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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGATATGAAGGATAAGGTCCTACGCAGCTATGCTGAGATGGAGAATGTCCTTGCCAGAACAAAGCGTGAGTCAGAGAACACCAAGAAGTATGCCATACAGgttcgcgcatcatatttactcgtttggtttgtaggtttttattgtacaaggatttgataatatttgtctgtctctgaaacatgctcacacttgatggttc...

Basic information

species Zea mays
transcript GRMZM2G002440_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G002440_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os08g25090.2 (Oryza sativa), 5'ss of exon 3
AGATATGAAGGATAAGGTCCTACGCAGCTATGCTGAGATGGAGAATGTCCTTGCCAGAACAAAGCGTGAGTCAGAGAACACCAAGAAGTATGCCATACAGgttcgcgcatcatatttactcgtttggtttgtaggtttttattgtac---aaggatttgataatatttgtctgtctctgaaacatgctcacacttgatggttc
||| ||||||||||| || | ||||||||||| ||||||||||| ||| |||| |||||||||||||| ||||| || | ||||||||||| ||||||| | || | | || | ||| ||| | || || ||| || | | | | | | || ||| |
AGACATGAAGGATAAAGTTTTGCGCAGCTATGCAGAGATGGAGAACGTCATTGCGAGAACAAAGCGTGAATCAGATAATGCAAAGAAGTATGCAGTACAGgtctgtattctatgtctggtcatg-attttttagaatcttgttttactttggaaatgagctcacgtctattcatccctgtag---------------------

upper sequence: GRMZM2G002440_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT4G26780.1 (Arabidopsis thaliana), 5'ss of exon 2
AGATATGAAGGATAAGGTCCTACGCAGCTATGCTGAGATGGAGAATGTCCTTGCCAGAACAAAGCGTGAGTCAGAGAACACCAAGAAGTATGCCATACAGgttcgcgcatcatatttactcgtttggtttgtaggtttt-tattgtacaaggatttgataatatttgtctgtctctgaaacatgctcacacttgatggttc
| |||| || || || || |||| ||||||||||||||||||||| | | |||||||| ||||| | || |||||||| ||||||||| |||||||| | | |||| |||||||| || |||| | | || || ||| | | || | | | | | | ||| ||
GCAGTTGAAAGACAAAGTTCTTCGCACTTATGCTGAGATGGAGAATGTCATGGACAGAACAAGACGTGATGCTGAAAACACCAAAAAGTATGCCGTACAGgttag-------tctttaagaacttggtttgcagcttttgtttcatataatagttttctgaaatatatatattcactatatatgtatgcag----------
















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|50332490|gb|CO527616.1|CO527616
EST:     TTGCCAGAACAAAGCGTGAGTCAGAGAACACCAAGAAGTATGCCATACAG                         AGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTGTCTCGGGCATCA
genomic: TTGCCAGAACAAAGCGTGAGTCAGAGAACACCAAGAAGTATGCCATACAGgttcgcgcat ... ttacatacagAGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTGTCTCGGGCATCA
EST: gi|37394200|gb|CF634371.1|CF634371
EST:     TTGCCAGAACAAAGCGTGAGTCAGAGAACACCAAGAAGTATGCCATACAG                         AGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTGTCTCGGGCATCA
genomic: TTGCCAGAACAAAGCGTGAGTCAGAGAACACCAAGAAGTATGCCATACAGgttcgcgcat ... ttacatacagAGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTGTCTCGGGCATCA
EST: gi|148953359|gb|EE152852.2|EE152852
EST:     TTGCCAGAACAAAGCGTGAGTCAGAGAACACCAAGAAGTATGCCATACAG                         AGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTGTCTCGGGCATCA
genomic: TTGCCAGAACAAAGCGTGAGTCAGAGAACACCAAGAAGTATGCCATACAGgttcgcgcat ... ttacatacagAGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTGTCTCGGGCATCA
EST: gi|5847121|gb|AW000200.1|AW000200
EST:     TTGCCAGAACAAAGCGTGAGTCAGAGAACACCAAGAAGTATGCCATACAG                         AGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTGTCTCGGGCATCA
genomic: TTGCCAGAACAAAGCGTGAGTCAGAGAACACCAAGAAGTATGCCATACAGgttcgcgcat ... ttacatacagAGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTGTCTCGGGCATCA
EST: gi|13237180|gb|BG355194.1|BG355194
EST:     ATGCCATACAG                         AGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTGTCTCGGGCATCA
genomic: ATGCCATACAGgttcgcgcat ... ttacatacagAGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTGTCTCGGGCATCA
EST: gi|78088183|gb|DV516576.1|DV516576
EST:     TTGCCAGAACAAAGCGTGAGTCAGAGAACACCAAGAAGTATGCCATACAG                         AGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTGTCTCGGGCATCA
genomic: TTGCCAGAACAAAGCGTGAGTCAGAGAACACCAAGAAGTATGCCATACAGgttcgcgcat ... ttacatacagAGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTGTCTCGGGCATCA
EST: gi|74234070|gb|DT641984.1|DT641984
EST:     TTGCCAGAACAAAGCGTGAGTCAGAGAACACCAAGAAGTATGCCATACAG                         AGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTGTCTCGGGCATCA
genomic: TTGCCAGAACAAAGCGTGAGTCAGAGAACACCAAGAAGTATGCCATACAGgttcgcgcat ... ttacatacagAGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTGTCTCGGGCATCA
EST: gi|74240578|gb|DT648492.1|DT648492
EST:     TTGCCAGAACAAAGCGTGAGTCAGAGAACACCAAGAAGTATGCCATACAG                         AGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTGTCTCGGGCATCA
genomic: TTGCCAGAACAAAGCGTGAGTCAGAGAACACCAAGAAGTATGCCATACAGgttcgcgcat ... ttacatacagAGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTGTCTCGGGCATCA
EST: gi|67042408|gb|CO468663.1|CO468663
EST:     TTGCCAGAACAAAGCGTGAGTCAGAGAACACCAAGAAGTATGCCATACAG                         AGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTGTCTCGGGCATCA
genomic: TTGCCAGAACAAAGCGTGAGTCAGAGAACACCAAGAAGTATGCCATACAGgttcgcgcat ... ttacatacagAGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTGTCTCGGGCATCA
EST: gi|5895637|gb|AW036883.1|AW036883
EST:     TTGCCAGAACAAAGCGTGAGTCAGAGAACACCACGAAGTATGCCATACAG                         AGCTTCTCCAAGAGACTTGGTAGATGGTGCAGACCATTTTGTCTCGGGCAT
genomic: TTGCCAGAACAAAGCGTGAGTCAGAGAACACCAAGAAGTATGCCATACAGgttcgcgcat ... ttacatacagAGCTTCTCCAAGAG-CTTGTTAGATGTTGCAGACAATTT-GTCTCGGGCAT
EST: gi|74234069|gb|DT641983.1|DT641983
EST:     AAGAAGTATGCCATACAG                         AGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTGTCTCGGGCATCA
genomic: AAGAAGTATGCCATACAGgttcgcgcat ... ttacatacagAGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTGTCTCGGGCATCA
EST: gi|148956597|gb|EC902445.2|EC902445
EST:     TTGCCAGAACAAAGCGTGAGTCAGAGAACACCAAGAAGTATGCCATACAG                         AGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTGTCTCGGGCATCA
genomic: TTGCCAGAACAAAGCGTGAGTCAGAGAACACCAAGAAGTATGCCATACAGgttcgcgcat ... ttacatacagAGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTGTCTCGGGCATCA
EST: gi|5343189|gb|AI795374.1|AI795374
EST:     TTGCCAGAACAAAGCGTGAGTCAGAGAACACCAAGAAGTATGCCATACAG                         AGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTGTCTCGGGCATCA
genomic: TTGCCAGAACAAAGCGTGAGTCAGAGAACACCAAGAAGTATGCCATACAGgttcgcgcat ... ttacatacagAGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTGTCTCGGGCATCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGATATGAAGGATAAGGTCCTACGCAGCTATGCTGAGATGGAGAATGTCCTTGCCAGAACAAAGCGTGAGTCAGAGAACACCAAGAAGTATGCCATACAGgttcgcgcatcatatttactcgtttggtttgtaggtttttattgtacaaggatttgataatatttgtctgtctctgaaacatgctcacacttgatggttc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT