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'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcatgcactagaattcaattcatcacaagaacatgtatgatcccccctatccttgaataaagtgtactctgcaaatgatttgctacaactgctttccagTGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAG

Basic information

species Zea mays
transcript GRMZM2G034143_T02
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G034143_T03 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os11g16370.1 (Oryza sativa), 3'ss of exon 11
-ttcatgcactagaattcaattcatcacaagaacatgtatgatcccccctatccttgaataaagtgtactctgcaaatgatttgctacaactgctttccagTGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAG
 ||||    || |      ||||     |  ||  | |     |  || |     | |||| | |      ||  ||| ||||  ||||| ||||||||||||| || || ||||||||||| || || |||||||||||||||||||| ||||||||||||||||||||  | ||||||||||||||  |||||
attcaatttcttgttaaagattctgttaataaagctcttcatacatccttgagtataaataca-taactattgtcaattatttcttacaattgctttccagTGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGTAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGAGAAGGAGACAATGGCAAACAG

upper sequence: GRMZM2G034143_T03 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os02g17320.2 (Oryza sativa), 3'ss of exon 11
---ttcatgcactagaattcaattcatcacaagaacatgt-atgatcccccctatccttgaataaagtgta-ctctgcaaatgatttgctacaactgctttccagTGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAG
   ||||| |  |   |   |  |  | |  | | ||  | || |        ||     |  || |  || || ||  ||| |||| || ||||| || |||||||| || || ||||||||||| || || |||||||| ||||||||||| ||||||||||||||||||||  ||||||||||||||||  |||||
ggattcattccttgtcaagtatcttgttagtaaagcacatcataaatttttgaat-----agaaaggcataactatgttaattattttctgcaacttctctccagTGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAG

upper sequence: GRMZM2G034143_T03 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA02G47270.1 (Glycine max), 3'ss of exon 11
ttcatgcactagaattcaattcatcacaagaacatgtatgatcccccctatccttgaataaagtgtactctgcaaatgatttgcta--caactgctttccagTGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAG
||| |       |||| | |   |   | |   |  ||||||| |  | ||  ||  |||||  | | |   |     ||||| ||  |||     || |||||| || || ||||| |||||  ||||||||||||| |||||||| ||||||||||| |||||||||||| | ||||| |||||||| ||||||
ttcttctttcctaatt-actcggtttaatgtggacctatgatcactgcaatt-ttatataaatagaatttgtccttaaatttgatatgcaatctaatttcagTGGGGAGAGTATGGAAAATGCTCTACGAGCATGCTGCAAAGGTATCAAGATTGGGAAAATTCTTATTCATAGAGAAGGTGACAATGGTCAACAG

upper sequence: GRMZM2G034143_T03 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA14G01480.1 (Glycine max), 3'ss of exon 8
----------------------------------------ttcatgcactagaattcaattcatcacaagaacatgtatgatcccccctatccttgaataaagtgtactctgcaaatgatttgctacaactgctttccagTGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAG
                                        ||| | |   |  | ||| ||       |    ||| || |   |   | |   | || | | | |   ||  || |   |   | |||     || |||||| || || ||||| ||||| |||||||||||||| |||||||| ||||||||||| |||||                               
ttgaaaatattatccaacctatattctaagaaactagttcttctttcctaattactcagtttgatgtgaacctatg-atcactgcaattttttataaacagAATTTGTCCTTAAATTTGATA--TGCAATCTAATTTCAGTGGGGAGAGTATGGAAAATGCTTTACGAGCATGCTGCAAAGGTATCAAGATTGGGAAAATTCT-------------------------------

upper sequence: GRMZM2G034143_T03 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA18G08180.1 (Glycine max), 3'ss of exon 11
-ttcatgcactagaattcaattcatcacaagaacatgtatgatcccccctatccttgaataaagtgtactctgcaaatgatttgctacaactgctttccagTGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAG-
  | | | |      |     || |  || |   ||   | ||       |   |    ||   |   |      ||  | ||  || |      || |||||| || || ||||||||||| ||  ||||||||||||||||||| ||||||||||| ||| | |||||  | ||||| |||||||| || ||| 
ccttaagaaaccttgtgtgtatctttgca-gtctataatttattgtttagaaattcatttactattatcataattaaaaaattaatatatgctaatttcagTGGGGAGAGTATGGAGAATGCTTTGAGAGCATGCTGTAAAGGTATCAAGATTGGGAAAATTTTAATTCACAGAGAAGGTGACAATGGTCAGCAGG

upper sequence: GRMZM2G034143_T03 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA08G45270.1 (Glycine max), 3'ss of exon 11
-ttcatgcactagaattcaattcatcacaagaacatgtatgatcccccctatccttgaataaagtgtactctgcaaatgatttgctacaactgctttccagTGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAG
    | | |      |     ||    || |   ||   | ||       |   |    |   ||   |      ||| ||||  || |    | || |||||| || || ||||||||||| ||  ||||||||||||||||||||||||||||||| ||| | |||||  | ||||| |||||||| || |||
ccctaagaaaccttgtgtgtctctctgca-gtttataatttattgttaagaaattcattttctgttatcataattaataatttaatatatgctcatttcagTGGGGAGAGTATGGAGAATGCTTTGAGAGCATGCTGTAAAGGTATAAAGATTGGGAAAATTTTAATTCACAGAGAAGGTGACAATGGTCAGCAG

upper sequence: GRMZM2G034143_T03 (Zea mays), 3'ss of exon 12
lower sequence: AT1G55810.1 (Arabidopsis thaliana), 3'ss of exon 11
ttcatgcactagaattcaattcatcacaagaacatgtatgatcccccctatccttgaataaagtgtactctgca-aatgatttgctacaactgctttccagTGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAG
                             | | |   || | |      |    |   ||| ||  |  ||  | ||||||||  |    |||      || || || || |||||||| ||  |  |||||||||| ||||| || || |||||||||||||| |||||| | ||||| |||||||| ||||||
-----------------------------gtaaagaaatcagcttaaacactaatagttaacgtcaatactatataatgattt--tgtctctgaacat-agCGGTGAGAGTATGGAGAACGCTCTTAGAGCATGCTGCAAAGGCATCAAAATTGGGAAGATTCTGATTCATAGAGAAGGCGACAATGGTCAACAG

upper sequence: GRMZM2G034143_T03 (Zea mays), 3'ss of exon 12
lower sequence: AT4G26510.2 (Arabidopsis thaliana), 3'ss of exon 11
ttcatgcactagaattcaattcatcacaagaacatgtatgatcccccctatccttgaataaagtgtactct-gcaaa--tgatt-tgctacaactgctttccagTGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAG
 |  |   ||| |  | |  |  |       |||  || || |  ||| ||||||  |||       ||||  | ||  ||||  || |   |     | | ||||| || |||||||||||||||||||||||||| || |||||||| ||||| |||||||| || |||||  | ||||| |||||||| ||||||
gtactttcctatatcttagctt-tagtttataca-ataggaacttccccatcctttcatatcccactctctcaccaacttgatggtgttttgaaataatgctagTGGTGAGAGCATGGAGAATGCGTTACGAGCATGTTGCAAAGGTATCAAGATCGGGAAGATCCTAATTCACAGAGAAGGTGACAATGGTCAACAG

upper sequence: GRMZM2G034143_T03 (Zea mays), 3'ss of exon 12
lower sequence: Vv19s0015g01730.t01 (Vitis vinifera), 3'ss of exon 11
ttcatgcactagaattcaattcatcacaagaacatgtatgatccc-ccctatccttgaataaagtgtactc-tgcaaatgatttgctacaactgctttccagTGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAG
   | | |  |||| |  |   | || |        ||||  |||    | || |||  |   |  |  |  |   ||  || | ||   |||| |  ||||||| || || ||||||||||| || |||||||| || |||||||| || ||||||||||||||||| ||| ||||||| || || || || |||
-aaaggaaaaagaagtgcaaaaagcatattcctggttatggacccattttctctttgtcttttgcattttggtttgaaccatcttctcttactgatg-ccagTGGTGAGAGTATGGAGAATGCTTTGCGAGCATGTTGCAAAGGTATCAAAATTGGGAAGATTCTTATCCATAGGGAAGGGGATAACGGTCAGCAG

upper sequence: GRMZM2G034143_T03 (Zea mays), 3'ss of exon 12
lower sequence: PP1S83_234V6.4 (Physcomitrella patens), 3'ss of exon 11
-------------------------ttcatgcacta---gaattcaattcatcacaagaacatgtatgatcccccctatccttgaataaagtgtactctgcaaatgatttgctacaactgctttccagTGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAG
                           ||   | ||   |||||   |   |   |     ||||  |      |  ||      | ||        ||    || |||  |     ||||   | || || || ||||||||||||||  | || || ||||| ||||| || |||||||| |||||| | || ||||| |||||||| ||||| ||||||
gtattattcctcattacgagttaccaccagtgattatgtgaattggctgtgtggaactggtatgtggggctgatctaatgtcattacaagtgagttgctaattattattgtcgggttctgcaaactagCGGGGAGAGCATGGAGAATGCACTGCGGGCGTGCTGCAAAGGCATCAAGATTGGAAAGATTTTGATACATCGCGAAGGAGATAATGGGCAACAG

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|148943393|gb|EC888452.2|EC888452
EST:     ACTGGTGTGGAGTTCTCCAAAAGGTTGTGTGGTGTCTCAGTGATCAGGAG                         TGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGAT
genomic: ACTGGTGTGGAGTTCTCCAAAAGGTTGTGTGGTGTCTCAGTGATCAGGAGgtaccaactt ... tgctttccagTGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGAT
EST: gi|32826219|gb|CD965897.1|CD965897
EST:     ACTGGTGTGGAGTTCTCCAAAAGGTTGTGTGGTGTCTCAGTGATCAGGAG                         TGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGAT
genomic: ACTGGTGTGGAGTTCTCCAAAAGGTTGTGTGGTGTCTCAGTGATCAGGAGgtaccaactt ... tgctttccagTGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGAT
EST: gi|37385350|gb|CF629812.1|CF629812
EST:     ACTGGTGTGGAGTTCTCCAAAAGGTTGTGTGGTGTCTCAGTGATCAGGAG                         TGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGAT
genomic: ACTGGTGTGGAGTTCTCCAAAAGGTTGTGTGGTGTCTCAGTGATCAGGAGgtaccaactt ... tgctttccagTGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGAT
EST: gi|60340284|gb|DN207257.1|DN207257
EST:     ACTGGTGTGGAGTTCTCCAAAAGGTTGTGTGGTGTCTCAGTGATCAGGAG                         TGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGAT
genomic: ACTGGTGTGGAGTTCTCCAAAAGGTTGTGTGGTGTCTCAGTGATCAGGAGgtaccaactt ... tgctttccagTGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGAT
EST: gi|110957674|gb|EE177726.1|EE177726
EST:     ACTGGTGTGGAGTTCTCCAAAAGGTTGTGTGGTGTCTCAGTGATCAGGAG                         TGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGAT
genomic: ACTGGTGTGGAGTTCTCCAAAAGGTTGTGTGGTGTCTCAGTGATCAGGAGgtaccaactt ... tgctttccagTGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGAT
EST: gi|24766852|gb|CA401999.1|CA401999
EST:     AGTTCTCCAAAAGGTTGTGTGGTGTCTCAGTGATCAGGAG                         TGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGAT
genomic: AGTTCTCCAAAAGGTTGTGTGGTGTCTCAGTGATCAGGAGgtaccaactt ... tgctttccagTGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGAT
EST: gi|67012645|gb|CO441394.1|CO441394
EST:     CAAAA-GTTGTGTGGTGTCTCAGTTTTCAGGAG                         TGGCGAAAGCATGGAGAATCGCGTTACGAGCATGCTGTAAAGGTATAAAGA
genomic: CAAAAGGTTGTGTGGTGTCTCAGTGATCAGGAGgtaccaactt ... tgctttccagTGGCGAAAGCATGGAGAAT-GCGTTACGAGCATGCTGTAAAGGTATAAAGA
EST: gi|78113248|gb|DV531642.1|DV531642
EST:     ACTGGTGTGGAGTTCTCCAAAAGGTTGTGTGGTGTCTCAGTGATCAGGAG                         TAGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGAT
genomic: ACTGGTGTGGAGTTCTCCAAAAGGTTGTGTGGTGTCTCAGTGATCAGGAGgtaccaactt ... tgctttccagTGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccctatccttgaataaagtgtactctgcaaatgatttgctacaactgctttccagTGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAG
                                            ctgctttcc  CT-rich tract
        ttgaataaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcatgcactagaattcaattcatcacaagaacatgtatgatcccccctatccttgaataaagtgtactctgcaaatgatttgctacaactgctttccagTGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA