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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTTTTATGATGCTAAATCAGTTATTTATCCATGAATCGAGAGAAGATTCTGACCCTCACTGGGACATGAGGCTGGACATTGATGATATGAGTTATGAGgtagtaagattgtaagaaagaacctagataattagtatcacaaaccaacacaggatgtgttctgtaactaatgtaagtttctatgctgttatctgcag

Basic information

species Zea mays
transcript GRMZM2G118344_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G118344_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os05g07070.8 (Oryza sativa), 5'ss of exon 6
CGTTTTATGATGCTAAATCAGTTATTTATCCATGAATCGAGAGAAGATTCTGACCCTCACTGGGACATGAGGCTGGACATTGATGATATGAGTTATGAGgtagtaagattgtaagaaagaacctagataattagtatcacaaaccaacacaggatgtgttctgtaactaatgtaagtttctatgctgttatctgcag
|| |||||||||||  |||||||| ||||||||||||| |||||||  |  || ||||||||||||||||| |||||||||||||| ||||| |||||||||| |||| |  |          |   |  ||| || ||||  |      || |||   | |  ||| |||| || ||| |       |||   |||
CGGTTTATGATGCTGGATCAGTTAGTTATCCATGAATCAAGAGAAGCATTCGATCCTCACTGGGACATGAGACTGGACATTGATGACATGAGCTATGAGgtagaaagaatcaa---------ttttctctttaataccacag-cagctttagaatgctattta-aacaaatgcaacttttt------ctatacacag

upper sequence: GRMZM2G118344_T02 (Zea mays), 5'ss of exon 6
lower sequence: Vv13s0019g04100.t01 (Vitis vinifera), 5'ss of exon 5
CGTTTTATGATGCTAAATCAGTTATTTATCCATGAATCGAGAGAAGATTCTGACCCTCACTGGGACATGAGGCTGGACATTGATGATATGAGTTATGAGgtagtaagattgtaagaaagaacctagataattagtatcacaaaccaacacaggatgtgttctgtaactaatgtaagtttctatgctgttatctgcag
  | | || ||| |  |    | ||   |  |||  || ||| |    | ||| |   |  ||||||||||||||||||||||||| ||||||||||||||    |  ||  |        |||  |     | | | |          |    | |  | |  || || || |   ||    || |          
GCTGTCATAATGGTGGACAGCTCATCCTTGTATGGTTCCAGAAATTTGTTTGATCAGTATGGGGACATGAGGCTGGACATTGATGACATGAGTTATGAGgttactatgtt-cacattgatccctttacttccattcttattgtttctagctccctttaattttaaagtactgca---tttggggcag----------
















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:     CTGACCCTCACTGGGACATGAGGCTGGACATTGATGATATGAGTTATGAG                         GAGCTGCTGGCTTTGGGAGAACGAATAGGCAATGTCAACACGGGCCTAGCT
genomic: CTGACCCTCACTGGGACATGAGGCTGGACATTGATGATATGAGTTATGAGgtagtaagat ... ttatctgcagGAGCTGCTGGCTTTGGGAGAACGAATAGGCAATGTCAACACGGGCCTAGCT
EST: gi|4646562|gb|AI491300.2|AI491300
EST:     TTGACCCTCACTGGGACATGAGGCTGGACATTGATGATATGAGTTATGAG                         GAGCTGCTGGCTTTGGGAGAACGAATAGGCAATGTCAACACGGGCCTAGCT
genomic: CTGACCCTCACTGGGACATGAGGCTGGACATTGATGATATGAGTTATGAGgtagtaagat ... ttatctgcagGAGCTGCTGGCTTTGGGAGAACGAATAGGCAATGTCAACACGGGCCTAGCT
EST: gi|91871238|gb|EB401314.1|EB401314
EST:     TTGACCCTCACTGGGACATGAGGCTGGACATTGATGATATGAGTTATGAG                         GAGCTGCTGGCTTTGGGAGAAGGAATAGGCAATGTCAACACGGGCCTAGCT
genomic: CTGACCCTCACTGGGACATGAGGCTGGACATTGATGATATGAGTTATGAGgtagtaagat ... ttatctgcagGAGCTGCTGGCTTTGGGAGAACGAATAGGCAATGTCAACACGGGCCTAGCT
EST: gi|50334693|gb|CO529819.1|CO529819
EST:     CTGACCCTCACTGGGACATGAGGCTGGACATTGATGATATGAGTTATGAG                         GAGCTGCTGGCTTTGGGAGAACGAATAGGCAATGTCAACACGGGCCTAGCT
genomic: CTGACCCTCACTGGGACATGAGGCTGGACATTGATGATATGAGTTATGAGgtagtaagat ... ttatctgcagGAGCTGCTGGCTTTGGGAGAACGAATAGGCAATGTCAACACGGGCCTAGCT
EST: gi|6563804|gb|AW231336.1|AW231336
EST:     CTGACCCTCACTGGGACATGAGGCTGGACATTGATGATATGAGTTATGAG                         GAGCTGCTGGCTTTGGGAGAACGAATAGGCAATGTCAACACGGGCCTAGCT
genomic: CTGACCCTCACTGGGACATGAGGCTGGACATTGATGATATGAGTTATGAGgtagtaagat ... ttatctgcagGAGCTGCTGGCTTTGGGAGAACGAATAGGCAATGTCAACACGGGCCTAGCT
EST: gi|60347420|gb|DN214393.1|DN214393
EST:     CTGACCCTCACTGGGACATGAGGCTGGACATTGATGATATGAGTTATGAG                         GAGCTGCTGGCTTTGGGAGAACGAATAGGCAATGTCAACACGGGCCTAGCT
genomic: CTGACCCTCACTGGGACATGAGGCTGGACATTGATGATATGAGTTATGAGgtagtaagat ... ttatctgcagGAGCTGCTGGCTTTGGGAGAACGAATAGGCAATGTCAACACGGGCCTAGCT
EST: gi|67019275|gb|CO448024.1|CO448024
EST:     CTGACCCTCACTGGGACATGAGGCTGGACATTGATGATATGAGTTATGAG                         GAGCTGCTGGCTTTGGGAGAACGAATAGGCAATGTCAACACGGGCCTAGCT
genomic: CTGACCCTCACTGGGACATGAGGCTGGACATTGATGATATGAGTTATGAGgtagtaagat ... ttatctgcagGAGCTGCTGGCTTTGGGAGAACGAATAGGCAATGTCAACACGGGCCTAGCT
EST: gi|88748917|gb|DY533058.1|DY533058
EST:     CTGACCCTCACTGGGACATGAGGCTGGACATTGATGATATGAGTTATGAG                         GAGCTGCTGGCTTTGGGAGAACGAATAGGCAATGTCAACACGGGCCTAGCT
genomic: CTGACCCTCACTGGGACATGAGGCTGGACATTGATGATATGAGTTATGAGgtagtaagat ... ttatctgcagGAGCTGCTGGCTTTGGGAGAACGAATAGGCAATGTCAACACGGGCCTAGCT
EST: gi|116823896|gb|EC867473.1|EC867473
EST:     CTGACCCTCACTGGGACATGAGGCTGGACATTGATGATATGAGTTATGAG                         GAGCTGCTGGCTTTGGGAGAACGAATAGGCAATGTCAACACGGGCCTAGCT
genomic: CTGACCCTCACTGGGACATGAGGCTGGACATTGATGATATGAGTTATGAGgtagtaagat ... ttatctgcagGAGCTGCTGGCTTTGGGAGAACGAATAGGCAATGTCAACACGGGCCTAGCT
EST: gi|71427069|gb|DR808119.1|DR808119
EST:     CTGACCCTCACTGGGACATGAGGCTGGACATTGATGATATGAGTTATGAG                         GAGCTGCTGGCTTTGGGAGAACGAATAGGCAATGTCAACACGGGCCTAGCT
genomic: CTGACCCTCACTGGGACATGAGGCTGGACATTGATGATATGAGTTATGAGgtagtaagat ... ttatctgcagGAGCTGCTGGCTTTGGGAGAACGAATAGGCAATGTCAACACGGGCCTAGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGTTTTATGATGCTAAATCAGTTATTTATCCATGAATCGAGAGAAGATTCTGACCCTCACTGGGACATGAGGCTGGACATTGATGATATGAGTTATGAGgtagtaagattgtaagaaagaacctagataattagtatcacaaaccaacacaggatgtgttctgtaactaatgtaagtttctatgctgttatctgcag

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