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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcacacctttttttctttttggttcattttgttttattataacttttatttcagcattccttatccatgttatgctttgcttggacctactctgagctcagTCGGATGAGCAATGCTGTAATTCTTGCGAAGAAGTCAGGGAAGCATATAAGAAGAAAGGGTGGGCTCTAACAAATCCTGACCTAATTGACCAG

Basic information

species Zea mays
transcript GRMZM2G161019_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G161019_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g41120.1 (Oryza sativa), 3'ss of exon 5
gtatgcacacctttttttctttttggttcattttgttttattataacttttatttcagcattccttatccatgttatgctttgcttggaccta-------------ctctgagct-cagTCGGATGAGCAATGCTGTAATTCTTGCGAAGAAGTCAGGGAAGCATATAAGAAGAAAGGGTGGGCTCTAACAAATCCTGACCTAATTGACCAG
||||||||| |||| | | | ||||||||| || | |||||||||| ||| | | || | ||||| | ||| |||| || ||||||||||| ||||||||||||||||| |||||||| ||||||||||||||||||||||| ||||| || ||||||||||| || |||||||||
gtatgcacaatcttttctaatgggaatgtattttgttt-atacctcttattatttcagctttctgaacttaccttgttctttgttacattctaactccggatggctttctggacttcagTCGGATGAACAATGCTGTAATTCTTGTGAAGAAGTTAGGGAAGCATATAAGAAGAAAGGATGGGCCCTTACAAATCCTGATCTGATTGACCAG

upper sequence: GRMZM2G161019_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA08G07840.1 (Glycine max), 3'ss of exon 5
gtatgcacaccttt-ttttctttttggttcattttgttttattataacttttatttcagcattccttatccatgttatgctttg-cttggacctactctgagctcagTCGGATGAGCAATGCTGTAATTCTTGCGAAGAAGTCAGGGAAGCATATAAGAAGAAAGGGTGGGCTCTAACAAATCCTGACCTAATTGACCAG
| || | | |||| | | || || || | | | | | |||| ||| ||||| | | |||||||| || || ||| | ||||| ||||| || || |||||||||||||||||||| | |||||||||| ||| ||||| ||||| | |||||| || | ||||| |||
-tgtgtatttgtacactttcatgtcagtgcaacttatactctccaa----tcgtttcttaatttcttatacgt-ctatgctttttctctcactcgttctca-tgcagTCAGATGAACACTGTTGTAATTCTTGCGAAGAAGTGCGTGAAGCATATAGGAAAAAAGGCTGGGCAATGACAAATATGGATTTGATTGATCAG
















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|71331223|gb|DR802438.1|DR802438
EST:     GGCTTGACAAAGGTGAACAATATTGTGGCACGTGTTATGGTGCTGAAGAG                         TCGGATGAGCAATGCTGTAATTCTTGCGAAGAAGTCAGGGAAGCATATAAG
genomic: GGCTTGACAAAGGTGAACAATATTGTGGCACGTGTTATGGTGCTGAAGAGgtatgcacac ... ctgagctcagTCGGATGAGCAATGCTGTAATTCTTGCGAAGAAGTCAGGGAAGCATATAAG
EST: gi|149112736|gb|EE295558.2|EE295558
EST:     GGCTTGACAAAGGTGAACAATATTGTGGCACGTGTTATGGTGCTGAAGAG                         TCCGATGAGCAATGCT
genomic: GGCTTGACAAAGGTGAACAATATTGTGGCACGTGTTATGGTGCTGAAGAGgtatgcacac ... ctgagctcagTCGGATGAGCAATGCT
EST: gi|149015010|gb|EE044754.2|EE044754
EST:     GGCTTGACAAAGGTGAACAATATTGTGGCACGTGTTATGGTGCTGAAGAG                         TCGGATGAGCAATGCTGTAATTCTTGCGAAGAAGTCAGGGAAGCATATAAG
genomic: GGCTTGACAAAGGTGAACAATATTGTGGCACGTGTTATGGTGCTGAAGAGgtatgcacac ... ctgagctcagTCGGATGAGCAATGCTGTAATTCTTGCGAAGAAGTCAGGGAAGCATATAAG
EST: gi|71772297|gb|DR970233.1|DR970233
EST:     GGCTTGACAAAGGTGAACAATATTGTGGCACGTGTTATGGTGCTGAAGAG                         TCGGATGAGCAATGCTGTAATTCTTGCGAAGAAGTCAGGGAAGCATATAAG
genomic: GGCTTGACAAAGGTGAACAATATTGTGGCACGTGTTATGGTGCTGAAGAGgtatgcacac ... ctgagctcagTCGGATGAGCAATGCTGTAATTCTTGCGAAGAAGTCAGGGAAGCATATAAG
EST: gi|149089164|gb|EE178352.2|EE178352
EST:     GGCTTGACAAAGGTGAACAATATTGTGGCACGTGTTATGGTGCTGAAGAG                         TCGGATGAGCAATGCTGTAATTCTTGCGAAGAAGTCAGGGAAGCATATAAG
genomic: GGCTTGACAAAGGTGAACAATATTGTGGCACGTGTTATGGTGCTGAAGAGgtatgcacac ... ctgagctcagTCGGATGAGCAATGCTGTAATTCTTGCGAAGAAGTCAGGGAAGCATATAAG
EST: gi|74232610|gb|DT640524.1|DT640524
EST:     GGCTTGACAAAGGTGAACAATATTGTGGCACGTGTTATGGTGCTGAAGAG                         TCGGATGAGCAATGCTGTAATTCTTGCGAAGAAGTCAGGGAAGCATATAAG
genomic: GGCTTGACAAAGGTGAACAATATTGTGGCACGTGTTATGGTGCTGAAGAGgtatgcacac ... ctgagctcagTCGGATGAGCAATGCTGTAATTCTTGCGAAGAAGTCAGGGAAGCATATAAG
EST: gi|71328273|gb|DR800766.1|DR800766
EST:     GGCTTGACAAAGGTGAACAATATTGTGGCACGTGTTATGGTGCTGAAGAG                         TCGGATGAGCAATGCTGTAATTCTTGCGAAGAAGTCAGGGAAGCATATAAG
genomic: GGCTTGACAAAGGTGAACAATATTGTGGCACGTGTTATGGTGCTGAAGAGgtatgcacac ... ctgagctcagTCGGATGAGCAATGCTGTAATTCTTGCGAAGAAGTCAGGGAAGCATATAAG
EST: gi|148948260|gb|EC893776.2|EC893776
EST:     GGCTTGACAAAGGTGAACAATATTGTGGCACGTGTTATGGTGCTGAAGAG                         TCGGATGAGCAATGCTGTAATTCTTGCGAAGA-GTCAGGGAAGCATATAAG
genomic: GGCTTGACAAAGGTGAACAATATTGTGGCACGTGTTATGGTGCTGAAGAGgtatgcacac ... ctgagctcagTCGGATGAGCAATGCTGTAATTCTTGCGAAGAAGTCAGGGAAGCATATAAG
EST: gi|149071871|gb|EE160258.2|EE160258
EST:     GGCTTGACAAAGGTGAACAATATTGTGGCACGTGTTATGGTGCTGAAGAG                         TCGGATGAGCAATGCTGTAATTCTTGCGAAGAAGTCAGGGAAGCATATAAG
genomic: GGCTTGACAAAGGTGAACAATATTGTGGCACGTGTTATGGTGCTGAAGAGgtatgcacac ... ctgagctcagTCGGATGAGCAATGCTGTAATTCTTGCGAAGAAGTCAGGGAAGCATATAAG
EST: gi|86465733|gb|DY232106.1|DY232106
EST:     GGCTTGACAAAGGAGAACAATATTGTGGCACGTGTTATGGTGCTGAAGAG                         TCGGATGAGCAATGCTGTAATTCTTGC
genomic: GGCTTGACAAAGGTGAACAATATTGTGGCACGTGTTATGGTGCTGAAGAGgtatgcacac ... ctgagctcagTCGGATGAGCAATGCTGTAATTCTTGC
EST: gi|74242178|gb|DT650092.1|DT650092
EST:     GGCTTGACAAAGGTGAACAATATTGTGGCACGTGTTATGGTGCTGAAGAG                         TCGGATGAGCAATGCTGTAATTCTTGCGAAGAAGTCAGGGAAGCATATAAG
genomic: GGCTTGACAAAGGTGAACAATATTGTGGCACGTGTTATGGTGCTGAAGAGgtatgcacac ... ctgagctcagTCGGATGAGCAATGCTGTAATTCTTGCGAAGAAGTCAGGGAAGCATATAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttcagcattccttatccatgttatgctttgcttggacctactctgagctcagTCGGATGAGCAATGCTGTAATTCTTGCGAAGAAGTCAGGGAAGCATATAAGAAGAAAGGGTGGGCTCTAACAAATCCTGACCTAATTGACCAG
                                       cctactct  CT-rich tract
 atgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcacacctttttttctttttggttcattttgttttattataacttttatttcagcattccttatccatgttatgctttgcttggacctactctgagctcagTCGGATGAGCAATGCTGTAATTCTTGCGAAGAAGTCAGGGAAGCATATAAGAAGAAAGGGTGGGCTCTAACAAATCCTGACCTAATTGACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA