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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGCTGATTTTTCACCACCTTGGAAGATCTTGGAGAAAGCCCCCAGAGAAGgtgagagagatatggcttgaccaccaatgcaaagaaaaaatgaggaatttctgctcagttatagtaggtgatggagctctttaattcttaatgtagggttgcttataattaccaaatgttcatatgcag

Basic information

species Zea mays
transcript GRMZM2G064212_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G064212_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g27350.2 (Oryza sativa), 5'ss of exon 4
GCGCTGATTTTTCACCACCTTGGAAGATCTTGGAGAAAGCCCCCAGAGAAGgtgagagagat-atggcttgaccaccaatgcaaagaaaaaatgaggaatttctgct--cagttatagtaggtgatggagctcttt-aattcttaatgtagggttgcttataattaccaaatgttcatatgcag
||  ||||||| ||||| |||||||| ||||||||||||||| || ||||||||||| | || |   | ||  |    ||   ||||  |||| |  | |||||| |   |||| |||||||||||||| |||||| ||||  ||||||||||||||||||||| | | |||||||||||||||
GCATTGATTTTCCACCATCTTGGAAGGTCTTGGAGAAAGCCCTCACAGAAGgtgagatacatgactacctgttc--tgatcttaagactaaataaa-attttctgtttttagttgtagtaggtgatggacctcttttaatttgtaatgtagggttgcttataatgatcgaatgttcatatgcag

upper sequence: GRMZM2G064212_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g27350.2 (Oryza sativa), 5'ss of exon 4
GCGCTGATTTTTCACCACCTTGGAAGATCTTGGAGAAAGCCCCCAGAGAAGgtgagagagat-atggcttgaccaccaatgcaaagaaaaaatgaggaatttctgct--cagttatagtaggtgatggagctcttt-aattcttaatgtagggttgcttataattaccaaatgttcatatgcag
||  ||||||| ||||| |||||||| ||||||||||||||| || ||||||||||| | || |   | ||  |    ||   ||||  |||| |  | |||||| |   |||| |||||||||||||| |||||| ||||  ||||||||||||||||||||| | | |||||||||||||||
GCATTGATTTTCCACCATCTTGGAAGGTCTTGGAGAAAGCCCTCACAGAAGgtgagatacatgactacctgttc--tgatcttaagactaaataaa-attttctgtttttagttgtagtaggtgatggacctcttttaatttgtaatgtagggttgcttataatgatcgaatgttcatatgcag

upper sequence: GRMZM2G064212_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os04g58560.1 (Oryza sativa), 5'ss of exon 4
GCGCTGATTTTTCACCACCTTGGAAGATCTTGGAGAAAGCCCCCAGAGAAGgtgagagagatatggcttgaccaccaatgcaaagaaaaaatgaggaatttctgctcagttatagtaggtgatggagctctttaattcttaatgtagggttgcttataattaccaaatgttcatatgcag
||  ||||||| ||||| ||||| ||||||||||||| ||||   |||||||||||| | ||   |  |  |  |  ||   |||| ||    |    | | |  |||||| |||||||||||||  ||||||                     || ||| | |||||||||||||||||
GCATTGATTTTCCACCATCTTGGCAGATCTTGGAGAAGgcccttggagaaggtgagatacat---gactacctgctgatcttaagacaatgaaaattttcttttttcagttgtagtaggtgatgggcctcttt---------------------tacaatgatcaaatgttcatatgcag

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|91050792|gb|EB161210.1|EB161210
EST:     CGCTGATTTTTCACCACCTTGGAAGATCTTGGAGAAAGCCCCCAGAGAAG                         CCATACAACCCAGATTATATAGGGGTCTTACACCTATTCGGTGATTCTGAA
genomic: CGCTGATTTTTCACCACCTTGGAAGATCTTGGAGAAAGCCCCCAGAGAAGgtgagagaga ... tcatatgcagCCATACAACCCAGATTATATAGGGGTCTTACACCTATTCGGTGATTCTGAA
EST: gi|93284688|gb|EB676952.1|EB676952
EST:     CGCTGATTTTTCACCACCTTGGAAGATCTTGGAGAAA-CCCCCAGAGAAG                         CCATACAACCCAGAT-ATATAGGGGTCTTAC
genomic: CGCTGATTTTTCACCACCTTGGAAGATCTTGGAGAAAGCCCCCAGAGAAGgtgagagaga ... tcatatgcagCCATACAACCCAGATTATATAGGGGTCTTAC
EST: gi|60341279|gb|DN208252.1|DN208252
EST:     CGCTGATTTTTCACCACCTTGGAAGATCTTGGAGAAAGCCCCCAGAGAAG                         CCATACAACCCAGATTATATAGGGGTCTTACACCTATTCGGTGATTCTGAA
genomic: CGCTGATTTTTCACCACCTTGGAAGATCTTGGAGAAAGCCCCCAGAGAAGgtgagagaga ... tcatatgcagCCATACAACCCAGATTATATAGGGGTCTTACACCTATTCGGTGATTCTGAA
EST: gi|76926912|gb|DV171049.1|DV171049
EST:     CGCTGATTTTTCACCACCTTGGAAGATCTTGGAGAAAGCCCCCAGAGAAG                         CCATACAACCCAGATTATATAGGGGTCTTACACCTATTCGGTGATTCTGAA
genomic: CGCTGATTTTTCACCACCTTGGAAGATCTTGGAGAAAGCCCCCAGAGAAGgtgagagaga ... tcatatgcagCCATACAACCCAGATTATATAGGGGTCTTACACCTATTCGGTGATTCTGAA
EST: gi|71320082|gb|DR796796.1|DR796796
EST:     CGCTGATTTTTCACCACCTTGGAAGATCTTGGAGAAAGCCCCCAGAGAAG                         CCATACAACCCAGATTATATAGGGGTCTTACACCTATTCGGTGATTCTGAA
genomic: CGCTGATTTTTCACCACCTTGGAAGATCTTGGAGAAAGCCCCCAGAGAAGgtgagagaga ... tcatatgcagCCATACAACCCAGATTATATAGGGGTCTTACACCTATTCGGTGATTCTGAA
EST: gi|211065965|gb|FK946610.1|FK946610
EST:     CGCTGATTTTTCACCACCTTGGAAGATCTTGGAGAAAGCCCCCAGAGAAG                         CCATACAACCCAGATTATATAGGGGTCTTACACCTATTCGGTGATTCTGAA
genomic: CGCTGATTTTTCACCACCTTGGAAGATCTTGGAGAAAGCCCCCAGAGAAGgtgagagaga ... tcatatgcagCCATACAACCCAGATTATATAGGGGTCTTACACCTATTCGGTGATTCTGAA
EST: gi|148958416|gb|EC904649.2|EC904649
EST:     CGCTGATTTTTCACCACCTTGGAAGATCTTGGAGAAAGCCCCCAGAGAAG                         CCATACAACCCAGATTATATAGGGGTCTTACACCTATTCGGTGATTCTGAA
genomic: CGCTGATTTTTCACCACCTTGGAAGATCTTGGAGAAAGCCCCCAGAGAAGgtgagagaga ... tcatatgcagCCATACAACCCAGATTATATAGGGGTCTTACACCTATTCGGTGATTCTGAA
EST: gi|148965028|gb|EE015858.2|EE015858
EST:     CGCTGATTTTTCACCACCTTGGAAGATCTTGGAGAAAGCCCCCAGAGAAG                         CCATACAACCCAGATTATATAGGGGTCTTACACCTATTCGGTGATTCTGAG
genomic: CGCTGATTTTTCACCACCTTGGAAGATCTTGGAGAAAGCCCCCAGAGAAGgtgagagaga ... tcatatgcagCCATACAACCCAGATTATATAGGGGTCTTACACCTATTCGGTGATTCTGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGCTGATTTTTCACCACCTTGGAAGATCTTGGAGAAAGCCCCCAGAGAAGgtgagagagatatggcttgaccaccaatgcaaagaaaaaatgaggaatttctgctcagttatagtaggtgatggagctctttaattcttaatgtagggttgcttataattaccaaatgttcatatgcag

- GCTGAT
- - - - - - - - - - TGGAAG
- - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - -  GGAGAA