Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatattctaatcttttgcgtatgctgttaactctgtttagctggaaataacaaagacaacattaaataccacgatttatttagataatatcagaacacatgcgattatcctgaatgagctagtattgtaaattgtagttctacttcaaccaaatcaatttatggttctaatcatgctaactttgtgcagGGACATCACCACTACATTTCCGAGCTTTGTCTTCCATTCTCAGGTCGATGATACCTGAATTTCTGAAAACTAATGAATGTCAGAAGGTGGACTGCTTGCT

Basic information

species Zea mays
transcript GRMZM2G112672_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G112672_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os03g42840.1 (Oryza sativa), 3'ss of exon 7
gtaagatattctaatcttttgcgtatgctgttaactctgtttagctggaaataacaaagacaacattaaataccacgatttatttagataatatcagaacacatgcgattatcctgaatgagctagtattgtaaattgtagttctacttcaaccaaatcaatttatggttctaatcatgctaactttgtgcagGGACATCACCACTACATTTCCGAGCTTTGTCTTCCATTCTCAGGTCGATGATACCTGAATTTCTGAAAACT---------AATG-AATGTCAGAAGGTGGACTGCTTGCT
                                                                                      |||    || | | || |    |  ||||   | |  | |  |  |   | ||   || | ||||  || | | |  ||     |||| |||   ||||||| ||||||||||||| ||||||||||| |||||||||||||||||||| ||||| ||||| |||| | |||| || |         |||| |||| ||||||   |          
--------------------------------------------------------------------------------------gatttagtctggatactttttttcttcctattttacttcgattgctctttggttactccatttca--cagacctaagtac----ctaaccatatcaactttg-gcagGGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGATACTTGAAAT-CTGAGAATTTCCCCCTCCAATGGAATGCCAGAAGACAGT---------

upper sequence: GRMZM2G112672_T02 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA18G08230.1 (Glycine max), 3'ss of exon 9
gtaagatattctaatcttttgcgtatgctgttaactctgtttagctggaaataacaaagacaacattaaataccacgatttatttagataatatcagaacacatgcgattatcctgaatgagctagtattgtaaattgtagttctacttcaaccaaatcaatttatggttctaatcatgctaactttgtgcagGGACATCACCACTACATTTCCGAGCTTTGTCTTCCATTCTCAGGTCGATGATACCTGAATTTCTGAAAACTAATGAATGTCAGAAGGTGGACTGCTTGCT--
                                                                                        |  | |    |||| |||  | | |    |  | |   | || |   || |   | || ||||      |   ||| || |     |  |  |   |||| |||||||||||||||| ||||| ||||||||||| || ||||| || || || ||||| ||||  |       |  |||  | ||      ||| |||| ||    
---------------------------------------------------------------------------------------gtcct-ttgatacacttgccgtgaact---actaacatctgtttttcctttttcctgtatttcactggtgt---tttctgatatcctttttaatgtgtttgggcaggGACATCACCACAACATTCCCGAGCTTTGTATTTCATTCACAAGTAGACGATACTTGAAGATAATTTCTCCCATGGCT-TCTTCCTTTGGGCTGCATGGCCA

upper sequence: GRMZM2G112672_T02 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA08G44580.1 (Glycine max), 3'ss of exon 8
gtaagatattctaatcttttgcgtatgctgttaactctgtttagctggaaataacaaagacaacattaaataccacgatttatttagataatatcagaacacatgcgattatcctgaatgagctagtattgtaaattgtagttctacttcaaccaaatcaatttatggttctaatcatgctaactttgtgcagGGACATCACCACTACATTTCCGAGCTTTGTCTTCCATTCTCAGGTCGATGATACCTGAATTTCTGAAAACTAATGAATGTCAGAAGGTGGACTGCTTGCT-
                                                                                 | | ||||  | | ||| || |    |||||     |||| |||  ||  |   ||   ||  | ||     |       ||| || |     |  |  |   |  | |||||||||||||||| ||||| ||||||||||| |||||||| || || || ||||| ||||  |       |  |||  | ||      ||| |||| ||   
--------------------------------------------------------------------------------cagtgagatg-tgt-agatcatagaacattat-----atgaactaacatctttttttcctgtatttctctggtct------tttctgatatcctttttaatgtgtacgagcagGGACATCACCACAACATTCCCGAGCTTTGTATTCCATTCACAAGTAGACGATACTTGAAGATAATTTCTCCTATGGCT-TCTTCCTTTGGGCTGCATGGCC

upper sequence: GRMZM2G112672_T02 (Zea mays), 3'ss of exon 7
lower sequence: AT4G26560.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaagatattctaatcttttgcgtatgctgttaactctgtttagctggaaataacaaagacaacattaaataccacgatttatttagataatatcagaacacatgcgattatcctgaatgagctagt-attgtaaattgtagttctacttcaaccaaatcaatttatggttctaatcatgctaactttgtgcagGGACATCACCACTACATTTCCGAGCTTTGTCTTCCATTCTCAGGTCGATGATACCTGAATTTCTGAAAACTAATGAATGTCAGAAGGTGGACTGCTTGCT
                                                                                        | |  ||  || ||    || || || ||  |   |||  | || || ||  | || | || || |       ||| |       |    || ||  | |||||||||| ||||| |||||||||||||||||||| || || || || || || |||||||||                                          
---------------------------------------------------------------------------------------gtgagctcctaa-accaaagactaacccga--ggtttagccaatgcaacttcaaatttttctgcatcacgtattattaacaccatgatatctgata-ttgtgtgcagGGATATCACAACTACATTTCCGAGCTTTGTGTTACACTCGCAAGTGGAAGATACCTGA------------------------------------------

upper sequence: GRMZM2G112672_T02 (Zea mays), 3'ss of exon 7
lower sequence: AT5G55990.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaagatattctaatcttttgcgtatgctgttaactctgtttagctggaaataacaaagacaacattaaataccacgatttatttagataatatcagaacacatgcgattatcctgaatgagctagtattgtaaattgtagt-tctacttcaaccaaatcaatttatggttctaat-catgctaactttgtgcagGGACATCACCACTACATTTCCGAGCTTTGTCTTCCATTCTCAGGTCGATGATACCTGAATTTCTGAAAACTAATGAATGTCAGAAGGTGGACTGCTTGCT-
                                                          |  |     ||||    | |||||| ||   |  ||  |||   || | |  |   |   |       |  | |   || || | || |    |   ||   |  |  || | ||  |   ||||  || ||  |||||| ||||| ||||| ||||| |||||||| |||||||||||||| || ||||||||||      ||| | || | | | |||  |   |||  | |  | 
----------------------------------------------------------gtgagttccaaatctttctatttatataaccaggatt-gaatctattcaaccaaattccttctctggtttctctttcttctattctccatgatatgtaataaaggtcgtgatcctgttgtgtgcttgctctg--cagGGATATCACGACTACGTTTCCAAGCTTTGTGTTCCATTCTCAGGTTGAAGATACCTGAAAAAGCAAAAGCAAAAGCAAG-CAGCGGCAAGACATCATTGTA

upper sequence: GRMZM2G112672_T02 (Zea mays), 3'ss of exon 7
lower sequence: AT4G26570.2 (Arabidopsis thaliana), 3'ss of exon 8
gtaagatattctaatcttttgcgtatgctgttaactctgtttagctggaaataacaaagacaacattaaataccacgatttatttagataatatcagaacacatgcgattatcctgaatgagctagtattgtaaattgtagttctacttcaaccaaatcaatttatggttctaatcatgctaactttgtgcagGGACATCACCACTACATTTCCGAGCTTTGTCTTCCATTCTCAGGTCGATGATACCTGAATTTCTGAAAACTAATGAATGTCAGAAGGTG-GACTGCTTGCT----
                                                                                      |  | |  |  |||  |  |  ||||||   | |     | | || || ||  | || |   |     |      ||  |    |  |||      | | |||||||||| || || |||||||||||||||||||| ||||| || ||||| || |||||||||       ||||| |  | || | || ||  | |||   |||      
--------------------------------------------------------------------------------------gtgagttcctaaaccaagac--ttatcc--gaggtttaggcaatgcaacttccaattttttctgtgtta------ttattaacaccgatctctgatattgtgtgcagGGATATAACAACTACATTTCCGAGCTTTGTGTTCCACTCGCAGGTGGAAGATACCTGAG-----AAAAACAATAGCATATTAGCAGAGGAGACAATTTGGGAATT

upper sequence: GRMZM2G112672_T02 (Zea mays), 3'ss of exon 7
lower sequence: Vv19s0015g01070.t01 (Vitis vinifera), 3'ss of exon 7
gtaagatattctaatcttttgcgtatgctgttaactctgtttagctggaaataacaaagacaacattaaataccacgatttatttagataatatcagaacacatgcgattatcctgaatgagctagtattgtaaattgtagttctacttcaaccaaatcaatttatggtt-ctaatcatgctaactttgtgcagGGACATCACCACTACATTTCCGAGCTTTGTCTTCCATTCTCAGGTCGATGATACCTGAATTTCTGAAAACTAATGAATGTCAGAAGGTGG-ACTGCTTGCT
                                                                                        |  |||||    |||     ||||    ||  |  |   |||| |   | |     |   |||| | | |||| | ||| |   |  |  |  |  |||||  ||||||||||||||| ||||| || ||||||||||| |||||||| || || || ||||||| | |   | |  || |       |    ||  | |  |||| 
---------------------------------------------------------------------------------------cttttatcattgtacac----ttatggacaa-aaaatgcaattggatgctatgagctt--ctcaaaccactcaactgatgttgatttgttttatttcctttgaacagGGACATCACCACCACATTCCCAAGCTTTGTCTTTCATTCTCAAGTTGACGACACCTGAAGTCCCATACATGAAAGTTGACTGGTTTTTGTTAATAATTGC-

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|22545746|gb|BU098105.1|BU098105
EST:     ACATGACACTACAATATCTCA-                         GGACATCACCACTACATTTCCGAGCTTTGTCTTCCATTCTCAGGTCGATGA
genomic: ACATGACACTACAATATCTCAAgtaagatatt ... ctttgtgcagGGACATCACCACTACATTTCCGAGCTTTGTCTTCCATTCTCAGGTCGATGA
EST: gi|211284965|gb|FL440139.1|FL440139
EST:     GTAGTGAGGCATCCCTCTTTATTGAAGAACATGACACTACAATATCTCAA                         GGACATCACCACTACATTTCCGAGCTTTGTCTTCCATTCTCAGGTCGATGA
genomic: GTAGTGAGGCATCCCTCTTTATTGAAGAACATGACACTACAATATCTCAAgtaagatatt ... ctttgtgcagGGACATCACCACTACATTTCCGAGCTTTGTCTTCCATTCTCAGGTCGATGA
EST: gi|4610024|gb|AI600863.1|AI600863
EST:     GTAGTGAGGCATCCCTCTTTATTGAAGAACATGACACTACAATATCTCAA                         GGACATCACCACTACATTTCCGAGCTTTGTCTTCCATTCTCAGGTCGATGA
genomic: GTAGTGAGGCATCCCTCTTTATTGAAGAACATGACACTACAATATCTCAAgtaagatatt ... ctttgtgcagGGACATCACCACTACATTTCCGAGCTTTGTCTTCCATTCTCAGGTCGATGA
EST: gi|6445548|gb|AW179511.1|AW179511
EST:     GTAGTGAGGCATCCCTCTTTATTGAAGAACATGACACTACAATATCTCAA                         GGACATCACCACTACATTTCCGAGCTTTGTCTTCCATTCTCAGGTCGATGA
genomic: GTAGTGAGGCATCCCTCTTTATTGAAGAACATGACACTACAATATCTCAAgtaagatatt ... ctttgtgcagGGACATCACCACTACATTTCCGAGCTTTGTCTTCCATTCTCAGGTCGATGA
EST: gi|83279282|gb|DV943290.1|DV943290
EST:     GTAGTGAGGCATCCCTCTTTATTGAAGAACATGACACTACAATATCTCAA                         GGACATCACCACTACATTTCCGAGCTTTGTCTTCCATTCTCAGGTCGATGA
genomic: GTAGTGAGGCATCCCTCTTTATTGAAGAACATGACACTACAATATCTCAAgtaagatatt ... ctttgtgcagGGACATCACCACTACATTTCCGAGCTTTGTCTTCCATTCTCAGGTCGATGA
EST: gi|5650045|gb|AI920405.1|AI920405
EST:     GTAGTGAGGCATCCCTCTTTATTGAAGAACATGACACTACAATATCTCAA                         GGACATCACCACTACATTTCCGAGCTTTGTCTTCCATTCTCAGGTCGATGA
genomic: GTAGTGAGGCATCCCTCTTTATTGAAGAACATGACACTACAATATCTCAAgtaagatatt ... ctttgtgcagGGACATCACCACTACATTTCCGAGCTTTGTCTTCCATTCTCAGGTCGATGA
EST: gi|5901062|gb|AW042162.1|AW042162
EST:     AGGCATCCCTCTTTATTGAAGAACATGACACTACAATATCTCAA                         GGACATCACCACTACATTTCCGAGCTTTGTCTTCCATTCTCAGGTCGATGA
genomic: AGGCATCCCTCTTTATTGAAGAACATGACACTACAATATCTCAAgtaagatatt ... ctttgtgcagGGACATCACCACTACATTTCCGAGCTTTGTCTTCCATTCTCAGGTCGATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagttctacttcaaccaaatcaatttatggttctaatcatgctaactttgtgcagGGACATCACCACTACATTTCCGAGCTTTGTCTTCCATTCTCAGGTCGATGATACCTGAATTTCTGAAAACTAATGAATGTCAGAAGGTGGACTGCTTGCT
                                       tgctaac  putative branch site (score: 1)
                aaatcaatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagatattctaatcttttgcgtatgctgttaactctgtttagctggaaataacaaagacaacattaaataccacgatttatttagataatatcagaacacatgcgattatcctgaatgagctagtattgtaaattgtagttctacttcaaccaaatcaatttatggttctaatcatgctaactttgtgcagGGACATCACCACTACATTTCCGAGCTTTGTCTTCCATTCTCAGGTCGATGATACCTGAATTTCTGAAAACTAATGAATGTCAGAAGGTGGACTGCTTGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA