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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgtaatacaaggagagttgctaaagccataactgtgaataagcatgttgataatatactgtttgtttttcttttccttgcagAGCTGGCGGTTTACAAGATAAAGATGGTGGCTTGCGAGAGTTGATTGTTGGGAAGGATGATGAGATCCTGAAAACAGAAACAAGAACTATAGCCAGGGCC

Basic information

species Zea mays
transcript GRMZM2G047219_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047219_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g01970.1 (Oryza sativa), 3'ss of exon 5
---------------------gttgtaatacaaggagagttgctaaagccataactgtgaataagcatgttgataatatactgtttgt-ttttcttttccttgcagAGCTGGCGGTTTACAAGATAAAGATGGTGGCTTGCGAGAGTTGATTGTTGGGAAGGATGATGAGATCCTGAAAACAGAAACAAGAACTATAGCCAGGGCC
                     |||| ||| |  | ||| ||  |  | |   ||    ||    ||||       | ||||| |||   |||| ||||   ||||| ||||| || ||||| ||||||||||||||  |||| |||||| ||||||||||||||||||||||| |||| |||||||||| ||||||  |||| || 
aaagaacaaaccctcagtgcagttgaaat-ctggaagaattattgtaacttgaatcaggagattgcat-----cgacatactcttttcattttgtttttaatgcagGGCTGGAGGATTACAGGATAAAGATGGTGGTGTGCGGGAGTTGCTTGTTGGGAAGGATGATGAGATCTTGAAGACAGAAACAAAAACTATTACCAGAGCA
















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|148955762|gb|EC901460.2|EC901460
EST:     AAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATATACAATTATAAG                         AGCTGGCGGTTTACAAGATAAAGATGGTGGCTTGCGAGAGTTGATTGTTGG
genomic: AAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATATACAATTATAAGgttgtaatac ... ttccttgcagAGCTGGCGGTTTACAAGATAAAGATGGTGGCTTGCGAGAGTTGATTGTTGG
EST: gi|211142589|gb|FL359509.1|FL359509
EST:     AAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATATACAATTATAAG                         AGCTGGCGGTTTACAAGGATAAAGATGGTGG
genomic: AAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATATACAATTATAAGgttgtaatac ... ttccttgcagAGCTGGCGGTTTACAAG-ATAAAGATGGTGG
EST: gi|211529297|gb|FL356731.1|FL356731
EST:     AAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATATACAATTATAAG                         AGCTGGCGGTTTACAAGGATAAAGATGGTGG
genomic: AAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATATACAATTATAAGgttgtaatac ... ttccttgcagAGCTGGCGGTTTACAAG-ATAAAGATGGTGG
EST: gi|17931616|gb|BM268576.1|BM268576
EST:     AAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATATACAATTATAAG                         AGCTGGCGGTTTACAAGATAAAGATGGTGGCTTGCGAGAGTTGATTGTTGG
genomic: AAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATATACAATTATAAGgttgtaatac ... ttccttgcagAGCTGGCGGTTTACAAGATAAAGATGGTGGCTTGCGAGAGTTGATTGTTGG
EST: gi|149015400|gb|EE045246.2|EE045246
EST:     AGGCAGAACAGTACCCTAGCAGACTCCGGTCTTCCATATACAATTATAAG                         AGCTGGCGGTTTACAAGATAAAGATGGTGGCTTGCGAGAGTTGATTGTTGG
genomic: AGGCAGAACAGTACC-TAGCAGACTCCGGTCTTCCATATACAATTATAAGgttgtaatac ... ttccttgcagAGCTGGCGGTTTACAAGATAAAGATGGTGGCTTGCGAGAGTTGATTGTTGG
EST: gi|12045929|gb|BF728159.1|BF728159
EST:     AAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATATACAATTATAAG                         AGCTGGCGGTTTACAAGATAAAGATGGTGGCTTGCGAGAGTTGATTGTTGG
genomic: AAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATATACAATTATAAGgttgtaatac ... ttccttgcagAGCTGGCGGTTTACAAGATAAAGATGGTGGCTTGCGAGAGTTGATTGTTGG
EST: gi|211072521|gb|FL326767.1|FL326767
EST:     AAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATATACAATTATAAG                         AGCTGGCGGTTTACAAGATAAAGATGGTGGCTTGCGAGAGTTGATTGTTGG
genomic: AAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATATACAATTATAAGgttgtaatac ... ttccttgcagAGCTGGCGGTTTACAAGATAAAGATGGTGGCTTGCGAGAGTTGATTGTTGG
EST: gi|148996959|gb|EE035773.2|EE035773
EST:     AAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATATACAATTATAAG                         AGCTGGCGGTTTACAAGATAAAGATGGTGGCTTGCGAGAGTTGATTGTTGG
genomic: AAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATATACAATTATAAGgttgtaatac ... ttccttgcagAGCTGGCGGTTTACAAGATAAAGATGGTGGCTTGCGAGAGTTGATTGTTGG
EST: gi|76293497|gb|DV033065.1|DV033065
EST:     AAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATATACAATTATAAG                         AGCTGGCGGTTTACAAGATAAAGATGGTGGCTTGCGAGAGTTGATTGTTGG
genomic: AAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATATACAATTATAAGgttgtaatac ... ttccttgcagAGCTGGCGGTTTACAAGATAAAGATGGTGGCTTGCGAGAGTTGATTGTTGG
EST: gi|211394348|gb|FL351051.1|FL351051
EST:     GGCAGAACAGTACCTAGCAGACTCCGGGTCTTC-ATTATACAATTATAAG                         AGCTGGCGGTTAACAAGATAAAGGATGGTGGCTTGC
genomic: GGCAGAACAGTACCTAGCAGACTCCGG-TCTTCCAT-ATACAATTATAAGgttgtaatac ... ttccttgcagAGCTGGCGGTTTACAAGATAAAG-ATGGTGGCTTGC
EST: gi|32940932|gb|CF045751.1|CF045751
EST:     ACCTAGCAGACTCCGGTCTTCCATATACAATTATAAG                         AGCTGGCGGTTTACAAGATAAAGATGGTGGCTTGCGAGAGTTGATTGTTGG
genomic: ACCTAGCAGACTCCGGTCTTCCATATACAATTATAAGgttgtaatac ... ttccttgcagAGCTGGCGGTTTACAAGATAAAGATGGTGGCTTGCGAGAGTTGATTGTTGG
EST: gi|148966373|gb|EE017367.2|EE017367
EST:     AAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATATACAATTATAAG                         AGCTGGCGGTTTCCAAGATAAAGATGGTGGCTTGCGAGAGTTGATTGTTGG
genomic: AAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATATACAATTATAAGgttgtaatac ... ttccttgcagAGCTGGCGGTTTACAAGATAAAGATGGTGGCTTGCGAGAGTTGATTGTTGG
EST: gi|89762676|gb|DY690164.1|DY690164
EST:     AAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATATACAATTATAAG                         AGCTGGCGGTTTACAAGATAAAGATGGTGGCTTGCGAGAGTTGATTGTTGG
genomic: AAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATATACAATTATAAGgttgtaatac ... ttccttgcagAGCTGGCGGTTTACAAGATAAAGATGGTGGCTTGCGAGAGTTGATTGTTGG
EST: gi|6742502|gb|AW313317.1|AW313317
EST:     AAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATATACAATTATAAG                         AGCTGGCGGTTTACAAGATAAAGATGGTGGCTTGCGAGAGTTGATTGTTGG
genomic: AAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATATACAATTATAAGgttgtaatac ... ttccttgcagAGCTGGCGGTTTACAAGATAAAGATGGTGGCTTGCGAGAGTTGATTGTTGG
EST: gi|71774203|gb|DR972081.1|DR972081
EST:     AAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATATACAATTATAAG                         AGCTGGCGGTTTACAAGATAAAGATGGTGGCTTGCGAGAGTTGATTGTTGG
genomic: AAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATATACAATTATAAGgttgtaatac ... ttccttgcagAGCTGGCGGTTTACAAGATAAAGATGGTGGCTTGCGAGAGTTGATTGTTGG
EST: gi|91055640|gb|EB166058.1|EB166058
EST:     AAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATATACAATTATAAG                         AGCTGGCGGTTTACAAGATAAAGATGGTGGCTTGCGAGAGTTGATTGTTGG
genomic: AAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATATACAATTATAAGgttgtaatac ... ttccttgcagAGCTGGCGGTTTACAAGATAAAGATGGTGGCTTGCGAGAGTTGATTGTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataactgtgaataagcatgttgataatatactgtttgtttttcttttccttgcagAGCTGGCGGTTTACAAGATAAAGATGGTGGCTTGCGAGAGTTGATTGTTGGGAAGGATGATGAGATCCTGAAAACAGAAACAAGAACTATAGCCAGGGCC
                            tactgtttgtttttct  CT-rich tract
                atgttgataatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgtaatacaaggagagttgctaaagccataactgtgaataagcatgttgataatatactgtttgtttttcttttccttgcagAGCTGGCGGTTTACAAGATAAAGATGGTGGCTTGCGAGAGTTGATTGTTGGGAAGGATGATGAGATCCTGAAAACAGAAACAAGAACTATAGCCAGGGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC