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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCAACAGCAGTTAAGGGTGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACAGGGAAGgtatatgcctgcctatattcttttaatcttaatttacaaatgtgtcaaacgtgttccataaaactaggacaatatttattgttgataaagaatggggaca...

Basic information

species Zea mays
transcript GRMZM2G064023_T03
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G064023_T04 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os11g33240.3 (Oryza sativa), 5'ss of exon 6
GGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCAACAGCAGTTAAGGGTGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACAGGGAAGgtatatgcctgcctatattcttttaatcttaatttacaaatgtgtcaaacgtgttccataaaa-----ctaggacaatatttattgttgataaagaatggggaca
|||||||||||||||||||||||| |||||||||||||||||| |||| ||||| ||||||||||| |||||||||||||||||||||||||| || ||||| |     |  |  |  |  |  |||| |  || |  |||   |  |   | | |||  |||      |     || |    ||||||||  || | | |    
GGGTCTCTCGATTCCAGAGTGCCAGAAAGTGCTGCCAACAGCAATTAAAGGTGGAGAACCTTTGCCGGAGGGTCTCCTTTGGCTTCTTTTGACTGGAAAGgtttggcttttgcctttcttatagaatccttgttga--aatagtttgatgatctgccaataaagttccttccagaaacagggcttgttgattcagtaggagc---

upper sequence: GRMZM2G064023_T04 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 5'ss of exon 7
GGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCAACAGCAGTTAAGGGTGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACAGGGAAGgtatatgcctgcctatattcttttaatcttaatttacaaatgtgtcaaacgtgttccataaaactaggacaatattta-ttgttgataaagaatgg-ggaca--------------
|||||||||||||||||||||||| ||||||||||| ||||||||||| | ||| || ||||||||||||||||| ||||||||||||||||| || ||||| |  | || | | | ||    |  | ||   ||  |||  ||     | |||||     |  |  | |   |||||  || |  |   || ||   |  |              
GGGTCTCTCGATTCCAGAGTGCCAGAAAGTGCTGCCGACAGCAGTTAAAGATGGGGAGCCTTTGCCTGAGGGTCTACTTTGGCTTCTTTTGACCGGAAAGgttt--ggcttcttttgtttaactgttttt--cttgtaaacttggttttcctgttctt---atttttgtcggcatttagctgctagtgtggactgataggtatttgtttgtttcag

upper sequence: GRMZM2G064023_T04 (Zea mays), 5'ss of exon 7
lower sequence: Vv13s0156g00180.t01 (Vitis vinifera), 5'ss of exon 7
GGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCAACAGCAGTTAAGGGTGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACAGGGAAGgtatatgcctgcctatattcttttaatcttaatttacaaatgtgtcaaacgtgttccataaaactaggacaatatttattgttgataaagaatggggaca--------
|||| | || || || || |||||||||||  | ||||  |||      ||||| || ||| ||||||||||||| |||||||||||||||||||| |||||   |   ||   | |        |    |  |||||         || |  |   | || |  ||||  | |||   |||      | ||| ||   |        
GGGTATGTCTATCCCTGAATGCCAAAAAGTATTACCAAATGCAACACCTGGTGGAGAGCCTCTGCCTGAGGGTCTGCTTTGGCTTCTTTTGACAGGAAAGgtgggtttgtgttaaaaac------aaaagacattacaggatacctgaatgaat--gaaaataggaggaagacattgcatgtcatatgaaaattggtttatgaggttt

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|211399063|gb|FL099822.1|FL099822
EST:     GTGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACAGGGAAG                         GTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
genomic: GTGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACAGGGAAGgtatatgcct ... cttgttttagGTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
EST: gi|8103179|gb|AW927835.1|AW927835
EST:     GTGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACAGGGAAG                         GTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
genomic: GTGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACAGGGAAGgtatatgcct ... cttgttttagGTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
EST: gi|76287895|gb|DV027463.1|DV027463
EST:     GTGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACAGGGAAG                         GTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
genomic: GTGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACAGGGAAGgtatatgcct ... cttgttttagGTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
EST: gi|4609628|gb|AI600467.1|AI600467
EST:     GTGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACAGGGAAG                         GTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
genomic: GTGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACAGGGAAGgtatatgcct ... cttgttttagGTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
EST: gi|149082725|gb|EE171943.2|EE171943
EST:     GTGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACAGGGAAG                         GTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
genomic: GTGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACAGGGAAGgtatatgcct ... cttgttttagGTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
EST: gi|71450120|gb|DR831170.1|DR831170
EST:     GTGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACAGGGAAG                         GTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
genomic: GTGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACAGGGAAGgtatatgcct ... cttgttttagGTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
EST: gi|213174510|gb|FM184748.1|FM184748
EST:     GTGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACAGGGAAG                         GTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
genomic: GTGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACAGGGAAGgtatatgcct ... cttgttttagGTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
EST: gi|149077813|gb|EE166538.2|EE166538
EST:     GTGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACAGGGAAG                         GTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
genomic: GTGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACAGGGAAGgtatatgcct ... cttgttttagGTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
EST: gi|211269893|gb|FL099813.1|FL099813
EST:     TGGTGAACCTTTGCCTGNAGG-TCTCCTTTGGCTTCTTTTGACAGGGAAG                         GTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
genomic: TGGTGAACCTTTGCCTG-AGGGTCTCCTTTGGCTTCTTTTGACAGGGAAGgtatatgcct ... cttgttttagGTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
EST: gi|32859373|gb|CD999054.1|CD999054
EST:     GTGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACAGGGAAG                         GTCCCAACCAAAGAGCAAGGTGATGCACTATCAAAGGAATTGCTTGCGCGC
genomic: GTGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACAGGGAAGgtatatgcct ... cttgttttagGTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
EST: gi|149090362|gb|EE179668.2|EE179668
EST:     GTGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACAGGGAAG                         GTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
genomic: GTGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACAGGGAAGgtatatgcct ... cttgttttagGTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCAACAGCAGTTAAGGGTGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACAGGGAAGgtatatgcctgcctatattcttttaatcttaatttacaaatgtgtcaaacgtgttccataaaactaggacaatatttattgttgataaagaatggggaca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cataaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ataaagaa