGTGAGCCACACGGTTCCAATCTATG
genomic: TGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTGgtaagatggc ... ctgtgtgcagGTATTGTGATGGATTCCGGTGATGGTGTGAGCCACACGGTTCCAATCTATG
EST: gi|18661174|gb|BM501270.1|BM501270
EST:     TGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTG                         GTATTGTGATGGATTCCGGTGATGGTGTGAGCCACACGGTTCCAATCTATG
genomic: TGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTGgtaagatggc ... ctgtgtgcagGTATTGTGATGGATTCCGGTGATGGTGTGAGCCACACGGTTCCAATCTATG
EST: gi|20300037|gb|BQ162980.1|BQ162980
EST:     TGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTG                         GTATTGTGATGGATTCCGGTGATGGTGTGAGCCACACGGTTCCAATCTATG
genomic: TGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTGgtaagatggc ... ctgtgtgcagGTATTGTGATGGATTCCGGTGATGGTGTGAGCCACACGGTTCCAATCTATG
EST: gi|211058166|gb|FL434265.1|FL434265
EST:     TGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTG                         GTATTGTGATGGATTCCGGTGATGGTGTGAGCCACACGGTTCCAATCTATG
genomic: TGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTGgtaagatggc ... ctgtgtgcagGTATTGTGATGGATTCCGGTGATGGTGTGAGCCACACGGTTCCAATCTATG
EST: gi|31353181|gb|CD437538.1|CD437538
EST:     TGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTG                         GTATTGTGATGGATTCCGGTGATGGTGTGAGCCACACGGTTCCAATCTATG
genomic: TGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTGgtaagatggc ... ctgtgtgcagGTATTGTGATGGATTCCGGTGATGGTGTGAGCCACACGGTTCCAATCTATG
EST: gi|91056023|gb|EB166441.1|EB166441
EST:     TGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTG                         GTATTGTGATGGATTCCGGTGATGGTGTGAGCCACACGGTTCCAATCTATG
genomic: TGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTGgtaagatggc ... ctgtgtgcagGTATTGTGATGGATTCCGGTGATGGTGTGAGCCACACGGTTCCAATCTATG
EST: gi|13178132|gb|BG349390.1|BG349390
EST:     TGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTG                         GTATTGTGATGGATTCCGGTGATGGTGTGAGCCACACGGTTCCAATCTATG
genomic: TGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTGgtaagatggc ... ctgtgtgcagGTATTGTGATGGATTCCGGTGATGGTGTGAGCCACACGGTTCCAATCTATG
EST: gi|22489111|gb|BU049034.1|BU049034
EST:     TGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTG                         GTATTGTGATGGATTCCGGTGATGGTGTGAGCCACACGGTTCCAATCTATG
genomic: TGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTGgtaagatggc ... ctgtgtgcagGTATTGTGATGGATTCCGGTGATGGTGTGAGCCACACGGTTCCAATCTATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGAAAATGACGCAGATTATGTTTGAAACCTTCGAATGCCCAGCAATGTATGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTGgtaagatggctgtcgcctcagatatatatagtgatatgcactacaaagatcatacatacatacggcaatcctgacacggtctctttgtcaaatatctctgtgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT