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

GATTTTCAAAGATTCCTGGACAACGTGCAATACAAAACAAGTGGGATATTACGTTATGAGCGTGTCTTTGGTGAAGGTTTTGTGAGCACTGGTGGAATCGgtgagcccatcaattgcctttgtttactgctaactcaccaatcatttatgctatacatagatcacactgtatccgtttcatgaacag

Basic information

species Zea mays
transcript GRMZM2G170400_T03
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G170400_T03 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os05g47545.1 (Oryza sativa), 5'ss of exon 7
GATTTTCAAAGATTCCTGGACAACGTGCAATACAAAACAAGTGGGATATTACGTTATGAGCGTGTCTTTGGTGAAGGTTTTGTGAGCACTGGTGGAATCGgtgagcccatcaattgcctttgtttactgctaactcaccaatcatttatgctatacatagatcacactgtatccgtttcatgaacag
|  || ||||||||||||||||| ||||| |||||||| | ||| || ||||| |||||||||||||| || || |||| ||| |||||||||||||| ||| ||   | ||||| ||||   |  ||  |||     ||| ||||||  | || || |   ||  || |||     | ||||||||
GGATTCCAAAGATTCCTGGACAATGTGCAGTACAAAACCACTGGAATCTTACGCTATGAGCGTGTCTTCGGAGAGGGTTATGTCAGCACTGGTGGAATTGgtcagttgaacaatttccttgcct--ctattaaaatgtcaa-catttactc-attcaaa---catgct-tat-----tgatgaacag

upper sequence: GRMZM2G170400_T03 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA07G11580.1 (Glycine max), 5'ss of exon 6
GATTTTCAAAGATTCCTGGACAACGTGCAATACAAAACAAGTGGGATATTACGTTATGAGCGTGTCTTTGGTGAAGGTTTTGTGAGCACTGGTGGAATCGgtgagcccatcaattgcctttgtttact-------gctaactcaccaatcatttatgctatacatagatcacactgtatccgtttcatgaacag--------
|  || || || ||| | || |  ||  | || ||    |  |  || |||| ||||||| |||| |||||| |||||||||||||||| || ||| | |||  |    ||| || ||||| | |  |       | ||  | |   |  ||||    |  |   || |     |||||  |    |||| |          
GGGTTCCAGAGGTTCTTAGATAGTGTTGAGTATAATCATAAGGATATTTTACTTTATGAGAGTGTTTTTGGTCAAGGTTTTGTGAGCACAGGAGGACTTGgtatgtt-gtcattttcctttctctcttatgctttgttatgtgatggagaattttcctttcattaaggtagggatgtatg-gaagaatgatctttctcaatg

upper sequence: GRMZM2G170400_T03 (Zea mays), 5'ss of exon 5
lower sequence: AT1G48600.1 (Arabidopsis thaliana), 5'ss of exon 6
GATTTTCAAAGATTCCTGGACAACGTGCAATACAAAACAAGTGGGATATTACGTTATGAGCGTGTCTTTGGTGAAGGTTTTGTGAGCACTGGTGGAATCGgtgagcccatcaat-tgcctttgtttac-tgctaactcac-caatcatttatgctatacatagatcacactgtatccgtttcatgaacag
||||| ||  | ||| ||||||| || ||||||||  | |||||||| || || ||||||||||||||||| ||||| | |||||||||||||||| | ||| |  ||||   |   | ||| | | | |    ||  ||  | |  | |   ||     |       |   | |   |||| | |||||
GATTTCCAGCGTTTCTTGGACAATGTTCAATACAAGTCTAGTGGGATCTTGCGCTATGAGCGTGTCTTTGGGGAAGGATATGTGAGCACTGGTGGATTTGgtaattccattcttactcttttatcttcatatggacatacgtacttgtattgtctgagtgttatctttatgttcttgttttccttaacag

upper sequence: GRMZM2G170400_T03 (Zea mays), 5'ss of exon 5
lower sequence: AT1G73600.1 (Arabidopsis thaliana), 5'ss of exon 7
GATTTTCAAAGATTCCTGGACAACGTGCAATACAAAACAAGTGGGATATTACGTTATGAGCGTGTCTTTGGTGAAGGTTTTGTGAGCACTGGTGGAATCGgtgagcccatcaattgcc---tttgt-ttactgctaactcaccaatcattta--tgctatacatagatcacactgtatccgtttcatgaacag--------------------------------------
|  || ||| | ||| ||||||| || || || ||  | ||||| || ||||| ||||||||||||||||| ||||| ||||| ||||| || ||| |||||  || | | | |   |   ||||| | |    |     |   ||  ||    |  |  |  ||  | | || | | || ||   ||||                                         
GGCTTCCAACGCTTCTTGGACAATGTCCAGTATAAGTCTAGTGGTATCTTACGCTATGAGCGTGTCTTTGGAGAAGGGTTTGTTAGCACAGGGGGACTCGgtatgctctttagtcatcgagtttgtatcaactttgcagtattgatggttctgtttttgaatttaagttatacag-aaccattaagtgaagctatcttttcttcttattatacttgtttcttttgatatag

upper sequence: GRMZM2G170400_T03 (Zea mays), 5'ss of exon 5
lower sequence: AT3G18000.1 (Arabidopsis thaliana), 5'ss of exon 7
GATTTTCAAAGATTCCTGGACAACGTGCAATACAAAACAAGTGGGATATTACGTTATGAGCGTGTCTTTGGTGAAGGTTTTGTGAGCACTGGTGGAATCGgtga--gccca--tcaattgcctttgtttactgctaactcac-caatcatttatgctatacatagatcacactgtatc-cgtttcatgaa-cag
|  || ||| | ||| ||||||| || ||||||||| | ||||| ||  |||| |||||||||||||||||  |||| |||||||||||||||||| | ||| |  || ||  || ||| |  |||| |  || |           ||||||| ||  ||| ||  |     | | ||  ||||| |||  |||
GGCTTCCAACGTTTCTTGGACAATGTCCAATACAAATCCAGTGGAATCCTACGCTATGAGCGTGTCTTTGGCCAAGGGTTTGTGAGCACTGGTGGACTTGgtaaaagctcaattcgatttcgcttgtgttgtgatgttctgtgtcttcattta-gcagtacttatgt-gtgttctgtcgtgtttcttgattcag

upper sequence: GRMZM2G170400_T03 (Zea mays), 5'ss of exon 5
lower sequence: Vv01s0011g05200.t01 (Vitis vinifera), 5'ss of exon 7
GATTTTCAAAGATTCCTGGACAACGTGCAATACAAAACAAGTGGGATATTACGTTATGAGCGTGTCTTTGGTGAAGGTTTTGTGAGCACTGGTGGAATCGgtgagcccatcaatt--gcctttgtttactgctaactcaccaa-tcatttatgctatacatagatcacac-tgtatcc-gtttcatgaacag--------
|  || ||| | |||||||| || || || || |||   || || |||||||| ||||| ||||||||||||||||| |||||||| || || ||| | |||  | | |        |  ||    ||    || | ||  || |   || | || |   |   |  | |   ||||  ||||||    | |        
GGGTTCCAACGTTTCCTGGATAATGTACAGTATAAATGCAGGGGCATATTACGCTATGAACGTGTCTTTGGTGAAGGCTTTGTGAGTACAGGGGGACTTGgtatgacaaatttccaagttttctcctaactttagcacaataacttgcttgtcctttgtttttgttgctcacatatcaagtttcagactccgaattttga

upper sequence: GRMZM2G170400_T03 (Zea mays), 5'ss of exon 5
lower sequence: Vv01s0011g05220.t01 (Vitis vinifera), 5'ss of exon 6
GATTTTCAAAGATTCCTGGACAACGTGCAATACAAAACAAGTGGGATATTACGTTATGAGCGTGTCTTTGGTGAAGGTTTTGTGAGCACTGGTGGAATCGgtgagcccatcaattgc-ctttgtttactgctaactcaccaatcatttatgctatac---atagatcacact---gtatccgtttcat---gaacag---
                              || ||    || || || ||||| ||||||||  ||||||||||||||||||| |||||||| ||| | |||  | | |  ||      ||| | ||     | |  |   |    || | || |||   || | ||  ||     |||  | | |||    | ||    
------------------------------TATAAGTGCAGGGGCATCTTACGATATGAGCGCATCTTTGGTGAAGGTTTTGTAAGCACTGGGGGACTTGgtatggctactaaccaagttttctctaacttcagcaaagtgacttattttactttacttgatggctcgtacattaatatgagctccatctcaaccaaatt

upper sequence: GRMZM2G170400_T03 (Zea mays), 5'ss of exon 5
lower sequence: PP1S60_199V6.1 (Physcomitrella patens), 5'ss of exon 5
GATTTTCAAAGATTCCTGGACAACGTGCAATACAAAACAAGTGGGATATTACGTTATGAGCGTGTCTTTGGTGAAGGTTTTGTGAGCACTGGTGGAATCGgtgagcccatcaattgcctttgtttactgctaactcaccaatcatt-tatgctatacatagatcac-actgtatccgtttcatgaacag-----------------------
  ||| || |  ||  |||||| |   || ||||   ||| ||| ||  | ||||| |||||| | ||||| ||||| ||||| ||||| |||||||||||||||      | |   | ||  |   | ||     |     ||   |   |||  | || ||| | | ||   | |||   |||  |                        
TGTTTCCAGAAGTTTTTGGACACCCAACAGTACACGTCAACTGGAATCCTGCGTTACGAGCGTATTTTTGGAGAAGGATTTGTTAGCACGGGTGGAATCGgtgagtattggagtctacatttctattttctctgggatgtgccaagatgctctaatcttaaatccctattgacactgttaactgattactgttacggatacttctgcttcag

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|211037925|gb|FK976248.1|FK976248
EST:     ACGTTATGAGCGTGTCTTTGGTGAAGGTTTTGTGAGCACTGGTGGAATCG                         AGACTACAAAGGAATTTGTGGGCATGCTCGATCTTAAACCGGGCCAGAAAG
genomic: ACGTTATGAGCGTGTCTTTGGTGAAGGTTTTGTGAGCACTGGTGGAATCGgtgagcccat ... tcatgaacagAGACTACAAAGGAATTTGTGGGCATGCTCGATCTTAAACCGGGCCAGAAAG
EST: gi|9952581|gb|BE639269.1|BE639269
EST:     ACGTTACGAGCGTGTCTTTGGTGAAGG-GTTGTGAGCACTGGTGGAATCG                         AGACAACAAAGGAATTTGTGGGCATGCTCGATCTTAAACCGGGCCAGAAAG
genomic: ACGTTATGAGCGTGTCTTTGGTGAAGGTTTTGTGAGCACTGGTGGAATCGgtgagcccat ... tcatgaacagAGACTACAAAGGAATTTGTGGGCATGCTCGATCTTAAACCGGGCCAGAAAG
EST: gi|211517250|gb|FL335505.1|FL335505
EST:     ACGTTACGAGCGTGTCTTTGGTGAAGGTTTTGTGAGCACTGGTGGAATCG                         AGACAACCAAGGAATTTGT
genomic: ACGTTATGAGCGTGTCTTTGGTGAAGGTTTTGTGAGCACTGGTGGAATCGgtgagcccat ... tcatgaacagAGACTACAAAGGAATTTGT
EST: gi|211422123|gb|FL330491.1|FL330491
EST:     ACGTTACGAGCGTGTCTTTGGTGAAGGTTTTGTGAGCACTGGTGGAATCG                         AGACAACAAAGGAATTTGTGGGCATGCTCGATCTTAAACC
genomic: ACGTTATGAGCGTGTCTTTGGTGAAGGTTTTGTGAGCACTGGTGGAATCGgtgagcccat ... tcatgaacagAGACTACAAAGGAATTTGTGGGCATGCTCGATCTTAAACC
EST: gi|211040372|gb|FK976256.1|FK976256
EST:     ACGTTACGAGCGTGTCTTTGGTGAAGGTTTTGTGAGCACTGGTGGAATCG                         AGACAACAAAGGAATTTGTGGGCATGCTCGATCTTAAACCGGGCCAGAAAG
genomic: ACGTTATGAGCGTGTCTTTGGTGAAGGTTTTGTGAGCACTGGTGGAATCGgtgagcccat ... tcatgaacagAGACTACAAAGGAATTTGTGGGCATGCTCGATCTTAAACCGGGCCAGAAAG
EST: gi|211040370|gb|FK976254.1|FK976254
EST:     ACGTTACGAGCGTGTCTTTGGTGAAGGTTTTGTGAGCACTGGTGGAATCG                         AGACAACAAAGGAATTTGTGGGCATGCTCGATCTTAAACCGGGCCAGAAAG
genomic: ACGTTATGAGCGTGTCTTTGGTGAAGGTTTTGTGAGCACTGGTGGAATCGgtgagcccat ... tcatgaacagAGACTACAAAGGAATTTGTGGGCATGCTCGATCTTAAACCGGGCCAGAAAG
EST: gi|211028113|gb|FK976189.1|FK976189
EST:     GTCTTTGGTGAAGGTTTTGTGAGCACTGGTGGAATCG                         AGACAACAAAGGAATTTGTGGGCATGCTCGATCTTAAACCGGGCCAGAAAG
genomic: GTCTTTGGTGAAGGTTTTGTGAGCACTGGTGGAATCGgtgagcccat ... tcatgaacagAGACTACAAAGGAATTTGTGGGCATGCTCGATCTTAAACCGGGCCAGAAAG
EST: gi|211040369|gb|FK976253.1|FK976253
EST:     ACGTTACGAGCGTGTCTTTGGTGAAGGTTTTGTGAGCACTGGTGGAATCG                         AGACAACAAAGGAATTTGTGGGCATGCTCGATCTTAAACCGGGCCAGAAAG
genomic: ACGTTATGAGCGTGTCTTTGGTGAAGGTTTTGTGAGCACTGGTGGAATCGgtgagcccat ... tcatgaacagAGACTACAAAGGAATTTGTGGGCATGCTCGATCTTAAACCGGGCCAGAAAG
EST: gi|211040366|gb|FK976250.1|FK976250
EST:     ACGTTACGAGCGTGTCTTTGGTGAAGGTTTTGTGAGCACTGGTGGAATCG                         AGACAACAAAGGAATTTGTGGGCATGCTCGATCTTAAACCGGGCCAGAAAG
genomic: ACGTTATGAGCGTGTCTTTGGTGAAGGTTTTGTGAGCACTGGTGGAATCGgtgagcccat ... tcatgaacagAGACTACAAAGGAATTTGTGGGCATGCTCGATCTTAAACCGGGCCAGAAAG
EST: gi|211028112|gb|FK976188.1|FK976188
EST:     TGTCTTTGGTGAAGGTTTTGTGAGCACTGGTGGAATCG                         AGACAACAAAGGAATTTGTGGGCATGCTCGATCTTAAACCGGGCCAGAAAG
genomic: TGTCTTTGGTGAAGGTTTTGTGAGCACTGGTGGAATCGgtgagcccat ... tcatgaacagAGACTACAAAGGAATTTGTGGGCATGCTCGATCTTAAACCGGGCCAGAAAG
EST: gi|211148345|gb|FL363504.1|FL363504
EST:     ACGTTACGAGCGTGTCTTTGGTGAAGGTTTTGTGAGCACTGGTGGAATCG                         AGACAACAAAGGAATTTGTGGGCATGCTCGATCTTAAACCGGGCCAGAAAG
genomic: ACGTTATGAGCGTGTCTTTGGTGAAGGTTTTGTGAGCACTGGTGGAATCGgtgagcccat ... tcatgaacagAGACTACAAAGGAATTTGTGGGCATGCTCGATCTTAAACCGGGCCAGAAAG
EST: gi|211028109|gb|FK976185.1|FK976185
EST:     TGTCTTTGGTGAAGGTTTTGTGAGCACTGGTGGAATCG                         AGACAACAAAGGAATTTGTGGGCATGCTCGATCTTAAACCGGGCCAGAAAG
genomic: TGTCTTTGGTGAAGGTTTTGTGAGCACTGGTGGAATCGgtgagcccat ... tcatgaacagAGACTACAAAGGAATTTGTGGGCATGCTCGATCTTAAACCGGGCCAGAAAG
EST: gi|87156028|gb|DY400817.1|DY400817
EST:     TGAAGGTTTTGTGAGCACTGGTGGAATCG                         AGACAACAAAGGAATTTGTGGGCATGCTCGATCTTAAACCGGGCCAGAAAG
genomic: TGAAGGTTTTGTGAGCACTGGTGGAATCGgtgagcccat ... tcatgaacagAGACTACAAAGGAATTTGTGGGCATGCTCGATCTTAAACCGGGCCAGAAAG
EST: gi|211040371|gb|FK976255.1|FK976255
EST:     ACGTTACGAGCGTGTCTTTGGTGAAGGTTTTGTGAGCACTGGTGGAATCG                         AGACAACMAAGGAATTTGTGGGCATGCTCGATCTTAAACCGGGCCAGAAAG
genomic: ACGTTATGAGCGTGTCTTTGGTGAAGGTTTTGTGAGCACTGGTGGAATCGgtgagcccat ... tcatgaacagAGACTACAAAGGAATTTGTGGGCATGCTCGATCTTAAACCGGGCCAGAAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATTTTCAAAGATTCCTGGACAACGTGCAATACAAAACAAGTGGGATATTACGTTATGAGCGTGTCTTTGGTGAAGGTTTTGTGAGCACTGGTGGAATCGgtgagcccatcaattgcctttgtttactgctaactcaccaatcatttatgctatacatagatcacactgtatccgtttcatgaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA