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

...tagcttccaggaaacttctatttttggtgttaatttacttgctagctttcgaaatcatgtttttcccttgtgtgagccatgagttgtttccatgtcacagCAAAGTTATAGATGTCTTCATCAAGGCTGCAGAATATATGGAGATGCCAGTTCGACGCAGTGATGATGAACCCCTGCAAAAATTGTTTGTAGCTGTTAGA

Basic information

species Zea mays
transcript GRMZM2G007871_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G007871_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os04g24180.1 (Oryza sativa), 3'ss of exon 6
-tagcttccaggaaacttctatttttggtgttaatttacttgctagctttcgaaat--catgtttttcccttgtgtgagccatgag----ttgtttccatgtcacagCAAAGTTATAGATGTCTTCATCAAGGCTGCAGAATATATGGAGATGCCAGTTCGACGCAGTGATGATGAACCCCTGCAAAAATTGTTTGTAGCTGTTAGA
  |  ||      | | ||  ||| || | | | ||      |||| | |  ||||  |  ||||||  | | | ||| || ||      |||  |  ||||  ||||||||| || ||||||||||| ||||||||||| ||||||||||||||||| || |||||||| ||||||||| |||| ||||| |||||||||||||| 
ccaaattgtcctgagcatcc-tttctgttatcagtt------ctagatatgaaaatgcctcgtttttgacatatctgatccgtggaactattggctgtatgttgcagCAAAGTCATGGATGTCTTCATTAAGGCTGCAGAGTATATGGAGATGCCAGTCCGGCGCAGTGACGATGAACCCTTGCAGAAATTATTTGTAGCTGTTAGG

upper sequence: GRMZM2G007871_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA15G20400.1 (Glycine max), 3'ss of exon 6
-tagcttccaggaaacttctatttttggtgttaatttacttgctagctttcgaaatcatgtttttccc--ttgtgtgagccatgagttgtttccatgtcacagCAAAGTTATAGATGTCTTCATCAAGGCTGCAGAATATATGGAGATGCCAGTTCGACGCAGTGATGATGAACCCCTGCAAAAATTGTTTGTAGCTGTTAGA
  || |  |      |  |  | |      || ||  | | |||| ||||   | |      ||||    ||   | |    ||| |   ||   ||  |||||||||| || |||||||||||||||||||| ||||||||||| || ||||||||  | | |||||||||||| || || ||  | ||| |    || || 
tgagttatccccccgcccccctctccca-attcatacaatagctatcttttatactttaaactttcaaagtttaattatttgtgaata--ttatgtggtacagCAAAGTCATGGATGTCTTCATCAAGGCTGCTGAATATATGGAAATTCCAGTTCGTAGGACTGATGATGAACCTCTTCAGAAGCTTTTTATGTTGGTAAGG

upper sequence: GRMZM2G007871_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA09G08830.1 (Glycine max), 3'ss of exon 6
tagcttccagg--aaacttctatttttggtgttaatttacttgctagctttcgaaatc---atgtttttcccttgtgtgagccatgagttgtttccatgtcacagCAAAGTTATAGATGTCTTCATCAAGGCTGCAGAATATATGGAGATGCCAGTTCGACGCAGTGATGATGAACCCCTGCAAAAATTGTTTGTAGCTGTTAGA
  | ||  |     |  |       ||    || ||  | | | || ||||   | |    ||||||     ||   | |    ||| |   ||   |   |||||||||| || |||||||||||||||||||| ||||||||||| || ||||| ||  | | |||||| ||||| || |||||  | ||| |    || || 
--gattgaaaattgagttatcccccttccaattgatacaataggtatcttttatactttaaatgtttaaagttta-attatttgtgaata--ttatgttgtacagCAAAGTAATGGATGTCTTCATCAAGGCTGCTGAATATATGGAAATTCCAGTCCGTAGAACTGATGACGAACCTCTTCAAAAGCTTTTTATGTTGGTAAGG

upper sequence: GRMZM2G007871_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT1G79940.3 (Arabidopsis thaliana), 3'ss of exon 6
-tagcttccaggaaacttctatttttggtgttaatttacttgctagctttcgaa---atcatgtttttccct-tgtgtgagccatgagttg---tttccatgtcacagCAAAGTTATAGATGTCTTCATCAAGGCTGCAGAATATATGGAGATGCCAGTTCGACGCAGTGATGATGAACCCCTGCAAAAATTGTTTGTAGCTGTTAGA
 ||  |||    | ||   |||   |     | ||    ||| |   |  | ||       ||||||    | | |||  | ||||  ||    |||  ||    |||||||||||| || || |||| |||||| || || || |||||||| ||||||||  | | |||||||||||| ||||| ||  | ||| |  ||||||| 
gtatattcactcatacccatatacattcaagtgatgctattggtgcatgacaaatgggctgtgttttcgtttgtttgtatgacatgttttaaaatttttattgtccagCAAAGTTATGGAAGTTTTCACCAAGGCAGCTGAGTACATGGAGATTCCAGTTCGTAGAACTGATGATGAACCTCTGCAGAAGCTCTTTATGTCTGTTAGG

upper sequence: GRMZM2G007871_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv16s0050g01460.t01 (Vitis vinifera), 3'ss of exon 5
tagcttccaggaaacttctatttttg-gtgttaatttacttgctagctttcgaaatcatgtttttcccttgtgtgagcc-atgagttgtttccatgtcacagCAAAGTTATAGATGTCTTCATCAAGGCTGCAGAATATATGGAGATGCCAGTTCGACGCAGTGATGATGAACCCCTGCAAAAATTGTTTGTAGCTGTTAGA
  |      ||    || | ||| |   ||||  | |   |  |||  |  ||  ||   | |     |||| |  |   ||| | |   |   | | ||||||||||||| ||||||||||| |||||||||||||| ||||| || ||||| ||  | | |||  |||| ||||| || ||| ||||  |    || || 
--gaaaaatgggtgtttatgtttatatatgtttttatgtatcttagtgtgtgatttctattataagttttgtttatgatgatgtgataacttggttttacagCAAAGTTATGGATGTCTTCATTAAGGCTGCAGAATACATGGAAATTCCAGTCCGTAGGACTGACAATGAGCCCCTTCAGAAACTGTTCATGTTAGTAAGG

upper sequence: GRMZM2G007871_T02 (Zea mays), 3'ss of exon 5
lower sequence: PP1S241_31V6.1 (Physcomitrella patens), 3'ss of exon 5
tagcttccaggaaacttctatttttggtgttaatttacttgctagctttcgaaatcatgtttttcccttgtgtgagc-catga-gttgtttccatgtca-cagCAAAGTTATAGATGTCTTCATCAAGGCTGCAGAATATATGGAGATGCCAGTTCGACGCAGTGATGATGAACCCCTGCAAAAATTGTTTGTAGCTGTTAGA
   | |    |    || |||||    |  |||  | |   | |||        | |||          |  | | | ||  | |||| |    |     |||||||||  | |||||  |  | || ||   ||| || || ||| |||||||||||||||||||||| || ||||||||||| || ||  | | |||| ||
--tcgtattaggcgattatatttagcttcctaaagtgcac-caagcagggtttctgatggcaccagaaagcatcaactcacaatgttggtctggtcctggcagCAAAGTGTTGGATGTGCTTGTGAAAGCACAAGAGTACATTGAGTTGCCAGTTCGACGCAGTGATGAAGAGCCCCTGCAAAAGTTATTCCTTGTTGTTCGA

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|32838158|gb|CD977836.1|CD977836
EST:     CAAACTTTGTCCACTTACTACTACTTTATGAAGCCATCTCTTGCTCCAAG                         CAAAGTTATAGATGTCTTCATCAAGGCTGCAGAATATATGGAGATGCCAGT
genomic: CAAACTTTGTCCACTTACTACTACTTTATGAAGCCATCTCTTGCTCCAAGgtatgaactt ... catgtcacagCAAAGTTATAGATGTCTTCATCAAGGCTGCAGAATATATGGAGATGCCAGT
EST: gi|22715113|gb|BU197585.1|BU197585
EST:     CAAACTTTGTCCACTTACTACTACTTTATGAAGCCATCTCTTGCTCCAAG                         CAAAGTTATAGATGTCTTCATCAAGGCTGCAGAATATATGGAGATGCCAGT
genomic: CAAACTTTGTCCACTTACTACTACTTTATGAAGCCATCTCTTGCTCCAAGgtatgaactt ... catgtcacagCAAAGTTATAGATGTCTTCATCAAGGCTGCAGAATATATGGAGATGCCAGT
EST: gi|22935564|gb|BU571839.1|BU571839
EST:     CAAACTTTGTCCACTTACTACTACTTTATGAAGCCATCTCTTGCTCCAAG                         CAAAGTTATAGATGTCTTCATCAAGGCTGCAGAATATATGGAGATGCCAGT
genomic: CAAACTTTGTCCACTTACTACTACTTTATGAAGCCATCTCTTGCTCCAAGgtatgaactt ... catgtcacagCAAAGTTATAGATGTCTTCATCAAGGCTGCAGAATATATGGAGATGCCAGT
EST: gi|26560014|gb|CA832249.1|CA832249
EST:     CAAACTTTGTCCACTTACTACTACTTTATGAAGCCATCTCTTGCTCCAAG                         CAAAGTTATAGATGTCTTCATCAAGGCTGCAGAATATATGGAGATGCCAGT
genomic: CAAACTTTGTCCACTTACTACTACTTTATGAAGCCATCTCTTGCTCCAAGgtatgaactt ... catgtcacagCAAAGTTATAGATGTCTTCATCAAGGCTGCAGAATATATGGAGATGCCAGT
EST: gi|32837602|gb|CD977280.1|CD977280
EST:     CAAACTTTGTCCACTTACTACTACTTTATGAAGCCATCTCTTGCTCCAAG                         CAAAGTTATAGATGTCTTCATCAAGGCTGCAGAATATATGGAGATGCCAGT
genomic: CAAACTTTGTCCACTTACTACTACTTTATGAAGCCATCTCTTGCTCCAAGgtatgaactt ... catgtcacagCAAAGTTATAGATGTCTTCATCAAGGCTGCAGAATATATGGAGATGCCAGT
EST: gi|87156492|gb|DY401281.1|DY401281
EST:     CAAACTTTGTCCACTTACTACTACTTTATGAAGCCATCTCTTGCTCCAAG                         CAAAGTTATAGATGTCTTCATCAAGGCTGCAGAATATATGGAGATGCCAGT
genomic: CAAACTTTGTCCACTTACTACTACTTTATGAAGCCATCTCTTGCTCCAAGgtatgaactt ... catgtcacagCAAAGTTATAGATGTCTTCATCAAGGCTGCAGAATATATGGAGATGCCAGT
EST: gi|32836675|gb|CD976353.1|CD976353
EST:     CAAACTTTGTCCACTTACTACTACTTTATGAAGCCATCTCTTGCTCCAAG                         CAAAGTTATAGATGTCTTCATCAAGGCTGCAGAATATATGGAGATGCCAGT
genomic: CAAACTTTGTCCACTTACTACTACTTTATGAAGCCATCTCTTGCTCCAAGgtatgaactt ... catgtcacagCAAAGTTATAGATGTCTTCATCAAGGCTGCAGAATATATGGAGATGCCAGT
EST: gi|22542214|gb|BU092652.1|BU092652
EST:     CAAACTTTGTCCACTTACTACTACTTTATGAAGCCATCTCTTGCTCCAAG                         CAAAGTTATAGATGTCTTCATCAAGGCTGCAGAATATATGGAGATGCCAGT
genomic: CAAACTTTGTCCACTTACTACTACTTTATGAAGCCATCTCTTGCTCCAAGgtatgaactt ... catgtcacagCAAAGTTATAGATGTCTTCATCAAGGCTGCAGAATATATGGAGATGCCAGT
EST: gi|87157186|gb|DY401975.1|DY401975
EST:     CAAACTTTGTCCACTTACTACTACTTTATGAAGCCATCTCTTGCTCCAAG                         CAAAGTTATAGATGTCTTCATCAAGGCTGCAGAATATATGGAGATGCCAGT
genomic: CAAACTTTGTCCACTTACTACTACTTTATGAAGCCATCTCTTGCTCCAAGgtatgaactt ... catgtcacagCAAAGTTATAGATGTCTTCATCAAGGCTGCAGAATATATGGAGATGCCAGT
EST: gi|87157024|gb|DY401813.1|DY401813
EST:     CAAACTTTGTCCACTTACTACTACTTTATGAAGCCATCTCTTGCTCCAAG                         CAAAGTTATAGATGTCTTCATCAAGGCTGCAGAATATATGGAGATGCCAGT
genomic: CAAACTTTGTCCACTTACTACTACTTTATGAAGCCATCTCTTGCTCCAAGgtatgaactt ... catgtcacagCAAAGTTATAGATGTCTTCATCAAGGCTGCAGAATATATGGAGATGCCAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttcgaaatcatgtttttcccttgtgtgagccatgagttgtttccatgtcacagCAAAGTTATAGATGTCTTCATCAAGGCTGCAGAATATATGGAGATGCCAGTTCGACGCAGTGATGATGAACCCCTGCAAAAATTGTTTGTAGCTGTTAGA
                                      ttgtttcc  CT-rich tract
           atgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagcttccaggaaacttctatttttggtgttaatttacttgctagctttcgaaatcatgtttttcccttgtgtgagccatgagttgtttccatgtcacagCAAAGTTATAGATGTCTTCATCAAGGCTGCAGAATATATGGAGATGCCAGTTCGACGCAGTGATGATGAACCCCTGCAAAAATTGTTTGTAGCTGTTAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- gcttcca
- - - - - - - - - - - - tggtgtt
- - - - - - - - - - - - - - - - - -tacttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gccatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttgttt