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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataaaatctgcggtgccagtgccggtctactgggtcagtcactggatgttctggcacgtttttatcacatgtaatccatgtggtccatttcttcctacagAGTGTTCTTGGGATCATCCTTGGAGGGGGTGCTGGGACAAGGCTGTATCCACTGACGAAGAAGAGGGCGAAACCAGCAGTGCCGTTGGGCGCCAACTACA

Basic information

species Zea mays
transcript GRMZM2G106213_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G106213_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os09g12660.2 (Oryza sativa), 3'ss of exon 1
---ataaaatctgcggtgccagtgccggtctactgggtcagtcactggatgttctggcacgtttttatcacatgtaatccatgtggtccatttcttcctacagAGTGTTCTTGGGATCATCCTTGGAGGGGGTGCTGGGACAAGGCTGTATCCACTGACGAAGAAGAGGGCGAAACCAGCAGTGCCGTTGGGCGCCAACTACA
   | | ||  ||     | || ||   ||  |||      ||  |  ||  ||||       ||| |   ||    |  |  |      |||  |||| ||||||||||||||||||||||||||||| ||||||||||||||||||||||| ||||| |||||||||||||| || || ||||||||||| || || ||||
agtacagaacttggaactcaagagcatttcatctg---ttatctatatatagtctgatgatgatttgtattattatttttacatccaatttttaatcctgcagAGTGTTCTTGGGATCATCCTTGGAGGTGGTGCTGGGACAAGGCTGTATCCGCTGACAAAGAAGAGGGCGAAGCCGGCGGTGCCGTTGGGTGCTAATTACA

upper sequence: GRMZM2G106213_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA02G47460.1 (Glycine max), 3'ss of exon 1
ataaaatctgcggtgccagtgccggtctactgggtc--agtcactggatgttctggcacgtttttatcacatgtaatccatgtggtccatttcttcctacagAGTGTTCTTGGGATCATCCTTGGAGGGGGTGCTGGGACAAGGCTGTATCCACTGACGAAGAAGAGGGCGAAACCAGCAGTGCCGTTGGGCGCCAACTACA
|| || | |    |        |    || ||  |     ||    ||| ||   |   | || |    |   |  |   ||   |       |   || ||||||| ||||| || || |||||||| |||||||||||  | || ||||||||||| ||||||||||| || ||||| || ||  | || || ||||| |
atgaatttttttttttttagatcacaatagtgaattttgatcgtgcgatattt--gattgattctggttctgattgtgattgcaatttgaaaatgtttatagAGTGTGCTTGGCATTATACTTGGAGGTGGTGCTGGGACTCGTCTTTATCCACTGACCAAGAAGAGGGCAAAGCCAGCTGTTCCTCTTGGAGCTAACTATA

upper sequence: GRMZM2G106213_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA14G01290.1 (Glycine max), 3'ss of exon 1
--ataaaatct--gcggtgccagtgccggtctactgggtcagtcactggatgttctggcacgtttttatcacatgtaatccatgtggtccatttcttcctacagAGTGTTCTTGGGATCATCCTTGGAGGGGGTGCTGGGACAAGGCTGTATCCACTGACGAAGAAGAGGGCGAAACCAGCAGTGCCGTTGGGCGCCAACTACA
   | | |||      ||   | |   | |||  ||        | |||||||   ||   | || |    |   |  |   |    |  |     |  || ||||||| ||||| || || |||||||| |||||||||||  |||| |||||||| || ||||||||||| || ||||| || ||  | || || ||||| |
tttttagatcacaatagtttgaattttgatcttgtgatatttgtattggatgt---ggattggttctggttctgattctgattccaatttaaaatgtt-tatagAGTGTGCTTGGCATTATACTTGGAGGTGGTGCTGGGACTCGGCTTTATCCACTCACCAAGAAGAGGGCAAAGCCAGCTGTTCCTCTTGGAGCTAACTATA

upper sequence: GRMZM2G106213_T02 (Zea mays), 3'ss of exon 1
lower sequence: AT5G48300.1 (Arabidopsis thaliana), 3'ss of exon 1
----ataaaatctgcggtgccagtgccggtctactgggtcagtcactggatgttctggcacgtttttatcacatgtaatccatgtggtccatttcttcctacagAGTGTTCTTGGGATCATCCTTGGAGGGGGTGCTGGGACAAGGCTGTATCCACTGACGAAGAAGAGGGCGAAACCAGCAGTGCCGTTGGGCGCCAACTACA
      |  ||||    |     |       |  | | | |  |  ||     | | |    ||   |||| ||   | |  | |  |   | ||    | ||||||||| | ||||| ||| | ||||| || ||||| ||  | || |||||||| ||||||||||| ||||||||||| |||||  | || || ||||| |
gtaagcatcatctatcttcttcttcttatctttgttgtttaagctttgaggaatgtag----ttgagatcaaattggaactgt-taattgttgtcaatttgcagAGTGTTTTGGGGATAATCTTAGGAGGTGGAGCTGGAACTCGTCTTTATCCACTTACGAAGAAGAGAGCGAAACCAGCTGTGCCTCTTGGTGCTAACTATA

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|211188665|gb|FL114950.1|FL114950
EST:     TTTCGGACTCGCGGAGCTCGCAAACGTGCCTTGATCCGGACGCCAGTACG                         AGTGTTCTTGGGATCATCCTTGGAGGGGGTGCTGGGACAAGGCTGTATCCA
genomic: TTTCGGACTCGCGGAGCTCGCAAACGTGCCTTGATCCGGACGCCAGCACGgtacgcgata ... cttcctacagAGTGTTCTTGGGATCATCCTTGGAGGGGGTGCTGGGACAAGGCTGTATCCA
EST: gi|211188667|gb|FL114952.1|FL114952
EST:     TTTCGGACTCGCGGAGCTCGCAAACGTGCCTTGATCCGGACGCCAGCACG                         AGTGTTCTTGGGATCATCCTTGGAGGGGGTGCTGGGACAAGGCTGTATCCA
genomic: TTTCGGACTCGCGGAGCTCGCAAACGTGCCTTGATCCGGACGCCAGCACGgtacgcgata ... cttcctacagAGTGTTCTTGGGATCATCCTTGGAGGGGGTGCTGGGACAAGGCTGTATCCA
EST: gi|148987334|gb|EE031175.2|EE031175
EST:     TTTCGGACTCGCGGAGCTCGCAAACGTGCCTTGATCCGGACGCCAGCACG                         AGTGTTCTTGGGATCATCCTTGGAGGGGGTGCTGGGACAAGGCTGTATCCA
genomic: TTTCGGACTCGCGGAGCTCGCAAACGTGCCTTGATCCGGACGCCAGCACGgtacgcgata ... cttcctacagAGTGTTCTTGGGATCATCCTTGGAGGGGGTGCTGGGACAAGGCTGTATCCA
EST: gi|60355358|gb|DN222331.1|DN222331
EST:     TTTCGGACTCGCGGAGCTCGCAAACGTGCCTTGATCCGGACGCCAGCACG                         AGTGTTCTTGGGATCATCCTTGGAGGGGGTGCTGGGACAAGGCTGTATCCA
genomic: TTTCGGACTCGCGGAGCTCGCAAACGTGCCTTGATCCGGACGCCAGCACGgtacgcgata ... cttcctacagAGTGTTCTTGGGATCATCCTTGGAGGGGGTGCTGGGACAAGGCTGTATCCA
EST: gi|67027741|gb|CO456490.1|CO456490
EST:     TTTCGGACTCGCGGAGCTCGCAAACGTGCCTTGATCCGGACGCCAGCACG                         AGTGTTCTTGGGATCATCCTTGGAGGGGGTGCTGGGACAAGGCTGTATCCA
genomic: TTTCGGACTCGCGGAGCTCGCAAACGTGCCTTGATCCGGACGCCAGCACGgtacgcgata ... cttcctacagAGTGTTCTTGGGATCATCCTTGGAGGGGGTGCTGGGACAAGGCTGTATCCA
EST: gi|211186267|gb|FL114942.1|FL114942
EST:     TTTCGGACTCGCGGAGCTCGCAAACGTGCCTTGATCCGGACGCCAGCACG                         AGTGTTCTTGGGATCATCCTTGGAGGGGGTGCTGGGACAAGGCTGTATCCA
genomic: TTTCGGACTCGCGGAGCTCGCAAACGTGCCTTGATCCGGACGCCAGCACGgtacgcgata ... cttcctacagAGTGTTCTTGGGATCATCCTTGGAGGGGGTGCTGGGACAAGGCTGTATCCA
EST: gi|71303914|gb|DR788076.1|DR788076
EST:     TTTCGGACTCGCGGAGCTCGCAAACGTGCCTTGATCCGGACGCCAGCACG                         AGTGTTCTTGGGATCATCCTTGGAGGGGGTGCTGGGACAAGGCTGTATCCA
genomic: TTTCGGACTCGCGGAGCTCGCAAACGTGCCTTGATCCGGACGCCAGCACGgtacgcgata ... cttcctacagAGTGTTCTTGGGATCATCCTTGGAGGGGGTGCTGGGACAAGGCTGTATCCA
EST: gi|148966536|gb|EE017559.2|EE017559
EST:     TTTCGGACTCGCGGAGCTCGCAAACGTGCCTTGATCCGGACGCCAGCACG                         AGTGTTCTTGGGATCATCCTTGGAGGGGGTGCTGGGACAAGGCTGTATCCA
genomic: TTTCGGACTCGCGGAGCTCGCAAACGTGCCTTGATCCGGACGCCAGCACGgtacgcgata ... cttcctacagAGTGTTCTTGGGATCATCCTTGGAGGGGGTGCTGGGACAAGGCTGTATCCA
EST: gi|148950461|gb|EC896031.2|EC896031
EST:     TTTCGGACTCGCGGAGCTCGCAAACGTGCCTTGATCCGGACGCCAGCACG                         AGTGTTCTTGGGATCATCCTTGGAGGGGGTGCTGGGACAAGGCTGTATCCA
genomic: TTTCGGACTCGCGGAGCTCGCAAACGTGCCTTGATCCGGACGCCAGCACGgtacgcgata ... cttcctacagAGTGTTCTTGGGATCATCCTTGGAGGGGGTGCTGGGACAAGGCTGTATCCA
EST: gi|31354893|gb|CD439250.1|CD439250
EST:     TTTCGGACTCGCGGAGCTCGCAAACGTGCCTTGATCCGGACGCCAGCACG                         AGTGTTCTTGGGATCATCCTTGGAGGGGGTGCTGGGACAAGGCTGTATCCA
genomic: TTTCGGACTCGCGGAGCTCGCAAACGTGCCTTGATCCGGACGCCAGCACGgtacgcgata ... cttcctacagAGTGTTCTTGGGATCATCCTTGGAGGGGGTGCTGGGACAAGGCTGTATCCA
EST: gi|154130546|gb|EC872338.2|EC872338
EST:     TTTCGGACTCGCGGAGCTCGCAAACGTGCCTTGATCCGGACGCCAGCACG                         AGTGTTCTTGGGATCATCCTTGGAGGGGGTGCTGGGACAAGGCTGTATCCA
genomic: TTTCGGACTCGCGGAGCTCGCAAACGTGCCTTGATCCGGACGCCAGCACGgtacgcgata ... cttcctacagAGTGTTCTTGGGATCATCCTTGGAGGGGGTGCTGGGACAAGGCTGTATCCA
EST: gi|211191070|gb|FL114967.1|FL114967
EST:     TTTCGGACTCGCGGAGCTCGCAAACGTGCCTTGATCCGGACGCCAGCACG                         AGTGTTCTTGGGATCATCCTTGGAGGGGGTGCTGGGACAAGGCTGTATCCA
genomic: TTTCGGACTCGCGGAGCTCGCAAACGTGCCTTGATCCGGACGCCAGCACGgtacgcgata ... cttcctacagAGTGTTCTTGGGATCATCCTTGGAGGGGGTGCTGGGACAAGGCTGTATCCA
EST: gi|211186262|gb|FL114937.1|FL114937
EST:     TTTCGGACTCGCGGAGCTCGCAAACGTGCCTTGATCCGGACGCCAGCACG                         AGTGTTCTTGGGATCATCCTTGGAGGGGGTGCTGGGACAAGGCTGTATCCA
genomic: TTTCGGACTCGCGGAGCTCGCAAACGTGCCTTGATCCGGACGCCAGCACGgtacgcgata ... cttcctacagAGTGTTCTTGGGATCATCCTTGGAGGGGGTGCTGGGACAAGGCTGTATCCA
EST: gi|148995829|gb|EE035064.2|EE035064
EST:     TTTCGGACTCGCGGAGCTCGCAAACGTGCCTTGATCCGGACGCCAGCACG                         AGTGTTCTTGGGATCATCCTTGGAGGGGGTGCTGGGACAAGGCTGTATCCA
genomic: TTTCGGACTCGCGGAGCTCGCAAACGTGCCTTGATCCGGACGCCAGCACGgtacgcgata ... cttcctacagAGTGTTCTTGGGATCATCCTTGGAGGGGGTGCTGGGACAAGGCTGTATCCA
EST: gi|31356252|gb|CD440609.1|CD440609
EST:     TTTCGGACTCGCGGAGCTCGCAAACGTGCCTTGATCCGGACGCCAGCACG                         AGTGTTCTTGGGATCATCCTTGGAGGGGGTGCTGGGACAAGGCTGTATCCA
genomic: TTTCGGACTCGCGGAGCTCGCAAACGTGCCTTGATCCGGACGCCAGCACGgtacgcgata ... cttcctacagAGTGTTCTTGGGATCATCCTTGGAGGGGGTGCTGGGACAAGGCTGTATCCA
EST: gi|211191066|gb|FL114963.1|FL114963
EST:     TTTCGGACTCGCGGAGCTCGCAAACGTGCCTTGATCCGGACGCCAGCACG                         AGTGTTCTTGGGATCATCCTTGGAGGGGGTGCTGGGACAAGGCTGTATCCA
genomic: TTTCGGACTCGCGGAGCTCGCAAACGTGCCTTGATCCGGACGCCAGCACGgtacgcgata ... cttcctacagAGTGTTCTTGGGATCATCCTTGGAGGGGGTGCTGGGACAAGGCTGTATCCA
EST: gi|148967973|gb|EE019294.2|EE019294
EST:     TTTCGGACTCGCGGAGCTCGCAAACGTGCCTTGATCCGGACGCCAGCACG                         AGTGTTCTTGGGATCATCCTTGGAGGGGGTGCTGGGACAAGGCTGTATCCA
genomic: TTTCGGACTCGCGGAGCTCGCAAACGTGCCTTGATCCGGACGCCAGCACGgtacgcgata ... cttcctacagAGTGTTCTTGGGATCATCCTTGGAGGGGGTGCTGGGACAAGGCTGTATCCA
EST: gi|211191068|gb|FL114965.1|FL114965
EST:     TTTCGGACTCGCGGAGCTCGCAAACGTGCCTTGATCCGGACGCCAGCACG                         AGTGTTCTTGGGATCATCCTTGGAGGGGGTGCTGGGACAAGGCTGTATCCA
genomic: TTTCGGACTCGCGGAGCTCGCAAACGTGCCTTGATCCGGACGCCAGCACGgtacgcgata ... cttcctacagAGTGTTCTTGGGATCATCCTTGGAGGGGGTGCTGGGACAAGGCTGTATCCA
EST: gi|211191069|gb|FL114966.1|FL114966
EST:     TTTCGGACTCGCGGAGCTCGCAAACGTGCCTTGATCCGGACGCCAGCACG                         AGTGTTCTTGGGATCATCCTTGGAGGGGGTGCTGGGACAAGGCTGTATCCA
genomic: TTTCGGACTCGCGGAGCTCGCAAACGTGCCTTGATCCGGACGCCAGCACGgtacgcgata ... cttcctacagAGTGTTCTTGGGATCATCCTTGGAGGGGGTGCTGGGACAAGGCTGTATCCA
EST: gi|18659860|gb|BM500559.1|BM500559
EST:     TTTCGGACTCGCGGA-CTCGCAAACGTGCCTTGATCCGGACGCCAGCACG                         AGTGTTCTTGGGATCATCCTTGGAGGGGGTGCTGGGACAAGGCTGTATCCA
genomic: TTTCGGACTCGCGGAGCTCGCAAACGTGCCTTGATCCGGACGCCAGCACGgtacgcgata ... cttcctacagAGTGTTCTTGGGATCATCCTTGGAGGGGGTGCTGGGACAAGGCTGTATCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgttctggcacgtttttatcacatgtaatccatgtggtccatttcttcctacagAGTGTTCTTGGGATCATCCTTGGAGGGGGTGCTGGGACAAGGCTGTATCCACTGACGAAGAAGAGGGCGAAACCAGCAGTGCCGTTGGGCGCCAACTACA
                                      tccatttcttcctac  CT-rich tract
             tttttatca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataaaatctgcggtgccagtgccggtctactgggtcagtcactggatgttctggcacgtttttatcacatgtaatccatgtggtccatttcttcctacagAGTGTTCTTGGGATCATCCTTGGAGGGGGTGCTGGGACAAGGCTGTATCCACTGACGAAGAAGAGGGCGAAACCAGCAGTGCCGTTGGGCGCCAACTACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG