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'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   		26  
 5'  3'   		27  
 5'  3'   		28  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cggactaaaagaaatttctgtaagtcagtaattagtaattacacaatactttgttgtatgtgcttctcatatttgtatgccctccttttgacgcaaccagAGACCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTCGATCAACAGCGTAGCCAGGCGCTTGAAGCCCATGCAGCATCTTTTGCAACATTTAAG

Basic information

species Zea mays
transcript GRMZM2G057576_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 5
-cggactaaaagaaatttctgtaagtcagtaattagtaattacacaatactttgttgtatgtgcttctcatatttgtatgccctccttttgacgcaaccagAGACCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTCGATCAACAGCGTAGCCAGGCGCTTGAAGCCCATGCAGCATCTTTTGCAACATTTAAG
     ||| |   |   |     |||   |||    | |||||  ||| ||||||| ||| |  | || | |||  | ||| ||| |||| || ||  ||||| |||||||||||||||||||||||||||||||||||||| ||||| || ||||| ||||| |||||||||||||||||||| |||||| ||||||||
atatgctacacctatgctggagcagttcttaaaagtttattacgtaatgctttgttctatatcatcctaacattgatgtgctctctttttcaccca-tcagAGGCCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTGGATCAGCAACGTAGTCAGGCACTTGAAGCCCATGCAGCATCCTTTGCATCATTTAAG

upper sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 5
-cggactaaaagaaatttctgtaagtcagtaattagtaattacacaatactttgttgtatgtgcttctcatatttgtatgccctccttttgacgcaaccagAGACCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTCGATCAACAGCGTAGCCAGGCGCTTGAAGCCCATGCAGCATCTTTTGCAACATTTAAG
     ||| |   |   |     |||   |||    | |||||  ||| ||||||| ||| |  | || | |||  | ||| ||| |||| || ||  ||||| |||||||||||||||||||||||||||||||||||||| ||||| || ||||| ||||| |||||||||||||||||||| |||||| ||||||||
atatgctacacctatgctggaacagtttttaaaagtttattacgtaatgctttgttctatatcatcctaacattgatgtgctctctttttcaccca-tcagAGGCCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTGGATCAGCAACGTAGTCAGGCACTTGAAGCCCATGCAGCATCCTTTGCATCATTTAAG

upper sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 5
cggactaaaagaaatttctgtaagtcagtaattagtaattacacaatactttgttgtatgtgcttctcatatttgt-atgccctcct-tttgacgcaaccagAGACCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTCGATCAACAGCGTAGCCAGGCGCTTGAAGCCCATGCAGCATCTTTTGCAACATTTAAG
     |  |     ||| | |   |  |      |               |||||  || | ||  |  |    || ||| | |  | ||||  |    |||||||| ||||| || || |||||||||||||| || ||||| ||||||||| | |||||||| |||||||| ||||| || || ||||| ||||||| |
--ttttttatttttttttttttttttgggggggggggggggggggggttgttgttaaatttcctatttgttggagtgatgacattttatttgttggttacagAGACCGCAACTTGTAAAAGGAAATATGCAACTCTTCTCTGTGGATCAACAGAGGAGCCAGGCTCTTGAAGCACATGCTGCCTCATTTGCCACATTTAGG

upper sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 5
cggactaaaagaaatttctgtaagtcagtaattag-taattacacaatactttgttgtatgt-gcttctcatatttgt-------atgccctcct-tttgacgcaaccagAGACCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTCGATCAACAGCGTAGCCAGGCGCTTGAAGCCCATGCAGCATCTTTTGCAACATTTAAG
           || |||||   |   | ||||| | ||||||     |  || |  || |||    | || |||||||       |||   |  | ||||  |    |||||||||||||| || || |||||||||||||| || ||||| ||||| ||| | |||||||| |||||||| ||||| || || ||||| ||||||| |
---------ttaattttcttgcataaattaattggctaattatgtttt-tttgggggtgtgttaaatttcctatttgttggagtgatggaattttatttgttggttacagAGACCACAACTTGTAAAAGGAAATATGCAACTCTTCTCTGTGGATCAGCAGAGGAGCCAGGCTCTTGAAGCACATGCTGCCTCATTTGCCACATTTAGG

upper sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 5
-cggactaaaagaaatttctgtaagtcagtaattagtaattacacaatactttgt-tgtatgtgcttctcatatttgtat-gccctccttttgacgcaaccagAGACCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTCGATCAACAGCGTAGCCAGGCGCTTGAAGCCCATGCAGCATCTTTTGCAACATTTAAG
  ||  |    ||   | ||  ||  || | ||      ||  || |||  |  |     | || |     | ||| | | |      || ||  |     |||| |||||| |||| || ||||| |||||||| || ||||| ||||||||||| |||||||| |||||||| ||||| ||||| |||||   ||| || 
ttgggattgttga---tccttgaaaacaatcatggtcttttttactataactcctacaagtctgatctaggttttttttttgggtatgttgtgttgtctatagAGGCCACAATTGGTTAAAGGAAACATGCAACTCTTCTCTGTGGATCAACAGCGGAGCCAGGCTCTTGAAGCACATGCGGCATCATTTGCTCAATTCAAA

upper sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 5
cggactaaaagaaatttctgtaagtcagtaattagtaattacacaatactttgtt-gtatgtgcttctcatatttgtatgccctccttttgacgcaac-cagAGACCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTCGATCAACAGCGTAGCCAGGCGCTTGAAGCCCATGCAGCATCTTTTGCAACATTTAAG
    ||      ||||     |     || ||   |  ||||     | ||     |  ||  ||  |    ||| | |  ||   || |   |||    |||| || ||| |||| |||||||| ||||||||||| ||||| |||||||| ||||| ||||| |||||||| ||||| ||||| |||||   |||||| 
ttatctgtgtataattgtacaagaattgtgatcttt--ttaccatgaatttaacaagcctgatctattttggtttatttctccatattattttgcattgtagAGGCCGCAATTGGTAAAGGGAAACATGCAACTTTTCTCTGTGGATCAACAACGTAGTCAGGCTCTTGAAGCTCATGCCGCATCATTTGCCCAATTTAAA

upper sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 5
cggactaaaagaaatttctgtaagtcagtaattagtaattacacaatactttgttgtatgtg--cttctcatatttgtatgccctccttttgacgcaac-cagAGACCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTCGATCAACAGCGTAGCCAGGCGCTTGAAGCCCATGCAGCATCTTTTGCAACATTTAAG
   |       | | || | ||||  | |  | |    ||   |   | |||     |  ||  ||  |    ||| | |  ||   || |   |||    ||||  ||||| |||| |||||||| ||||||||||| || || |||||||| ||||| ||||| |||||||| ||||| ||||| |||||   |||||| 
-ttatctgtgtataattgtataag--aattgtgatcttttcaccgtgattttaacaaacctgatctattttggtttatttttccatattattttgcattgtagAGGGCACAATTGGTAAAGGGAAACATGCAACTTTTCTCAGTGGATCAACAACGTAGTCAGGCTCTTGAAGCTCATGCTGCATCATTTGCCCAATTTAAA

upper sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 4
cggactaaaagaaatttctgtaagtcagt--aattagtaattacacaatactttgttgtatgtgcttctcatatttgtatgccctccttttgacgcaaccagAGACCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTCGATCAACAGCGTAGCCAGGCGCTTGAAGCCCATGCAGCATCTTTTGCAACATTTAAG
    |  ||    |  | | |  || | |  ||||  | |  |   ||   | ||   |   |  || | | | |  | |   | | |||||        ||||||||||||| || || ||||| |||||||| || ||||| ||||| || ||||| ||||| |||||||| ||||| || || |||||  | ||||  
--tcccgaagcttacatttttgtgttatttaaatttctgaacatcaaaccttgtgagattattaattgtaagaataattttatcacattttgtttgttgtagAGACCACAACTAGTAAAAGGAAACATGCAACTCTTCTCTGTGGATCAGCAACGTAGTCAGGCTCTTGAAGCACATGCTGCCTCATTTGCTTCGTTTAGA

upper sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 5
-cggactaaaagaaatttctgtaagtcagtaattagtaattacacaatactttgttg---tatgtgcttctcatatttgtatgccctccttttgacgcaaccagAGACCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTCGATCAACAGCGTAGCCAGGCGCTTGAAGCCCATGCAGCATCTTTTGCAACATTTAAG
 | ||     | |  ||| ||| | | |  ||||  | |  |||  | || ||||     |||     | | | | |  | |   ||| |||||        ||||||||||||| || || ||||| |||||||| || ||||| ||||| || ||||| ||||| |||||||| ||||| || || ||||| |||||||  
cccgaagcttacatttttatgtgattta--aatttctga--acattaaaccttgtgagcttattaatgtgtaagaataattttatctcattttgtttgttgtagAGACCACAACTAGTAAAAGGAAACATGCAACTCTTCTCTGTGGATCAGCAACGTAGTCAGGCTCTTGAAGCACATGCTGCCTCGTTTGCTACATTTAGA

upper sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 5
-cggactaaaagaaatttctgt-aagtcagtaattagtaattacacaatactt-tgttgtatgtgcttctcatatttgtatgccctccttttgacgcaaccagAGACCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTCGATCAACAGCGTAGCCAGGCGCTTGAAGCCCATGCAGCATCTTTTGCAACATTTAAG
      | |  |       | | | ||||  ||     |   | ||     |  |||||||  | |||  |  || | | |        | ||        |||||| |||| |||| || ||||||||||| ||||| ||||| ||||||||||| || ||||| ||||| || ||||| ||||| |||||    ||||||
gtaagtttactgcgccacatattaggtcaaaaaaagacatcaaaactgctttcatgttgtagattcttgactgatct-tgtcattattatctgttttctgtagAGACAACAATTGGTAAAAGGAAATATGCAGCTTTTCTCTGTGGATCAACAGCGGAGTCAGGCCCTTGAGGCACATGCTGCATCGTTTGCGCAGTTTAAG

upper sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 5
-cggactaaaagaaatttctgtaagtcagtaattagtaattaca-caatactt-tgttgtatgtgcttctcatatttgtatgccctccttttgacgcaaccagAGACCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTCGATCAACAGCGTAGCCAGGCGCTTGAAGCCCATGCAGCATCTTTTGCAACATTTAAG
   |  |    | |     | | ||   | | | ||  || | | |   | |  |||||||| |  ||  |  | |  | |       | ||  |      ||||||||||| ||||||| ||||||||||| ||||| ||||| ||||||||||| |||||||| |||||||| ||||| |||||||||||    ||||||
gtagggttcctgcaccacgtattaggttgaattaagacatcataacggcagtcatgttgtatatttttgacggaatcttgt----cattattatcctctgtagAGACCACAATTGGTGAAAGGAAATATGCAGCTTTTCTCTGTGGATCAACAGCGGAGCCAGGCCCTTGAAGCACATGCTGCATCTTTTGCTCAGTTTAAG

upper sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 5
cggactaaaagaaatttctgtaagtcagtaattagtaattacacaatactttgttgtatgtgcttctcatatttgtatgccctccttttga----cgcaacc--agAGACCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTCGATCAACAGCGTAGCCAGGCGCTTGAAGCCCATGCAGCATCTTTTGCAACATTTAAG
   |  |   |   ||||  | ||    |     |||     |||| |   |    | ||   || | | | |  |||    ||| | | |     |       |||| |||||||| || || || |||||||||||||| || || ||||| || ||||| ||||| |||||||| ||||| ||||| |||||  ||||||| 
---aggacctgctttttcaatgagc--attgcatgtagcctaacaacagcgtaaaat-tgattttttaacaatgatatatgttccatcttaaaattgtggttgtagAGGCCACAACTCGTCAAAGGGAATATGCAACTTTTCTCAGTGGATCAGCAACGTAGTCAGGCCCTTGAAGCACATGCTGCATCATTTGCCTCATTTAAA

upper sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S452_30V6.1 (Physcomitrella patens), 3'ss of exon 5
-cggactaaaagaaatttctgtaagtcagtaattagtaattacacaatactttgttgtatgtgcttctcatatttgtatgccctccttttgacgcaaccagAGACCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTCGATCAACAGCGTAGCCAGGCGCTTGAAGCCCATGCAGCATCTTTTGCAACATTTAAG
   ||||| ||     |  | ||  ||  |   |   | | | |     | |  ||  |   ||    |   ||  |    ||   |  |        ||| | ||||| || ||||||||||| |||||| | |||||||| ||||||||| | || || ||  | ||||| ||||||||||| || ||||| ||||||
tttgactataaatgcatcgtttatatcc-tctctgccattaatatggggcgtaatttaaatggccgaacggtttaatgataccatataatatgttctgcagCGCCCACAGCTTGTGAAGGGAAACATGCAATTATTTTCTGTGGATCAACAGAGGAGTCAAGCATTAGAAGCGCATGCAGCATCATTCGCAACTTTTAAG

upper sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 5
cggactaaaagaaatttctgtaagtcagtaattagtaattacacaatactttgttgtatgtgcttctcatatttgtatgccctccttttgacgcaaccagAGACCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTCGATCAACAGCGTAGCCAGGCGCTTGAAGCCCATGCAGCATCTTTTGCAACATTTAAG
                                            |    ||| ||| |   | ||||  ||  |          || ||         || | |||||||||||||| ||||| |||||||| ||||| |||||||| ||||| || || ||  | ||||| ||||| |||||||| || ||||| |||
------------------------------------------gtatccatttcttgaa-aagtttcttgtagctaacaaagaaactctt-------ttagCGTCCACAACTGGTGAAAGGAAACATGCAACTCTTTTCAGTCGATCAGCAGCGAAGTCAAGCTTTGGAAGCTCATGCTGCATCTTTCGCTACATTCAAG

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|22491519|gb|BU051442.1|BU051442
EST:     CAGCAGAGAAGTGGCTTGTGCTTATTGGAATTGCACCGGGAGCCCCAGAG                         AGACCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTCGATCAACAG
genomic: CAGCGGAGAAGTGGCTTGTGCTTATTGGAATTGCACCGGGAGCCCCAGAGgtacggtttt ... acgcaaccagAGACCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTCGATCAACAG
EST: gi|19350742|gb|BM895274.1|BM895274
EST:     CAGCAGAGAAGTGGCTTGTGCTTATTGGAATTGCACCGGGAGCCCCAGAG                         AGACCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTCGATCAACAG
genomic: CAGCGGAGAAGTGGCTTGTGCTTATTGGAATTGCACCGGGAGCCCCAGAGgtacggtttt ... acgcaaccagAGACCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTCGATCAACAG
EST: gi|89106255|gb|DY576472.1|DY576472
EST:     CAGCAGAGAAGTGGCTTGTGCTTATTGGAATTGCACCGGGAGCCCCAGAG                         AGACCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTCGATCAACAG
genomic: CAGCGGAGAAGTGGCTTGTGCTTATTGGAATTGCACCGGGAGCCCCAGAGgtacggtttt ... acgcaaccagAGACCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTCGATCAACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atactttgttgtatgtgcttctcatatttgtatgccctccttttgacgcaaccagAGACCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTCGATCAACAGCGTAGCCAGGCGCTTGAAGCCCATGCAGCATCTTTTGCAACATTTAAG
                                        ttttgac  putative branch site (score: 3)
                       atatttgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cggactaaaagaaatttctgtaagtcagtaattagtaattacacaatactttgttgtatgtgcttctcatatttgtatgccctccttttgacgcaaccagAGACCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTCGATCAACAGCGTAGCCAGGCGCTTGAAGCCCATGCAGCATCTTTTGCAACATTTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC