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

gtacacatcacttgtgctcctgtgtgctggattagtgatttgtaaatgtataacagttatgatgttttgaatatttaatgcagGTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGGCCTGGCCGCATAGACAGGAAGATTGAATTTCCAAATCCTAACGAGGAT

Basic information

species Zea mays
transcript GRMZM2G107362_T04
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107362_T04 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g11050.1 (Oryza sativa), 3'ss of exon 6
gtacacatcacttgtgctcctgtgtgctggattagtgatttgtaaatgtataacagtt----atgatgttttgaatatttaatgcagGTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGGCCTGGCCGCATAGACAGGAAGATTGAATTTCCAAATCCTAACGAGGAT
        ||||  |   | | |||  |   |    ||||  |||  ||  |  ||||     |||    || ||| ||  ||||||||| |||||||||| || || |||||||| |||||||| ||||||||||||||||| |||||||||||||| ||||||||||| |||||||| ||||||
--gtgtgccactgctttgcatatgttatatgt-gccgattaataaccgtgaaggagtttattgtgacacgttaaatgttccatgcagGTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGGCCTGGTCGCATAGACAGGAAAATTGAATTTCCTAATCCTAATGAGGAT

upper sequence: GRMZM2G107362_T04 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 6
---------------------------------------gtacacatcacttgtgctcctgtgtgctggattagtgatttgtaaatgta-----taacagttatgatgt---------tttga-----atatttaat-gcagGTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGGCCTGGCCGCATAGACAGGAAGATTGAATTTCCAAATCCTAACGAGGAT
                                        || |  |    ||   |||  ||| ||  |  ||  || |||||  ||      |||||| ||| || |         |||||     || || ||| | ||||||||||||| || ||  | || || ||  ||||||||||||| || || || || || |||||| |||| |||||||||||||| ||||| || || 
gtaaaggagctatactgtaatagtgtattaaggggaattttaaagctagtctgatgtccactgttctaaaa-agaaatatgtaacagttgaacttaacagatattatttaccctctcatttgagaaaaattttcaattgtagGTTTTGATGGCCACCAATCGGATTGATATCCTGGATCAAGCCCTCCTTAGACCAGGACGGATAGACCGGAAAATTGAATTTCCAAACCCTAATGAAGAG

upper sequence: GRMZM2G107362_T04 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA08G24000.1 (Glycine max), 3'ss of exon 6
----------------------------------------------------------------------------------------------gtacacatcacttgtgctcctgtgtgctggattagtgatttgtaaatg---tataacagttatgatgttttgaatatttaat-gcagGTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGGCCTGGCCGCATAGACAGGAAGATTGAATTTCCAAATCCTAACGAGGAT
                                                                                                | | || | ||   ||        |        ||| || | |||    | |    ||| ||| | |   ||| || ||| | ||||||||||||| || ||  | || || ||  ||||||||||||| || || ||||| || || ||| ||||||||||||||||||| ||||| || || 
gtaaaggagctatactgttatgtgtattaaggggaattttaaagctagtcttatgtccactgttctgaaaagaaatctgtaacagttgaacttaacagatattatttactctgtctgactcatttgagatgagttctcaattctttgtggaggttctgaagat--aaattttcaattgtagGTTTTGATGGCCACAAATCGGATTGATATCCTGGATCAAGCCCTCCTTAGACCTGGACGGATTGACCGGAAGATTGAATTTCCAAACCCTAATGAAGAG

upper sequence: GRMZM2G107362_T04 (Zea mays), 3'ss of exon 6
lower sequence: AT5G19990.1 (Arabidopsis thaliana), 3'ss of exon 6
-------------------------gtacacatcacttgtgctcctgtgtgctggatta--gtgatttgtaaatgtata-acagttatgatgttttgaatatttaatgcagGTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGGCCTGGCCGCATAGACAGGAAGATTGAATTTCCAAATCCTAACGAGGAT
                           |  ||| | |||            |||  |||  ||  | || || ||   | | ||| ||  | | || |||   |  |||||||||||||||| || ||  | || || ||| |||||||||| ||||| ||||||||  | || || ||||| ||||||||||| |||||||| || || 
gtacctattaagttgtaaaggaaaaaaaaccataagttgaataggatgagtctgtgttattgtagtctgaaattgctgacagagtcatattctctttaatgactgttgcagGTTTTGATGGCTACAAATCGTATTGATATTCTGGATCAAGCTCTTCTCAGGCCTGGAAGAATTGATAGGAAAATTGAATTTCCTAATCCTAATGAAGAG

upper sequence: GRMZM2G107362_T04 (Zea mays), 3'ss of exon 6
lower sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 6
-------------------gtacacatcacttgtgctcctgtgt--gctggattagtgat-ttgtaaat---gtata-acagttatga--tgttttgaatatttaatgcagGTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGGCCTGGCCGCATAGACAGGAAGATTGAATTTCCAAATCCTAACGAGGAT
                     | | |  | |  ||   |||     | |   |  ||| |  | | |||   | | | | |||| | |  | | || |||   |  |||||||||||||||| || ||  | || || ||| |||||||||| |||||  |||||||  | || || ||||| ||||||||||| |||||||| || || 
gtatgccttatgttgtgaatgaaaaaatagtcatgaagctgaaaaggataactctgtgttactctgaatttcgcagacaaagttgttaattctcttaaatgactgttgcagGTTTTGATGGCTACAAATCGTATTGATATTCTGGATCAAGCTCTTCTCCGGCCTGGAAGGATTGATAGGAAAATTGAATTTCCTAATCCTAATGAAGAG

upper sequence: GRMZM2G107362_T04 (Zea mays), 3'ss of exon 6
lower sequence: Vv04s0008g04690.t01 (Vitis vinifera), 3'ss of exon 6
gtacacatcacttgtgctcctgtgtgctggattagtga---tttgtaaatgta--taacagttatgatgttttgaatatttaatgcagGTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGGCCTGGCCGCATAGACAGGAAGATTGAATTTCCAAATCCTAACGAGGAT
|||| | ||| |  |    ||  ||      | ||| |   |||||   ||||  ||||  || | |||   |||  ||||| | |||||||||||||| || ||  | || || ||||||||||||||||| || |||||||| || || |||||||||||||| || |||||||| ||||| || 
gtactcctcaataatttctcttcgttggtagtaagttaaattttgtctctgtaaataactattgt-atgagatgaccatttattacagGTTTTGATGGCTACAAATCGCATTGATATTTTGGATCAAGCCCTCCTTAGGCCTGGACGAATTGACAGGAAGATTGAGTTCCCAAATCCCAACGAAGAG

upper sequence: GRMZM2G107362_T04 (Zea mays), 3'ss of exon 6
lower sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 6
--------------------------------------------------------------------------------------gtacacatcacttgtgctcctgtgtgctg--------gattagtgatttgtaaa-----tgtataacagttatgatgttttgaatatttaatgcagGTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGGCCTGGCCGCATAGACAGGAAGATTGAATTTCCAAATCCTAACGAGGAT
                                                                                      ||       | ||||  ||  ||    |         | || |  ||| ||  |     | | | | |  | |||     |||  | |   | |||||||| ||||| || ||  |||| || ||| | || |||||||| || ||||| || || || |||||||||||||| ||||||||||| || | ||| 
gtactattaataattgctaccctttttgcttctgctgtagttgtgtgtgcccacttgtattatatttgtgtatttatatgtattatgtgtgtggtatttgttatctagtagaatcagcaaaatggttggaaattggtggaatctgtatgtcatatctgtgacaacatgatcaatattttcagGTTTTAATGGCTACAAATCGAATTGATATTCTTGACCAAGCCCTCCTCAGGCCAGGACGGATTGACAGGAAGATTGAGTTTCCAAATCCCAATGGGGAG

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|20301129|gb|BQ164072.1|BQ164072
EST:     TTGAACTTCTAAACCAGCTCGATGGTTTTGAAGCATCAAACAAAATTAAG                         GTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGG
genomic: TTGAACTTCTAAACCAGCTCGATGGTTTTGAAGCATCAAACAAAATTAAGgtacacatca ... tttaatgcagGTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGG
EST: gi|32843443|gb|CD983124.1|CD983124
EST:     TTGAACTTCTAAACCAGCTTGATGGTTTTGAAGCATCAAACAAAATTAAG                         GTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGG
genomic: TTGAACTTCTAAACCAGCTCGATGGTTTTGAAGCATCAAACAAAATTAAGgtacacatca ... tttaatgcagGTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGG
EST: gi|33095260|gb|CF055254.1|CF055254
EST:     TTGAACTTCTAAACCAGCTTGATGGTTTTGAAGCATCAAACAAAATTAAG                         GTTTTGATGGCAACGAACAGAATAGACATTTTTGATCAAGCCCTTCTGAGG
genomic: TTGAACTTCTAAACCAGCTCGATGGTTTTGAAGCATCAAACAAAATTAAGgtacacatca ... tttaatgcagGTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGG
EST: gi|5847445|gb|AW000524.1|AW000524
EST:     TTGAACTTCTAAACCAGCTTGATGGTTTTGAAGCATCAAACAAAATTAAG                         GTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGG
genomic: TTGAACTTCTAAACCAGCTCGATGGTTTTGAAGCATCAAACAAAATTAAGgtacacatca ... tttaatgcagGTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggattagtgatttgtaaatgtataacagttatgatgttttgaatatttaatgcagGTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGGCCTGGCCGCATAGACAGGAAGATTGAATTTCCAAATCCTAACGAGGAT
                            ttatgatgttttgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacacatcacttgtgctcctgtgtgctggattagtgatttgtaaatgtataacagttatgatgttttgaatatttaatgcagGTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGGCCTGGCCGCATAGACAGGAAGATTGAATTTCCAAATCCTAACGAGGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT