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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtcacatcatccatttcaatttcaatttgtatttgtatttttgtgaagttcttaatacataaaatttgctagtagACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGTATTAAGAGAGAGTACAAG

Basic information

species Zea mays
transcript GRMZM2G056393_T02
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G056393_T02 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os03g36780.1 (Oryza sativa), 3'ss of exon 12
gtttgtcacatcatccatttcaatttcaatttgtatttgtatttttgtgaagttcttaatacataaaatttgctagtagACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGTATTAAGAGAGAGTACAAG
||||||    | |||  ||  | |||   | |  || | |   |||||||| ||  |||    |||| |||| | | ||||||||||||| |||||||||||||||||| ||||||| || |||||||| || | |||||||||||||
gtttgttttgttatctgttgtatttt---tctaaatctat-catttgtgaactt--taaagtgtaaattttgatcgcagACAATTATTTCTGGGATGGGTGAGCTGCATTTGGATATCTATGTTGAACGCATCAGGAGAGAGTACAAG

upper sequence: GRMZM2G056393_T02 (Zea mays), 3'ss of exon 12
lower sequence: Vv15s0021g02450.t01 (Vitis vinifera), 3'ss of exon 12
gtttg--tcacatcatccatttca-atttcaatttgtatttgtatttttgtgaagttc--ttaatacataaaa---tttgctagt--agACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGTATTAAGAGAGAGTACAAG
||||   | |   ||| ||||||| |  |   || |     | | |||| | | |       |  |||| |||    || || ||  ||||||||||||| || ||||| ||||||||| |||| || ||||||||||| |||  ||| ||||| |||
gtttaatttatgacatgcatttcacacattccttagaggaagaagttttatcatgcctaaccatgacatcaaaatgctttcttgtgcagACAATTATTTCTGGAATGGGAGAGCTGCATTTGGACATTTACGTTGAACGCATTCGGAGGGAGTATAAG

upper sequence: GRMZM2G056393_T02 (Zea mays), 3'ss of exon 12
lower sequence: PP1S20_94V6.1 (Physcomitrella patens), 3'ss of exon 10
----------------------------------------------------------------------------------gtttgtcacatcatccatttcaatttcaatttgtatttgt--atttttgtgaagttcttaatacataaaatttgcta--gtagACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGTATTAAGAGAGAGTACAAG
                                                                                   ||| |  ||  || |  |||||  | |||     |  |   |||| | ||| |  |             |  | |   | ||||||||||||| |||||||| ||||||||||| || ||||| |||||||| |||    | || ||||||
gtaaatcatttcacagcttgtttttacttgttccttgcttttgtggtacatttattggtattttcaatctccagtgacctaactttattgca--attctattcaaagtgaatggagttcagaggatttatctgaggggccgggactggggcttgagtttctgcagACAATTATTTCGGGGATGGGAGAGCTGCATCTTGACATATATGTTGAACGCATTCGTCGTGAATACAAG

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|32930091|gb|CF034903.1|CF034903
EST:     AAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAG                         ACAATTATTTCAGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGT
genomic: AAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAGgtttgtcaca ... ttgctagtagACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGT
EST: gi|91874831|gb|EB404788.1|EB404788
EST:     AAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAG                         ACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGT
genomic: AAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAGgtttgtcaca ... ttgctagtagACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGT
EST: gi|6194594|gb|AW146698.1|AW146698
EST:     AAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAG                         ACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGT
genomic: AAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAGgtttgtcaca ... ttgctagtagACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGT
EST: gi|6020648|gb|AW065681.1|AW065681
EST:     GGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAG                         ACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGT
genomic: GGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAGgtttgtcaca ... ttgctagtagACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGT
EST: gi|211410070|gb|FL355701.1|FL355701
EST:     AAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAG                         ACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGT
genomic: AAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAGgtttgtcaca ... ttgctagtagACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGT
EST: gi|32801951|gb|CD954187.1|CD954187
EST:     GATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAG                         ACAATTATTTCAGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGT
genomic: GATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAGgtttgtcaca ... ttgctagtagACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGT
EST: gi|118406757|gb|EH038205.1|EH038205
EST:     AAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAG                         ACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGT
genomic: AAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAGgtttgtcaca ... ttgctagtagACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGT
EST: gi|32788275|gb|CD940511.1|CD940511
EST:     GATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAG                         ACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGT
genomic: GATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAGgtttgtcaca ... ttgctagtagACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGT
EST: gi|211409847|gb|FL347405.1|FL347405
EST:     AAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAG                         ACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGT
genomic: AAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAGgtttgtcaca ... ttgctagtagACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGT
EST: gi|67017174|gb|CO445923.1|CO445923
EST:     AAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAG                         ACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGT
genomic: AAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAGgtttgtcaca ... ttgctagtagACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGT
EST: gi|211430479|gb|FL350077.1|FL350077
EST:     AAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAG                         ACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGT
genomic: AAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAGgtttgtcaca ... ttgctagtagACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcaatttgtatttgtatttttgtgaagttcttaatacataaaatttgctagtagACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGTATTAAGAGAGAGTACAAG
                             tcttaat  putative branch site (score: 3)
                         aagttcttaatacata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtcacatcatccatttcaatttcaatttgtatttgtatttttgtgaagttcttaatacataaaatttgctagtagACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGTATTAAGAGAGAGTACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA