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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattaattttgtctcctatctctctgtactctttagtgtttgttaccatttcacaatgatggtatctagatgatgcatttggtattctttagGTTTTACGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGCCGGCTGAGGAAAAAG

Basic information

species Zea mays
transcript GRMZM2G056099_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G056099_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g20310.2 (Oryza sativa), 3'ss of exon 4
gtattaattttgtctcctatctctctgtactctttagtgtttgttaccatttcacaatgatggtatctagatgatgcatttggtattctttagGTTTTACGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGCCGGCTGAGGAAAAAG
|| |||||||  |||||||| ||| ||| |     |||| |  ||| | ||||  ||||||||||| |||    |   |||| |||||| ||||| ||||| |||||||| |||||||||||||| ||||||||||| |||||||| ||||||
gtgttaattt-atctcctatttct-tgtgc-----agtgctacttatcctttcttaatgatggtatttaggaagtatgtttgttattctgtagGTGTTACGCCGGCTTGCTCAAAATCGTGAGGCTGCAAGAAAAAGTCGGCTGAGAAAAAAG

upper sequence: GRMZM2G056099_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA19G31050.3 (Glycine max), 3'ss of exon 6
gtattaattttgtctcctatctctctgtactctttagtgtttgttaccatttcacaatgatggtatctagatgatgcatttggtattctttagGTTTTACGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGCCGGCTGAGGAAAAAG
                 | | |  | ||| |  |  |    |   |  |        | |  || |    ||  | |||||   ||||   ||   ||| |||||||||| |||||||||||||| || || |||||||| ||||||||||||
---------------gttgtatg-cagtaattgtgtgcaaatagcataagccttttgttactgtgtgctaatttttcatttttcattc---agACATTAAGACGGCTTGCTCAAAATCGTGAGGCTGCCAGGAAAAGCCGACTGAGGAAAAAG

upper sequence: GRMZM2G056099_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA20G39050.2 (Glycine max), 3'ss of exon 4
-------gtattaattttgtctcctatctctctgtactctttagtgtttgttaccatttcacaatgatggtatctagatgatgcatttggtattcttt--agGTTTTACGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGCCGGCTGAGGAAAAAG
        | || | | | | |   || |   | | |  || | | | |   |   ||  |   |  | ||  |  ||| ||  ||||  || |  ||  ||  | | ||| ||||||| || ||||||||||||||||||||||| ||| |||| || || 
aaaacaaatgtttactctattttaaatttggttatgcggtt-aatatctaaaatt-ttaaatggtatttgttacgtgattattgattttttaattattgcagACTCTCCGAAGGCTTGCTCAGAATCGTGAGGCAGCAAGAAAAAGTCGGTTGAGAAAGAAA

upper sequence: GRMZM2G056099_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA03G28400.1 (Glycine max), 3'ss of exon 1
-------gtattaattttgtctcctatctctctgtactctttagtgtttgttaccatttcacaatgatggtatctagatgatgcatttggtattc-tttagGTTTTACGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGCCGGCTGAGGAAAAAG
        |   ||  ||   | |  |   | ||| |   |  |  |  |  | | |||    |  |||   |     |  |   |||  | ||| || ||   ||| |||||||||| |||||||||||||| || || |||||||| |||||||||| |
ttgaccaatcaaaaggttaaatgcagtaattgtgttcaaat-ggcataagcaagccttttgttactatgcattaatttttctttttttatttttcattcagACATTAAGACGGCTTGCTCAAAATCGTGAGGCTGCCAGGAAAAGCCGACTGAGGAAAATG

upper sequence: GRMZM2G056099_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA03G28320.2 (Glycine max), 3'ss of exon 6
gtattaattttgtctcctatctctctgtactctttagtgtttgttaccatttcacaatgatggtatctagatgatgcatttggtattctttagGTTTTACGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGCCGGCTGAGGAAAAAG
   ||   |        | | |     |    |      |||||||| ||    || | ||    | |   |  |  ||||   ||||   ||   ||| |||||||||| |||||||||||||| || || |||||||| ||||||||||||
--gttgtatgcagtaattgtgttcaaatggcataagccttttgttactat---gcattaat----ttttctttttttatttttcattc---agACATTAAGACGGCTTGCTCAAAATCGTGAGGCTGCCAGGAAAAGCCGACTGAGGAAAAAG

upper sequence: GRMZM2G056099_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT3G12250.5 (Arabidopsis thaliana), 3'ss of exon 4
gtattaattttgtctcctatctctctgtactctttagtgtttgttaccatttcacaatgatggtatctagatgatgcatttggtattctttagGTTTTACGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGCCGGCTGAGGAAAAAG
||  ||  ||  |||| | |   ||      | |  |||| | ||||   |   || | ||    | |   |  |     |  |  ||  |||    | ||  ||||||| ||||||||||||||||||||||||||| |  ||||||| |||
gtgatagattcatctc-tgtggatcaactagcatctgtgtatattacgcatatgca-taatctgttttgtttccttttcgttttgatccatagACCCTTCGTAGGCTTGCTCAAAATCGTGAGGCAGCAAGAAAAAGCAGATTGAGGAAGAAG

upper sequence: GRMZM2G056099_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv08s0007g05170.t01 (Vitis vinifera), 3'ss of exon 5
gtattaattttgtctcctatctctctgtactctttagtgtttgttaccatttcacaatgatggtatctagatgatgcatttggtattctttagGTTTTACGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGCCGGCTGAGGAAAAAG
   ||||  || |    ||  | | | ||     ||  | ||   |  ||     |||| |  ||  | | |  |    |   | ||||| ||   ||||| |||||||| ||||||||||| || || |||||||||||  | |||||||||
--gttaaaatt-taaattagttatatttagatgatacagcttagcataat-----aatgttcttaatttgttcctttgatcaatcttcttcagACATTACGCCGGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATTAAGGAAAAAG

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|78090121|gb|DV518495.1|DV518495
EST:     CTAATTCATCTGACCGGTCTGACAGATCTGACAAACCTATGGACCAGAAG                         GTTTTACGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGCCGGCTG
genomic: CTAATTCATCTGACCGGTCTGACAGATCTGACAAACCTATGGACCAGAAGgtattaattt ... tattctttagGTTTTACGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGCCGGCTG
EST: gi|60397549|gb|DN230365.1|DN230365
EST:     TGGACCAGAAG                         GTTTTACGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGCCGGCTG
genomic: TGGACCAGAAGgtattaattt ... tattctttagGTTTTACGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGCCGGCTG
EST: gi|211541917|gb|FL379337.1|FL379337
EST:     CTAATTCATCTGACCGGTCTGACAGATCTGACAAACCTATGGACCAGAAG                         GTTTTACGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGCCGGCTG
genomic: CTAATTCATCTGACCGGTCTGACAGATCTGACAAACCTATGGACCAGAAGgtattaattt ... tattctttagGTTTTACGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGCCGGCTG
EST: gi|76020899|gb|DT948069.1|DT948069
EST:     CTAATTCATCTGACCGGTCTGACAGATCTGACAAACCTATGGACCAGAAG                         GTTTTACGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGCCGGCTG
genomic: CTAATTCATCTGACCGGTCTGACAGATCTGACAAACCTATGGACCAGAAGgtattaattt ... tattctttagGTTTTACGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGCCGGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttgttaccatttcacaatgatggtatctagatgatgcatttggtattctttagGTTTTACGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGCCGGCTGAGGAAAAAG
                                             tattcttt  CT-rich tract
                                             tattcttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattaattttgtctcctatctctctgtactctttagtgtttgttaccatttcacaatgatggtatctagatgatgcatttggtattctttagGTTTTACGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGCCGGCTGAGGAAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA