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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagcctagtaatctgaattagtttatgattgcaccgagtcacgcgttcgggaagcaaaggcatgaagggagtttgccgtggtaatcgaatctcgtgacatgtttgaccttgcgttttcagCGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGTTTTCAG

Basic information

species Zea mays
transcript GRMZM2G147882_T04
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147882_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g09300.2 (Oryza sativa), 3'ss of exon 7
-------------------------gtaaagccta----gtaatctgaattagtttatgattgcaccgagtcacg-cgttcgggaagcaaaggcatgaagggagtttgccg-tggtaatcgaatctcgtgacatgtttgaccttgcgttttcagCGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGTTTTCAG
                         | ||    ||      | ||||| ||   |  ||   | |   | |   |  ||         || |   |  | ||  | ||||    || |  |||  || | ||||||||  |||    ||| ||| || ||||| ||||| |||||||| ||||||||| ||||||||||| |  |||||||
gtgagcttgctaatctaatcacttagcaatatttatgccaaattctgatttctgtgttggcagtataaaattgggatgtatcaatcataaggtattctacggcctatgccaactgttagtgaagatccttacatgttttccctctattttccagAGGTTTTATTGTCAATCTTGGCGATATGCTCGAACGGTGGAGTAACTGTATTTTCAG
















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|78077655|gb|DV506089.1|DV506089
EST:     GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGG                         CGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
genomic: GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGGgtaaagccta ... gcgttttcagCGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
EST: gi|32925957|gb|CF030769.1|CF030769
EST:     GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGG                         CGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
genomic: GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGGgtaaagccta ... gcgttttcagCGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
EST: gi|32926415|gb|CF031227.1|CF031227
EST:     GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGG                         CGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
genomic: GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGGgtaaagccta ... gcgttttcagCGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
EST: gi|32926466|gb|CF031278.1|CF031278
EST:     GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGG                         CGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
genomic: GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGGgtaaagccta ... gcgttttcagCGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
EST: gi|74241069|gb|DT648983.1|DT648983
EST:     GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGG                         CGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
genomic: GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGGgtaaagccta ... gcgttttcagCGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
EST: gi|32926635|gb|CF031447.1|CF031447
EST:     GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGG                         CGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
genomic: GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGGgtaaagccta ... gcgttttcagCGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
EST: gi|32926849|gb|CF031661.1|CF031661
EST:     GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGG                         CGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
genomic: GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGGgtaaagccta ... gcgttttcagCGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
EST: gi|71437198|gb|DR818248.1|DR818248
EST:     GACAAGAACGCTCAGCCTCAACTGTGGGGATACGTAGCTCCGTTGAAAGG                         CGGATTTATCGTCAACCTTGGCGAC
genomic: GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGGgtaaagccta ... gcgttttcagCGGATTTATCGTCAACCTTGGCGAC
EST: gi|32926430|gb|CF031242.1|CF031242
EST:     GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGG                         CGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
genomic: GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGGgtaaagccta ... gcgttttcagCGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
EST: gi|32926417|gb|CF031229.1|CF031229
EST:     GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGG                         CGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
genomic: GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGGgtaaagccta ... gcgttttcagCGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
EST: gi|32925395|gb|CF030207.1|CF030207
EST:     GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGG                         CGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
genomic: GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGGgtaaagccta ... gcgttttcagCGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
EST: gi|211415426|gb|FL477512.1|FL477512
EST:     GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGG                         CGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
genomic: GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGGgtaaagccta ... gcgttttcagCGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
EST: gi|71758494|gb|DR956431.1|DR956431
EST:     GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGG                         CGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
genomic: GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGGgtaaagccta ... gcgttttcagCGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
EST: gi|32926166|gb|CF030978.1|CF030978
EST:     GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGG                         CGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
genomic: GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGGgtaaagccta ... gcgttttcagCGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
EST: gi|32926025|gb|CF030837.1|CF030837
EST:     GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGG                         CGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
genomic: GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGGgtaaagccta ... gcgttttcagCGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
EST: gi|71299018|gb|DR785501.1|DR785501
EST:     GACAAGAACGTTCAGCTTCAACTGTGGGAATACGTAGCTCCGTTGAAAGG                         CGGATTTTTCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
genomic: GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGGgtaaagccta ... gcgttttcagCGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
EST: gi|32925152|gb|CF029964.1|CF029964
EST:     GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGG                         CGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
genomic: GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGGgtaaagccta ... gcgttttcagCGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
EST: gi|71429425|gb|DR810475.1|DR810475
EST:     GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGG                         CGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
genomic: GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGGgtaaagccta ... gcgttttcagCGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
EST: gi|76287314|gb|DV026882.1|DV026882
EST:     GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGG                         CGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
genomic: GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGGgtaaagccta ... gcgttttcagCGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
EST: gi|78117759|gb|DV536146.1|DV536146
EST:     GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGG                         CGGATTTATCGTCAACCTTGGCGACTTGCTCGAAAGGTGGAGTAACGGCGT
genomic: GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGGgtaaagccta ... gcgttttcagCGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
EST: gi|32926219|gb|CF031031.1|CF031031
EST:     GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGG                         CGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
genomic: GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGGgtaaagccta ... gcgttttcagCGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
EST: gi|78078283|gb|DV506698.1|DV506698
EST:     GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGG                         CGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
genomic: GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGGgtaaagccta ... gcgttttcagCGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
EST: gi|32858735|gb|CD998416.1|CD998416
EST:     GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGG                         CGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
genomic: GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGGgtaaagccta ... gcgttttcagCGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
EST: gi|32926072|gb|CF030884.1|CF030884
EST:     GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGG                         CGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
genomic: GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGGgtaaagccta ... gcgttttcagCGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
EST: gi|32926162|gb|CF030974.1|CF030974
EST:     GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGG                         CGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
genomic: GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGGgtaaagccta ... gcgttttcagCGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
EST: gi|32926197|gb|CF031009.1|CF031009
EST:     GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGG                         CGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
genomic: GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGGgtaaagccta ... gcgttttcagCGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
EST: gi|32925587|gb|CF030399.1|CF030399
EST:     GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGG                         CGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
genomic: GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGGgtaaagccta ... gcgttttcagCGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
EST: gi|32925272|gb|CF030084.1|CF030084
EST:     GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGG                         CGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
genomic: GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGGgtaaagccta ... gcgttttcagCGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
EST: gi|32925426|gb|CF030238.1|CF030238
EST:     GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGG                         CGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
genomic: GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGGgtaaagccta ... gcgttttcagCGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
EST: gi|32925266|gb|CF030078.1|CF030078
EST:     GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGG                         CGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT
genomic: GACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGGgtaaagccta ... gcgttttcagCGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agggagtttgccgtggtaatcgaatctcgtgacatgtttgaccttgcgttttcagCGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGTTTTCAG
                                   gtttgac  putative branch site (score: 4)
                                              cgttttc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagcctagtaatctgaattagtttatgattgcaccgagtcacgcgttcgggaagcaaaggcatgaagggagtttgccgtggtaatcgaatctcgtgacatgtttgaccttgcgttttcagCGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGTTTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG