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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcaatgaaaaataactagtttcttataggtttgctcattcttatcagaaaccatatgctatttgttgattgacttgggatttctcatctggatcccttagGTGAAAAGGATACATGAATATAAGCGGCAGCTGCTAAATATCCTTGGAATTGTCTACCGCTACAAGAAGATGAAAGAAATGAGCACAGAAGAAAGAGCAA

Basic information

species Zea mays
transcript GRMZM2G074158_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G074158_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os03g55090.1 (Oryza sativa), 3'ss of exon 10
gcaatgaaaaataactagtttcttataggtttgctcattcttatcagaaaccatatgctatttgttgattgacttgggatttctcatctggatcccttagGTGAAAAGGATACATGAATATAAGCGGCAGCTGCTAAATATCCTTGGAATTGTCTACCGCTACAAGAAGATGAAAGAAATGAGCACAGAAGAAAGAGCAA
                  | | | |||||      |||| | ||         | |   || | ||| || |||| |  ||| ||| |||||| |   ||||||||||||| ||||| |||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||  || |||| |||  ||
---------------gtatatttaatagg---aagcattttcat---------tctatcatgtattggttcacttagtttttgtcacctggattcac-agGTGAAAAGGATCCATGAGTATAAGCGACAGCTGCTAAATATCCTTGGAATTGTCTACCGCTACAAGAAGATGAAAGAAATGAGTGCAAAAGACAGAATAA

upper sequence: GRMZM2G074158_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA19G03490.1 (Glycine max), 3'ss of exon 10
gcaatgaaaaataactagtttcttataggtttgctcattcttatcagaaaccatatgctattt-gttgattgacttgggatt--tctcatctggatcccttagGTGAAAAGGATACATGAATATAAGCGGCAGCTGCTAAATATCCTTGGAATTGTCTACCGCTACAAGAAGATGAAAGAAATGAGCACAGAAGAAAGAGCAA
 ||||      | ||  ||   ||  |  | | | || ||   |   |  || |||    ||| | | |   | |     ||    | ||     |   ||||||||| || || |||||||||||||| ||  |  | || ||  |||||||||| ||||| |||||||||||||||||||||||  | | |||||| | | 
-caattttg--ttacgtgtgagttcaatttctacccaatccatttgtactccctatatagttttgctaaactattcactgttggctttattatttttgtttagGTGAAGAGAATCCATGAATATAAGCGACAATTAATGAACATATTTGGAATTGTTTACCGATACAAGAAGATGAAAGAAATGAGTGCGGCAGAAAGGGAAG

upper sequence: GRMZM2G074158_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA13G06040.1 (Glycine max), 3'ss of exon 10
gcaatgaaaaataactagtttcttataggtttgctcattcttatcagaaa-ccatatgctattt-gttgattgacttgggatt--tctcatctggatcccttagGTGAAAAGGATACATGAATATAAGCGGCAGCTGCTAAATATCCTTGGAATTGTCTACCGCTACAAGAAGATGAAAGAAATGAGCACAGAAGAAAGAGCAA
 || | |      ||| ||   ||  |  | | | || ||  ||||| |  || |||    ||| | | |   | |     ||    | |||    |   ||||||||| || || |||||||||||||| ||  |  | || ||  |||||||||| ||||| |||||||||||||||||||||||  | | ||||||   | 
-cagttatg--ctacttgtgaattcaatttctacccaatcc-atcagtattccctatatagttttgctaaactattcactgttggctttatcatttttgtttagGTGAAGAGAATCCATGAATATAAGCGACAATTATTGAACATATTTGGAATTGTTTACCGATACAAGAAGATGAAAGAAATGAGTGCTGCAGAAAGGAAAG

upper sequence: GRMZM2G074158_T01 (Zea mays), 3'ss of exon 10
lower sequence: AT3G29320.1 (Arabidopsis thaliana), 3'ss of exon 10
-----------------------------gcaatgaaaaataactagttt---cttataggtttgctcattcttatcagaaaccatatgctatttgttgattgacttgggatttctcatctggatccctt---agGTGAAAAGGATACATGAATATAAGCGGCAGCTGCTAAATATCCTTGGAATTGTCTACCGCTACAAGAAGATGAAAGAAATGAGCACAGAAGAAAGAGCAA
                               | |||  | |   | | ||    || | ||||||   | || | |  | |||  |  |    || |  |    |||    |||  |||    | |  ||   || | ||  | |||||||| || ||||| || |||||||||||| | |||||||| ||||||||||| |||||||| ||||||||  |    || ||||  |
gtcagttccaatggatcttggttacttttagattgatgagttgtttgcttgggtttttcggtttgagaagtcctttacgcaactctgagtagcttatgtagattcttttctttttgcattgaaaactttttgcagATCAAGCGTATACATGAGTACAAGCGACAACTGCTAAATATCTTGGGAATTGTTTACCGCTACAAAAAGATGAAGGAAATGAGTGCTAGTGAGAGAGAGA

upper sequence: GRMZM2G074158_T01 (Zea mays), 3'ss of exon 10
lower sequence: EFJ09932 (Selaginella moellendorffii), 3'ss of exon 9
gcaatgaaaaataactagtttcttataggtttgctcattcttatcagaaaccatatgctatttgttgattgacttgggatttctcatctggatccctta---gGTGAAAAGGATACATGAATATAAGCGGCAGCTGCTAAATATCCTTGGAATTGTCTACCGCTACAAGAAGATGAAAGAAATGAGCACAGAAGAAAGAGCAA
                                                                 | |     |  || | || |     ||    |||   ||||||||| || || || || ||||| || |||||||| ||  | |||    ||||||||||||| |||||||||||||||||  || |||| ||   | 
--------------------------------------------------------------gtctcaccatgtgaggttctcactaaaagactatttaacagGTGAAAAGAATCCACGAGTACAAGCGTCAACTGCTAAACATTTTAGGATGCATCTACCGCTACAAAAAGATGAAAGAAATGAGTCCAAAAGAGAGGAAAG

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|32809282|gb|CD961516.1|CD961516
EST:     GGGAGAAGACAGGATATATTGTCAGTCCAGATGCAATGTTTGATGTGCAG                         GTGAAAAGGATACATGAATATAAGCGGCAGCTGCTAAATATCCTTGGAATT
genomic: GGGAGAAGACAGGATATATTGTCAGTCCAGATGCAATGTTTGATGTGCAGgtatattttg ... gatcccttagGTGAAAAGGATACATGAATATAAGCGGCAGCTGCTAAATATCCTTGGAATT
EST: gi|211354262|gb|FK983836.1|FK983836
EST:     GGGAGAAGACAGGATATATTGTCAGTCCAGATGCAATGTTTGATGTGCAG                         GTGAAAAGGATACATGAATATAAGCGGCAGCTGCTAAATATCCTTGGAATT
genomic: GGGAGAAGACAGGATATATTGTCAGTCCAGATGCAATGTTTGATGTGCAGgtatattttg ... gatcccttagGTGAAAAGGATACATGAATATAAGCGGCAGCTGCTAAATATCCTTGGAATT
EST: gi|32809100|gb|CD961334.1|CD961334
EST:     GGGAGAAGACAGGATATATTGTCAGTCCAGATGCAATGTTTGATGTGCAG                         GTGAAAAGGATACATGAATATAAGCGGCAGCTGCTAAATATCCTTGGAATT
genomic: GGGAGAAGACAGGATATATTGTCAGTCCAGATGCAATGTTTGATGTGCAGgtatattttg ... gatcccttagGTGAAAAGGATACATGAATATAAGCGGCAGCTGCTAAATATCCTTGGAATT
EST: gi|33095807|gb|CF055801.1|CF055801
EST:     GGGAGAAGACAGGATATATTGTCAGTCCAGATGCAATGTTTGATGTGCAG                         GTGAAAAGGATACATGAATATAAGCGGCAGCTGCTAAATATCCTTGGAATT
genomic: GGGAGAAGACAGGATATATTGTCAGTCCAGATGCAATGTTTGATGTGCAGgtatattttg ... gatcccttagGTGAAAAGGATACATGAATATAAGCGGCAGCTGCTAAATATCCTTGGAATT
EST: gi|32934247|gb|CF039059.1|CF039059
EST:     GGGAGAAGACAGGATATATTGTCAGTCCAGATGCAATGTTTGATGTGCAG                         GTGAAAAGGATACATGAATATAAGCGGCAGCTGCTAAATATCCTTGGAATT
genomic: GGGAGAAGACAGGATATATTGTCAGTCCAGATGCAATGTTTGATGTGCAGgtatattttg ... gatcccttagGTGAAAAGGATACATGAATATAAGCGGCAGCTGCTAAATATCCTTGGAATT
EST: gi|32826811|gb|CD966489.1|CD966489
EST:     GGGAGAAGACAGGATATATTGTCAGTCCAGATGCAATGTTTGATGTGCAG                         GTGAAAAGGATACATGAATATAAGCGGCAGCTGCTAAATATCCTTGGAATT
genomic: GGGAGAAGACAGGATATATTGTCAGTCCAGATGCAATGTTTGATGTGCAGgtatattttg ... gatcccttagGTGAAAAGGATACATGAATATAAGCGGCAGCTGCTAAATATCCTTGGAATT
EST: gi|31356465|gb|CD440822.1|CD440822
EST:     GGGAGAAGACAGGATATATTGTCAGTCCAGATGCAATGTTTGATGTGCAG                         GTGAAAAGGATACATGAATATAAGCGGCAGCTGCTAAATATCCTTGGAATT
genomic: GGGAGAAGACAGGATATATTGTCAGTCCAGATGCAATGTTTGATGTGCAGgtatattttg ... gatcccttagGTGAAAAGGATACATGAATATAAGCGGCAGCTGCTAAATATCCTTGGAATT
EST: gi|211354266|gb|FK983840.1|FK983840
EST:     GGGAGAAGACAGGATATATTGTCAGTCCAGATGCAATGTTTGATGTGCAG                         GTGAAAAGGATACATGAATATAAGCGGCA-CTGCTAAATATCCTTGGAATT
genomic: GGGAGAAGACAGGATATATTGTCAGTCCAGATGCAATGTTTGATGTGCAGgtatattttg ... gatcccttagGTGAAAAGGATACATGAATATAAGCGGCAGCTGCTAAATATCCTTGGAATT
EST: gi|32808763|gb|CD960997.1|CD960997
EST:     GGGAGAAGACAGGATATATTGTCAGTCCAGATGCAATGTTTGATGTGCAG                         GTGAAAAGGATACATGAATATAAGCGGCAGCTGCTAAATATCCTTGGAATT
genomic: GGGAGAAGACAGGATATATTGTCAGTCCAGATGCAATGTTTGATGTGCAGgtatattttg ... gatcccttagGTGAAAAGGATACATGAATATAAGCGGCAGCTGCTAAATATCCTTGGAATT
EST: gi|67027583|gb|CO456332.1|CO456332
EST:     GGGAGAAGAC-GGATATATTGTCAGTCCAGATGCAATGTTGGATGTGCAG                         GTGAAAAGGATACATGAAATATAAGCG-CAGCTGCTAA-TATCCTTGGAAT
genomic: GGGAGAAGACAGGATATATTGTCAGTCCAGATGCAATGTTTGATGTGCAGgtatattttg ... gatcccttagGTGAAAAGGATACATGAA-TATAAGCGGCAGCTGCTAAATATCCTTGGAAT
EST: gi|32809530|gb|CD961764.1|CD961764
EST:     GGGAGAAGACAGGATATATTGTCAGTCCAGATGCAATGTTTGATGTGCAG                         GTGAAAAGGATACATGAATATAAGCGGCAGCTGCTAAATATCCTTGGAATT
genomic: GGGAGAAGACAGGATATATTGTCAGTCCAGATGCAATGTTTGATGTGCAGgtatattttg ... gatcccttagGTGAAAAGGATACATGAATATAAGCGGCAGCTGCTAAATATCCTTGGAATT
EST: gi|32792865|gb|CD945101.1|CD945101
EST:     GGGAGAAGACAGGATATATTGTCAGTCCAGATGCAATGTTTGATGTGCAG                         GTGAAAAGGATACATGAATATAAGCGGCAGCTGCTAAATATCCTTGGAATT
genomic: GGGAGAAGACAGGATATATTGTCAGTCCAGATGCAATGTTTGATGTGCAGgtatattttg ... gatcccttagGTGAAAAGGATACATGAATATAAGCGGCAGCTGCTAAATATCCTTGGAATT
EST: gi|211354261|gb|FK983835.1|FK983835
EST:     GGGAGAAGACAGGATATATTGTCAGTCCAGATGCAATGTTTGATGTGCAG                         GTGAAAAGGATACATGAATATAAGCGGCAGCTGCTAAATATCCTTGGAATT
genomic: GGGAGAAGACAGGATATATTGTCAGTCCAGATGCAATGTTTGATGTGCAGgtatattttg ... gatcccttagGTGAAAAGGATACATGAATATAAGCGGCAGCTGCTAAATATCCTTGGAATT
EST: gi|32809095|gb|CD961329.1|CD961329
EST:     GGGAGAAGACAGGATATATTGTCAGTCCAGATGCAATGTTTGATGTGCAG                         GTGAAAAGGATACATGAATATAAGCGGCAGCTGCTAAATATCCTTGGAATT
genomic: GGGAGAAGACAGGATATATTGTCAGTCCAGATGCAATGTTTGATGTGCAGgtatattttg ... gatcccttagGTGAAAAGGATACATGAATATAAGCGGCAGCTGCTAAATATCCTTGGAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaaaccatatgctatttgttgattgacttgggatttctcatctggatcccttagGTGAAAAGGATACATGAATATAAGCGGCAGCTGCTAAATATCCTTGGAATTGTCTACCGCTACAAGAAGATGAAAGAAATGAGCACAGAAGAAAGAGCAA
                     gattgac  putative branch site (score: 3)
                                               tccctt  putative PPT
             tatttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaatgaaaaataactagtttcttataggtttgctcattcttatcagaaaccatatgctatttgttgattgacttgggatttctcatctggatcccttagGTGAAAAGGATACATGAATATAAGCGGCAGCTGCTAAATATCCTTGGAATTGTCTACCGCTACAAGAAGATGAAAGAAATGAGCACAGAAGAAAGAGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - aaaaata
- - - - - - - - - - - - - - - -tgctcat
- - - - - - - - - - - - - - - - - - - - - - - - - -catatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgat