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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatggtgttaattattttctcataattacgcgaacatgaattcttgtcgtgtaactaatacagttgcattgtatgtagCGTTTTATGATGCTAAATCAGTTATTTATCCATGAATCGAGAGAAGATTCTGACCCTCACTGGGACATGAGGCTGGACATTGATGATATGAGTTATGAG

Basic information

species Zea mays
transcript GRMZM2G118344_T05
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G118344_T05 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os05g07070.1 (Oryza sativa), 3'ss of exon 4
gtaaatggtgttaattattttctcataattacgcgaacatgaattcttgt-cgtgtaactaatacagttgcattgtatgtagCGTTTTATGATGCTAAATCAGTTATTTATCCATGAATCGAGAGAAGATTCTGACCCTCACTGGGACATGAGGCTGGACATTGATGATATGAGTTATGAG-
||| ||  | ||   |  | | | |||      | |   | || | |||  |  | | |||||  | || || | | ||||||| |||||||||||  |||||||| ||||||||||||| |||||||  |  || ||||||||||||||||| |||||||||||||| ||||| |||||| 
gtagatattattctctcctct-tgatatcagtacaatgttaaaattttgaacacgcatctaatctattttcactctttgtagCGGTTTATGATGCTGGATCAGTTAGTTATCCATGAATCAAGAGAAGCATTCGATCCTCACTGGGACATGAGACTGGACATTGATGACATGAGCTATGAGG

upper sequence: GRMZM2G118344_T05 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os05g07070.8 (Oryza sativa), 3'ss of exon 5
gtaaatggtgttaattattttctcataattacgcgaacatgaattcttgt-cgtgtaactaatacagttgcattgtatgtagCGTTTTATGATGCTAAATCAGTTATTTATCCATGAATCGAGAGAAGATTCTGACCCTCACTGGGACATGAGGCTGGACATTGATGATATGAGTTATGAG
||| ||  | ||   |  | | | |||      | |   | || | |||  |  | | |||||  | || || | | ||||||| |||||||||||  |||||||| ||||||||||||| |||||||  |  || ||||||||||||||||| |||||||||||||| ||||| ||||||
gtagatattattctctcctct-tgatatcagtacaatgttaaaattttgaacacgcatctaatctattttcactctttgtagCGGTTTATGATGCTGGATCAGTTAGTTATCCATGAATCAAGAGAAGCATTCGATCCTCACTGGGACATGAGACTGGACATTGATGACATGAGCTATGAG

upper sequence: GRMZM2G118344_T05 (Zea mays), 3'ss of exon 6
lower sequence: Vv13s0019g04100.t01 (Vitis vinifera), 3'ss of exon 4
---gtaaatggtg-ttaattattttctcataattacgcgaacatg----aattcttgtcgtgt-aacta--------atacagttgca--ttgtatgtagCGTTTTATGATGCTAAATCAGTTATTTATCCATGAATCGAGAGAAGATTCTGACCCTCACTGGGACATGAGGCTGGACATTGATGATATGAGTTATGAG
    |  ||  |  || |||||  |   |     | | | |  |     | || |  |  ||| || ||        ||| |  ||    ||  ||| ||  | | || ||| |  |    | ||   |  |||  || ||| |    | ||| |   |  ||||||||||||||||||||||||| ||||||||||||
attctggattctccttgattatagtactactgcaaagtggatgtatagcagttttcattttgttaattatatgtcgcatatatctgttatttccatgcagGCTGTCATAATGGTGGACAGCTCATCCTTGTATGGTTCCAGAAATTTGTTTGATCAGTATGGGGACATGAGGCTGGACATTGATGACATGAGTTATGAG

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|74242191|gb|DT650105.1|DT650105
EST:     TTCGTCCACTGGTTATTGAAGAAAATAACTTGAGAGGACCAGCAACCGAG                         CGTTTTATGATGCTAAATCAGTTATTTATCCATGAATCGAGAGAAGATTCT
genomic: TTCGTCCACTGGTTATTGAAGAAAATAACTTGAGAGGACCAGCAACCGAGgtaaatggtg ... ttgtatgtagCGTTTTATGATGCTAAATCAGTTATTTATCCATGAATCGAGAGAAGATTCT
EST: gi|91871238|gb|EB401314.1|EB401314
EST:     TTCGTCCACTGGTTATTGAAGAAAATAACTTGAGAGGACCAGCAACCGAG                         CGTTTTATGATGCTAAATCAGTTATTTATCCATGAATCGAGAGAAGATTTT
genomic: TTCGTCCACTGGTTATTGAAGAAAATAACTTGAGAGGACCAGCAACCGAGgtaaatggtg ... ttgtatgtagCGTTTTATGATGCTAAATCAGTTATTTATCCATGAATCGAGAGAAGATTCT
EST: gi|50334693|gb|CO529819.1|CO529819
EST:     TTCGTCCACTGGTTATTGAAGAAAATAACTTGAGAGGACCAGCAACCGAG                         CGTTTTATGATGCTAAATCAGTTATTTATCCATGAATCGAGAGAAGATTCT
genomic: TTCGTCCACTGGTTATTGAAGAAAATAACTTGAGAGGACCAGCAACCGAGgtaaatggtg ... ttgtatgtagCGTTTTATGATGCTAAATCAGTTATTTATCCATGAATCGAGAGAAGATTCT
EST: gi|6563804|gb|AW231336.1|AW231336
EST:     AAATAACTTGAGAGGACCAGCAACCGAG                         CGGTTTATGATGCTAAATCAGTTATTTATCCATGAATCGAGAGAAGATTCT
genomic: AAATAACTTGAGAGGACCAGCAACCGAGgtaaatggtg ... ttgtatgtagCGTTTTATGATGCTAAATCAGTTATTTATCCATGAATCGAGAGAAGATTCT
EST: gi|60347420|gb|DN214393.1|DN214393
EST:     TTCGTCCACTGGTTATTGAAGAAAATAACTTGAGAGGACCAGCAACCGAG                         CGGTTTATGATGCTAAATCAGTTATTTATCCATGAATCGAGAGAAGATTCT
genomic: TTCGTCCACTGGTTATTGAAGAAAATAACTTGAGAGGACCAGCAACCGAGgtaaatggtg ... ttgtatgtagCGTTTTATGATGCTAAATCAGTTATTTATCCATGAATCGAGAGAAGATTCT
EST: gi|67019275|gb|CO448024.1|CO448024
EST:     TTCGTCCACTGGTTATTGAAGAAAATAACTTGAGAGGACCAGCAACCGAG                         CGGTTTATGATGCTAAATCAGTTATTTATCCATGAATCGAGAGAAGATTCT
genomic: TTCGTCCACTGGTTATTGAAGAAAATAACTTGAGAGGACCAGCAACCGAGgtaaatggtg ... ttgtatgtagCGTTTTATGATGCTAAATCAGTTATTTATCCATGAATCGAGAGAAGATTCT
EST: gi|88748917|gb|DY533058.1|DY533058
EST:     TTCGTCCACTGGTTATTGAAGAAAATAACTTGAGAGGACCAGCAACCGAG                         CGTTTTATGATGCTAAATCAGTTATTTATCCATGAATCGAGAGAAGATTCT
genomic: TTCGTCCACTGGTTATTGAAGAAAATAACTTGAGAGGACCAGCAACCGAGgtaaatggtg ... ttgtatgtagCGTTTTATGATGCTAAATCAGTTATTTATCCATGAATCGAGAGAAGATTCT
EST: gi|116823896|gb|EC867473.1|EC867473
EST:     TTCGTCCACTGGTTATTGAAGAAAATAACTTGAGAGGA-CAGCAACCGAG                         CGTTTTATGATGCTAAATCAGTTATTGATCCATGAATCGAGAGAAGATTCT
genomic: TTCGTCCACTGGTTATTGAAGAAAATAACTTGAGAGGACCAGCAACCGAGgtaaatggtg ... ttgtatgtagCGTTTTATGATGCTAAATCAGTTATTTATCCATGAATCGAGAGAAGATTCT
EST: gi|71427069|gb|DR808119.1|DR808119
EST:     TTCGTCCACTGGTTATTGAAGAAAATAACTTGAGAGGACCAGCAACCGAG                         CGTTTTATGATGCTAAATCAGTTATTTATCCATGAATCGAGAGAAGATTCT
genomic: TTCGTCCACTGGTTATTGAAGAAAATAACTTGAGAGGACCAGCAACCGAGgtaaatggtg ... ttgtatgtagCGTTTTATGATGCTAAATCAGTTATTTATCCATGAATCGAGAGAAGATTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattacgcgaacatgaattcttgtcgtgtaactaatacagttgcattgtatgtagCGTTTTATGATGCTAAATCAGTTATTTATCCATGAATCGAGAGAAGATTCTGACCCTCACTGGGACATGAGGCTGGACATTGATGATATGAGTTATGAG
                             aactaat  putative branch site (score: 2)
                            taactaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatggtgttaattattttctcataattacgcgaacatgaattcttgtcgtgtaactaatacagttgcattgtatgtagCGTTTTATGATGCTAAATCAGTTATTTATCCATGAATCGAGAGAAGATTCTGACCCTCACTGGGACATGAGGCTGGACATTGATGATATGAGTTATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA