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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctggtttggtaacactgattaacatgtttactactactgttaagtttttcagcatttgaatttgattttggtaactgactgctacaaattgcttgtagATTGGTGATTGACAAAGAGACCGGCAAGCCAAAAGGTTATGGCTTTTGCGAGTACAAGGATGAGGAAACTGCTTTAAGTGCACGCCGGAACCTTCAGGGT

Basic information

species Zea mays
transcript GRMZM2G096480_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G096480_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g07490.1 (Oryza sativa), 3'ss of exon 2
-ttctggtttggtaacactgattaacatgtttactactactgttaagtttttcagcatttgaatttgattttggtaactgactgctacaaattgcttgtagATTGGTGATTGACAAAGAGACCGGCAAGCCAAAAGGTTATGGCTTTTGCGAGTACAAGGATGAGGAAACTGCTTTAAGTGCACGCCGGAACCTTCAGGGT
| |||| || || | | ||| || | | || | | || | | | || | | | ||| |||||||| ||||| ||||| || || |||||||| |||||||| ||||| ||||||||||||||||| |||||| |||||||||||||||||||||| |||
tgccaagtttcctagcagctgcaagtgttttttaatctggtaacacgtggtaagatagtttcgactactcataagctcttaa-acatttggtgctttgcagATTGGTTATTGATAAAGAAACAGGGAAGCCAAAGGGTTATGGGTTTTGTGAGTACAAGGATGAGGAGACTGCTCTAAGTGCACGCCGGAACCTTCAAGGT

upper sequence: GRMZM2G096480_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA10G36350.1 (Glycine max), 3'ss of exon 2
------ttctggtttggtaacactgattaacatgtttactactactgttaagtttttcagcatttgaatttgattttggtaactgactgctacaaattgcttgtagATTGGTGATTGACAAAGAGACCGGCAAGCCAAAAGGTTATGGCTTTTGCGAGTACAAGGATGAGGAAACTGCTTTAAGTGCACGCCGGAACCTTCAGGGT
|| | | | | | || | | || | | | |||| | | | | |||| | | | || || || ||| | || ||||||| ||| || || || |||||||||||||| || || ||||| |||||||| || || ||||||||||| || || || |||||||||
tgagattttttctgtaatttcttggaactgccttttgcttcttgaccaaaggtttatttggttgaagacttgaact--attcccatcttctt----ttatccacagACTAGTTATTGACAGAGAAACTGGGAAACCAAAAGGTTATGGATTCTGTGAGTATAAGGATGAAGAGACGGCTTTAAGTGCTCGACGAAATCTTCAGGGT

upper sequence: GRMZM2G096480_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA20G31220.2 (Glycine max), 3'ss of exon 2
------ttctggtttggtaacactgattaacatgtttactact--actgttaagtttttcagcatttgaatttgattttggtaactgactgctacaaattgcttgtagATTGGTGATTGACAAAGAGACCGGCAAGCCAAAAGGTTATGGCTTTTGCGAGTACAAGGATGAGGAAACTGCTTTAAGTGCACGCCGGAACCTTCAGGGT
|| | | | | || || | | ||| || || || | || || | ||||| || || | | | | || | || || ||| | || ||||||| ||| || || || |||||||||||||| || || |||||||||||||| || || ||||| ||||| || || || |||||||||
tgagattttttctgtaatttcatggaactccct-tttgcttcttgaccaatggtttatttgg---ttgaa---gacttgaattattcccatcttctt-ttatctgcagACTAGTTATTGACAGAGAAACTGGGAAACCAAAAGGTTATGGATTCTGTGAGTACAAGGATGAAGAGACGGCTTTGAGTGCTCGACGAAATCTTCAGGGT

upper sequence: GRMZM2G096480_T03 (Zea mays), 3'ss of exon 2
lower sequence: Vv18s0001g01800.t01 (Vitis vinifera), 3'ss of exon 2
---ttctggtttggtaacactgattaacatgtttactactactgttaagtttttcagcatttgaatttgattttggtaactgactgctacaaattgcttgtagATTGGTGATTGACAAAGAGACCGGCAAGCCAAAAGGTTATGGCTTTTGCGAGTACAAGGATGAGGAAACTGCTTTAAGTGCACGCCGGAACCTTCAGGGT
| ||| ||| | | | | || || || || || | || ||| ||| | | | | | | | |||||| |||||||| ||||| ||| || || ||||||||||||||||| || || ||||| |||||||| || || || |||||||| || || || ||||||||
aatgaacgttttctccacatttccctcactttcttttagtaacagcaatttgttt--ctatttcctttttctttatttatttatttatttattttgctt-cagATTGGTTATTGATCGAGAAACAGGGAAGCCAAAAGGTTATGGATTCTGTGAGTATAAGGATGAAGAGACAGCATTAAGTGCTCGTCGTAATCTTCAGGGC

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|211352084|gb|FL106817.1|FL106817
EST:     GAGCAGCTCGTGCAGATTTGCGAAGAAGTCGGCCCAGTCGTATCCTTCAG                         ATTGGTGATTGACAAAGAGACCGGCAAGCCAAAAGGTTATGGCTTTTGCGA
genomic: GAGCAGCTCGTGCAGATTTGCGAAGAAGTCGGCCCAGTCGTATCCTTCAGgtgtgctttt ... ttgcttgtagATTGGTGATTGACAAAGAGACCGGCAAGCCAAAAGGTTATGGCTTTTGCGA
EST: gi|211354482|gb|FL106822.1|FL106822
EST:     GAGCAGCTCGTGCAGATTTGCGAGGAAGTCGGGCCAGTCGTATCCTTCAG                         ATGGGTGATTGACAAAGAGACGGGCAAGGCAAAA
genomic: GAGCAGCTCGTGCAGATTTGCGAAGAAGTCGGCCCAGTCGTATCCTTCAGgtgtgctttt ... ttgcttgtagATTGGTGATTGACAAAGAGACCGGCAAGCCAAAA
EST: gi|211354484|gb|FL106824.1|FL106824
EST:     GAGCAGCTCGTGCAGATTTGCGAAGAAGTCGGCCCAGTCGTATCCTTCAG                         ATTGGTGATTGACAAAGAGACCGGCAAGCCAAAAGGTTATGGCTTTTGCGA
genomic: GAGCAGCTCGTGCAGATTTGCGAAGAAGTCGGCCCAGTCGTATCCTTCAGgtgtgctttt ... ttgcttgtagATTGGTGATTGACAAAGAGACCGGCAAGCCAAAAGGTTATGGCTTTTGCGA
EST: gi|211354480|gb|FL106820.1|FL106820
EST:     GAGCAGCTCGTGCAGATTTGCGAAGAAGTCGGCCCAGTCGTATCCTTCAG                         AATTGGTGATTGACAAAGAGACCGGCAAGCCAAAAGGTTATGGCTTTTGCG
genomic: GAGCAGCTCGTGCAGATTTGCGAAGAAGTCGGCCCAGTCGTATCCTTCAGgtgtgctttt ... ttgcttgtagA-TTGGTGATTGACAAAGAGACCGGCAAGCCAAAAGGTTATGGCTTTTGCG
EST: gi|211354488|gb|FL106828.1|FL106828
EST:     GAGCAGCTCGTGCAGATTTGCGAAGAAGTCGGCCCAGTCGTATCCTTCAG                         ATTGGTGATTGACAAAGAGACCGGCAAGCCAAAAGGTTATGGCTTTTGCGA
genomic: GAGCAGCTCGTGCAGATTTGCGAAGAAGTCGGCCCAGTCGTATCCTTCAGgtgtgctttt ... ttgcttgtagATTGGTGATTGACAAAGAGACCGGCAAGCCAAAAGGTTATGGCTTTTGCGA
EST: gi|211354485|gb|FL106825.1|FL106825
EST:     GAGCAGCTCGTGCAGATTTGCGAAGAAGTCGGCCCAGTCGTATCCTTCAG                         ATTGGTGATTGACAAAGAGACCGGCAAGCCAAAAGGTTATGGCTTTTGCGA
genomic: GAGCAGCTCGTGCAGATTTGCGAAGAAGTCGGCCCAGTCGTATCCTTCAGgtgtgctttt ... ttgcttgtagATTGGTGATTGACAAAGAGACCGGCAAGCCAAAAGGTTATGGCTTTTGCGA
EST: gi|211352083|gb|FL106816.1|FL106816
EST:     GAGCAGCTCGTGCAGATTTGCGAAGAAGTCGGCCCAGTCGTATCCTTCAG                         ATTGGTGATTGACAAAGAGACCGGCAAGCCAAAAGGTTATGGCTTTTGCGA
genomic: GAGCAGCTCGTGCAGATTTGCGAAGAAGTCGGCCCAGTCGTATCCTTCAGgtgtgctttt ... ttgcttgtagATTGGTGATTGACAAAGAGACCGGCAAGCCAAAAGGTTATGGCTTTTGCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttttcagcatttgaatttgattttggtaactgactgctacaaattgcttgtagATTGGTGATTGACAAAGAGACCGGCAAGCCAAAAGGTTATGGCTTTTGCGAGTACAAGGATGAGGAAACTGCTTTAAGTGCACGCCGGAACCTTCAGGGT
                             aactgac  putative branch site (score: 2)
 atttgaatttgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctggtttggtaacactgattaacatgtttactactactgttaagtttttcagcatttgaatttgattttggtaactgactgctacaaattgcttgtagATTGGTGATTGACAAAGAGACCGGCAAGCCAAAAGGTTATGGCTTTTGCGAGTACAAGGATGAGGAAACTGCTTTAAGTGCACGCCGGAACCTTCAGGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG