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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attaccataggtccatagtctttcagtagtgtgctcttggtttctttgttgtttcctttttctcatatgatacgcttttgtggtttacaatgtcttgcagGGAGGATGTGGTGTCATTGTCGAATGGTGTATTTGCCAATGTGCTACATTTATGGGAAGAGGTTTGTTGGCCGAATCACACCACTTCTGTTGGAATTAAG

Basic information

species Zea mays
transcript GRMZM2G023798_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G023798_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g04710.2 (Oryza sativa), 3'ss of exon 5
--------------------------attaccataggtccatagtctttcagtagtgtgctc-ttggtttctttgttgt---ttcctttttctcatatgata---cgcttttgtggtttacaatgtcttgcagGGAGGATGTGGTGTCATTGTCGAATGGTGTATTTGCCAATGTGCTACATTTATGGGAAGAGGTTTGTTGGCCGAATCACACCACTTCTGTTGGAATTAAG
                          ||   |     |  |  || | | | || | |  || ||  |||  ||| |||   || | ||    |   | ||      ||  |    |||| |||    || |||| | |||||||||||||| || ||||| |||||||| ||||| ||||||||||| ||||||||||| |||| | | |||||| || | |||||||||||
gttgtgctccccctgtaggcatttatatcttctcctattgaatgtatatga-taatatattcattactttgcttgctgtagattacattagtgctagtaatttcttactgataaactttataattatgtgaagGGCGAATGTGGTGTCATTGCCGGATGGTTTATTTGCCTATGTGTTACATTTATGGAAAGAGGTTTGTGGGCCCAGTTACACCAATTATATTGGAATTAAG

upper sequence: GRMZM2G023798_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA01G00430.2 (Glycine max), 3'ss of exon 6
attaccataggtccatagtctttcagtagtgtgctcttggttt----ctttgttgtttcctttttctcatatgatacgcttttgtggtttac---aatgtcttgcagGGAGGATGTGGTGTCATTGTCGAATGGTGTATTTGCCAATGTGCTACATTTATGGGAAGAGGTTTGTTGGCCGAATCACACCACTTCTGTTGGAATTAAG
       ||  |   | ||||||    | ||||  | | ||||     |   ||  ||| || |    | | || |    |      ||||    ||||  || |||| |||||||||||||| || || ||||| |||||||| |||| |||| | ||||| |||||||||||||| | |||| |||||    | ||    || ||
-------taaattggttgtctttagtcattgtgaacattgtttgatgttccattcattctttatgtaaacaggaaataaatcatatttttatgctaatgcattacagGAAGGATGTGGTGTCACTGCCGGATGGTCTATTTGCCGATGTCCTACTTATATGGCAAGAGGTTTGTTGGTCCAATCTCACCAACAGTATTATCTTTGAG

upper sequence: GRMZM2G023798_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT2G07050.1 (Arabidopsis thaliana), 3'ss of exon 5
attaccataggtccatagtctttcagtagtgtgctcttggtttctttgttgtttcctttttctcata-tgatacgcttttgt--ggtttacaatgtcttgc---agGGAGGATGTGGTGTCATTGTCGAATGGTGTATTTGCCAATGTGCTACATTTATGGGAAGAGGTTTGTTGGCCGAATCACACCACTTCTGTTGGAATTAAG
      ||| |    |  | |   |  | |    | || |||  | ||    || || |    || | | |  |       |  | || |   | ||||||   ||| ||||||||||| ||||||||||||||||| ||||| ||||  ||  | ||||| || |||||||| || |  || ||  |   | | ||   | | ||
------atatggttttcttttgctacaacttgctttttagttcttatgcatattgctatagtgcacagtaaagcatcagaataagattaattttctcttgctccagGAAGGATGTGGTGCCATTGTCGAATGGTGTACTTGCCGATGTCGTATTTGTATGGAAAAAGGTTTGTGGGTCCCATAACGTCCACTGTTTTATCACTGAG

upper sequence: GRMZM2G023798_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv09s0054g01110.t01 (Vitis vinifera), 3'ss of exon 7
----attacca-taggtcca-tagtctttcag--tagtgtgctcttggtttctttgttgtttcctttttctcatatgatacgcttttgtggtttacaatgtcttgcagGGAGGATGTGGTGTCATTGTCGAATGGTGTATTTGCCAATGTGCTACATTTATGGGAAGAGGTTTGTTGGCCGAATCACACCACTTCTGTTGGAATTAAG
     |||||| ||  |     ||  ||||||  |  | |  ||||| |          |||  ||| |      || ||  |||||    |||    | |||   |||  | ||||||||||||||  |||||||||||||||| ||||  ||||| |||||||||||||||||||| | ||| |||||     |  |  | || ||
acaagttaccaataaattaggcagcttttcaggttgattttatcttgctgcaagcaggattttatttgtt---ggtggtaaacttttaaatttt----tatct-atagGACGAATGTGGTGTCATTGCAGAATGGTGTATTTGCCCATGTCGTACATATATGGGAAGAGGTTTGTTGGTCCAATTACACCTACAATTATTTATTTGAG

upper sequence: GRMZM2G023798_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv09s0054g01180.t01 (Vitis vinifera), 3'ss of exon 4
----attaccataggtcca--tagtctttcagtagtgtgctcttggtttctttgttgtttcctttttctcatatgatacgcttttgtggtttacaatgtcttgcagGGAGGATGTGGTGTCATTGTCGAATGGTGTATTTGCCAATGTGCTACATTTATGGGAAGAGGTTTGTTGGCCGAATCACACCACTTCTGTTGGAATTAAG
     |||||| |     |   ||  ||||||     |  | |     |  | |  |  |  | ||| ||| ||| ||  ||||     |||    | |||   |||  | |||||||||||||| ||||||||||||||||| ||||  ||||| |||||||||||||||||||| | ||| |||||     |  |    || ||
acaagttaccaaaaaattaggcagcttttcaggttgattttatctcactgctagcaggattttatttgtca-atggtaaactttcaaatttt----tatct-atagGACGAATGTGGTGTCATTGCCGAATGGTGTATTTGCCCATGTCGTACATATATGGGAAGAGGTTTGTTGGTCCAATTACACCCACAATTATTTCTTTGAG

upper sequence: GRMZM2G023798_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv09s0054g01120.t01 (Vitis vinifera), 3'ss of exon 4
----attaccataggtcca--tagtctttcagtagtgtgctcttggtttctttgttgtttcctttttctcatatgatacgcttttgtggtttacaatgtcttgcagGGAGGATGTGGTGTCATTGTCGAATGGTGTATTTGCCAATGTGCTACATTTATGGGAAGAGGTTTGTTGGCCGAATCACACCACTTCTGTTGGAATTAAG
     |||||| |     |  |||  |||||      |  | |    ||    |  |  |  | ||| |||  || ||  ||||     |||      |     |||  |||||   || | ||||||||||||||||||||| ||||  ||||| |||||||||||||||||||| |  || |||||     |  |    || ||
acaagttaccaaaaaattaggtagcttttcaagttgattttatctcattgcaagcaggattttatttgtca-gtggtaaactttcaaattttt-----ttccatagGACGGATGAATTGCCCTTGTCGAATGGTGTATTTGCCCATGTCGTACATATATGGGAAGAGGTTTGTTGGTCCGATTACACCCACAATTATTTCCTTGAG

upper sequence: GRMZM2G023798_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv09s0018g00630.t01 (Vitis vinifera), 3'ss of exon 5
----attacca-taggtcca-tagtctttcagtagtgtgctcttggtttctttgttgtttcctttttctcatatgatacgcttttgtggtttacaatgtcttgcagGGAGGATGTGGTGTCATTGTCGAATGGTGTATTTGCCAATGTGCTACATTTATGGGAAGAGGTTTGTTGGCCGAATCACACCACTTCTGTTGGAATTAAG
     |||||| ||  |     ||  ||||||     |  | |     |    |  |  |  | ||| |    |||||  ||||     |||    | |||   |||  | |||||||||||||| ||||||||||||||||| ||||  ||||| |||||||||||||||||||| | ||| |||||     |  |    || ||
acaagttaccaataaattaggcagcttttcaggttgattttatcttactgcaagcaggattttatttgttg-gtgataaactttcaaatttt----tatct-atagGACGAATGTGGTGTCATTGCCGAATGGTGTATTTGCCCATGTCGTACATATATGGGAAGAGGTTTGTTGGTCCAATTACACCTACAATTATTTCTTTGAG

upper sequence: GRMZM2G023798_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv09s0054g01250.t01 (Vitis vinifera), 3'ss of exon 2
----attacca-taggtcca-tagtctttcagtagtgtgctcttggtttctttgttgtttcctttttctcatatgatacgcttttgtggtttacaatgtcttgcagGGAGGATGTGGTGTCATTGTCGAATGGTGTATTTGCCAATGTGCTACATTTATGGGAAGAGGTTTGTTGGCCGAATCACACCACTTCTGTTGGAATTAAG
     |||||| ||  |     ||  ||||||   | |  | |     |    |     |  | ||| |    || || |||||     |||    | |||   |||  |||||||||||||||| |||||||| |||||||| ||||  ||||| |||||||||||||||||||| | ||| |||||     |  |    || ||
acaagttaccaataaattaggcagcttttcaggtttattttatctcactacaagcaagattttatttattg-gtggtaagctttcaaatttt----tatct-atagGACGGATGTGGTGTCATTGCCGAATGGTTTATTTGCCCATGTCATACATATATGGGAAGAGGTTTGTTGGTCTAATTACACCCACAATTATTTCTTTGAG

upper sequence: GRMZM2G023798_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv11s0065g00640.t01 (Vitis vinifera), 3'ss of exon 6
attaccataggtccatagtctttcagtagtgtgctcttggtttctttgttgtttcctttttctc-atatgatacgcttttgtggtttacaatgtcttgcagGGAGGATGTGGTGTCATTGTCGAATGGTGTATTTGCCAATGTGCTACATTTATGGGAAGAGGTTTGTTGGCCGAATCACACCACTTCTGTTGGAATTAAG
 | ||  ||  |   | |   || | |||||  ||  |   || |    | || |   | | || |    ||         |  ||| |||| |  |||||| |||||||||||||| ||  | ||||| |||||||| ||||  ||| | |||||||||||||||||||| |   |||||||     | |||   || ||
gtgactttatttggttggaaattaattagtgaacttgtaaattttcaaattttcctactctgtccaagaaatggagaagaattttttccaat-ttgtgcagGAAGGATGTGGTGTCACTGCAGGATGGTTTATTTGCCTATGTCATACTTATATGGGAAGAGGTTTGTTGGTCCTCTCACACCTACAGTATTGTCTTTGAG

upper sequence: GRMZM2G023798_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv09s0054g01090.t01 (Vitis vinifera), 3'ss of exon 5
----attacca-taggtcca-tagtctttcagtagtgtgctcttggtttctttgttgtttcctttttctcatatgatacgcttttgtggtttacaatgtcttgcagGGAGGATGTGGTGTCATTGTCGAATGGTGTATTTGCCAATGTGCTACATTTATGGGAAGAGGTTTGTTGGCCGAATCACACCACTTCTGTTGGAATTAAG
     |||||| ||  |     ||  ||||||     |  | |   | |    |  |  |  | ||| ||   || ||  ||||     |||    | |||   |||  |||||||||||||||| ||||||||||||||||| ||||  ||||| ||||| |||||||||||||| | ||| |||||     |  |    || ||
acaagttaccaataaattaggcagcttttcaggttgattttatctctctgcaagcaggattttatttgtcg-gtggtaaactttcaaatttt----tatct-atagGACGGATGTGGTGTCATTGCCGAATGGTGTATTTGCCCATGTCGTACATATATGGAAAGAGGTTTGTTGGTCCAATTACACCCACAATTATTTCTTTGAG

upper sequence: GRMZM2G023798_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv09s0054g01550.t01 (Vitis vinifera), 3'ss of exon 5
----attaccataggtcca--tagtctttcagtagtgtgctcttggtttctttgttgtttcctttttctcatatgatacgcttttgtggtttacaatgtcttgcagGGAGGATGTGGTGTCATTGTCGAATGGTGTATTTGCCAATGTGCTACATTTATGGGAAGAGGTTTGTTGGCCGAATCACA-CCACTTCTGTTGGAATTAAG
     ||||   |     |  | |  ||||||     |  | |    || |  |     |  | ||| | |  || ||  ||||     |||    | |||   |||  |||||||||||||||| ||||||||||||||||| ||||  ||  | |||||||||| ||||||||| | ||||||| ||||   | ||    || ||
acaagttactgaaaaattaggtggcttttcaggttgattttatctcgttgtaagcaagattttatttgtta-gtggtaaactttcaaatttt----tatct-atagGACGGATGTGGTGTCATTGCCGAATGGTGTATTTGCCCATGTCATATTTATATGGGAAGAAGTTTGTTGGTCCAATCACATCCACAATTATTTCT-TTGAG

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|211505955|gb|FL017761.1|FL017761
EST:     GGTGCCACCAGAAGTATGGCTACTGCCATATCTCCTCCCATTTCACCCAG                         GGAGGATGTGGTGTCATTGTCGAATGGTGTATTTGCCAATGTGCTACATTT
genomic: GGTGCCACCAGAAGTATGGCTACTGCCATATCTCCTCCCATTTCACCCAGgttctgcttt ... tgtcttgcagGGAGGATGTGGTGTCATTGTCGAATGGTGTATTTGCCAATGTGCTACATTT
EST: gi|211505957|gb|FL017763.1|FL017763
EST:     GGTGCCACCAGAAGTATGGCTACTGCCATATCTCCTCCCATTTCACCCAG                         GGAGGATGTGGTGTCATTGTCGAATGGTGTATTTGCCAATGNGCTACATTT
genomic: GGTGCCACCAGAAGTATGGCTACTGCCATATCTCCTCCCATTTCACCCAGgttctgcttt ... tgtcttgcagGGAGGATGTGGTGTCATTGTCGAATGGTGTATTTGCCAATGTGCTACATTT
EST: gi|211505958|gb|FL017764.1|FL017764
EST:     GGTGCCACCAGAAGTATGGCTACTGCCATATCTCCTCCCATTTCACCCAG                         GGAGGATGTGGTGTCATTGTCGAATGGTGTATTTGCCAATGTGCTACATTT
genomic: GGTGCCACCAGAAGTATGGCTACTGCCATATCTCCTCCCATTTCACCCAGgttctgcttt ... tgtcttgcagGGAGGATGTGGTGTCATTGTCGAATGGTGTATTTGCCAATGTGCTACATTT
EST: gi|211505959|gb|FL017765.1|FL017765
EST:     GGTGCCACCAGAAGTATGGCTACTGNCATATCTCCTCCCATTTCACCCAG                         GGAGGATGTGGTGTCATTGTCGAATGGTGTATTTGCCAATGTGCTACATTT
genomic: GGTGCCACCAGAAGTATGGCTACTGCCATATCTCCTCCCATTTCACCCAGgttctgcttt ... tgtcttgcagGGAGGATGTGGTGTCATTGTCGAATGGTGTATTTGCCAATGTGCTACATTT
EST: gi|211505960|gb|FL017766.1|FL017766
EST:     GGTGCCACCAGAAGTATGGCTACTGCCATATCTCCTCCCATTTCACCCAG                         GGAGGATGTGGTGTCATTGTCGAATGGTGTATTTGCCAATGTGCTACATTT
genomic: GGTGCCACCAGAAGTATGGCTACTGCCATATCTCCTCCCATTTCACCCAGgttctgcttt ... tgtcttgcagGGAGGATGTGGTGTCATTGTCGAATGGTGTATTTGCCAATGTGCTACATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttgtttcctttttctcatatgatacgcttttgtggtttacaatgtcttgcagGGAGGATGTGGTGTCATTGTCGAATGGTGTATTTGCCAATGTGCTACATTTATGGGAAGAGGTTTGTTGGCCGAATCACACCACTTCTGTTGGAATTAAG
                   atatgata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attaccataggtccatagtctttcagtagtgtgctcttggtttctttgttgtttcctttttctcatatgatacgcttttgtggtttacaatgtcttgcagGGAGGATGTGGTGTCATTGTCGAATGGTGTATTTGCCAATGTGCTACATTTATGGGAAGAGGTTTGTTGGCCGAATCACACCACTTCTGTTGGAATTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG