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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcacagcatccatccagtgccagcaatatattctttatcttttgacaacgcatcgttatctgtgcagaaattactcatgctgcttgcagaacgttaaaatattctctttgtttttttagGAGACGGTTTTCTTTGATGTCCTGTTCATTATCCAACACTACGTGTTGTACCCTGTCAAGAAGGACGAGAATGGTAAGGCAATCATTTCTGAAAGGGTAG

Basic information

species Zea mays
transcript GRMZM2G015869_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G015869_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os12g18110.1 (Oryza sativa), 3'ss of exon 7
gtgagcacagcatccatccagtgccagcaatatattctttatc----------ttttgacaacgcatcgttatctgtgc--------------agaaattactcatgctgcttgcagaac-------gttaaaata--ttctctttgtttttttagGAGACGGTTTTCTTTGATGTCCTGTTCATTATCCAACACTACGTGTTGTACCCTGTCAAGAAGGACGAGAATGGTAAGGCAATCATTTCTGAAAGGGTAG
|||||||  | |    |      | |  ||||   |||||| |          || | || ||    | || ||  ||               |  ||  |||| |  || ||||  |||         ||||||    | |||||| | || |||||    |||||||| ||  || | ||||| ||||||||||| ||| |||||||||||||    || |||||||||||||| |||||||||||||||||||
gtgagca--ggacttgttttactctaataatactatctttaccacttaaggatttctaactacaagcccttctcaatgttaaataataataataagaacaactcttaatgtttgctaaactcgagtaactaaaatgacatgtctttgatattgtagGAAGTCGTTTTCTTCGACATCTTATTCATAATCCAACACTATGTGCTGTACCCTGTCAAACGAGATGAGAATGGTAAGGCTATCATTTCTGAAAGGGTAG
















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|60338746|gb|DN205719.1|DN205719
EST:     ATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTG                         GAGACGGTTTTCTTTGATGTCCTGTTCATTATCCAACACTACGTGTTGTAC
genomic: ATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTGgtgagcacag ... gtttttttagGAGACGGTTTTCTTTGATGTCCTGTTCATTATCCAACACTACGTGTTGTAC
EST: gi|78092412|gb|DV520786.1|DV520786
EST:     ATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTG                         GAGACGGTTTTCTTTGATGTCCTGTTCATTATCCAACACTACGTGTTGTAC
genomic: ATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTGgtgagcacag ... gtttttttagGAGACGGTTTTCTTTGATGTCCTGTTCATTATCCAACACTACGTGTTGTAC
EST: gi|166698057|gb|EG194972.1|EG194972
EST:     TAACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTG                         GAGACGGTTTTCTT
genomic: T-ACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTGgtgagcacag ... gtttttttagGAGACGGTTTTCTT
EST: gi|78084914|gb|DV513307.1|DV513307
EST:     ATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTG                         GAGACGGTTTTCTTTGATGTCCTGTTCATTATCCAACACTACGTGTTGTAC
genomic: ATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTGgtgagcacag ... gtttttttagGAGACGGTTTTCTTTGATGTCCTGTTCATTATCCAACACTACGTGTTGTAC
EST: gi|5932718|gb|AW057079.1|AW057079
EST:     ATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTG                         GAGACGGTTTTCTTTGATGTCCTGGTCATTATCCAACACTACGTGTTGGAC
genomic: ATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTGgtgagcacag ... gtttttttagGAGACGGTTTTCTTTGATGTCCTGTTCATTATCCAACACTACGTGTTGTAC
EST: gi|50323027|gb|CO518153.1|CO518153
EST:     ATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTG                         GAGACGGTTTTCTTTGATGTCCTGTTCATTATCCAACACTACGTGTTGTAC
genomic: ATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTGgtgagcacag ... gtttttttagGAGACGGTTTTCTTTGATGTCCTGTTCATTATCCAACACTACGTGTTGTAC
EST: gi|84977496|gb|DW475918.1|DW475918
EST:     GGAAAACCCTTCTTTCATTG                         GAGACGGTTTTCTTTGATGTCCTGTTCATTATCCAACACTACGTGTTGTAC
genomic: GGAAAACCCTTCTTTCATTGgtgagcacag ... gtttttttagGAGACGGTTTTCTTTGATGTCCTGTTCATTATCCAACACTACGTGTTGTAC
EST: gi|78081909|gb|DV510321.1|DV510321
EST:     ATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTG                         GAGACGGNNNNNNNNGATGTCCTGTTCATTATCCAACACTACGTGTTGTAC
genomic: ATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTGgtgagcacag ... gtttttttagGAGACGGTTTTCTTTGATGTCCTGTTCATTATCCAACACTACGTGTTGTAC
EST: gi|211091569|gb|FL457271.1|FL457271
EST:     ATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTG                         GAGACGGTTTTCTTTGATGTCCTGTTCATTATCCAACACTACGTGTTGTAC
genomic: ATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTGgtgagcacag ... gtttttttagGAGACGGTTTTCTTTGATGTCCTGTTCATTATCCAACACTACGTGTTGTAC
EST: gi|50329143|gb|CO524269.1|CO524269
EST:     ATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTG                         GAGACGGTTTTCTTTGATGTCCTGTTCATTATCCAACACTACGTGTTGTAC
genomic: ATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTGgtgagcacag ... gtttttttagGAGACGGTTTTCTTTGATGTCCTGTTCATTATCCAACACTACGTGTTGTAC
EST: gi|14244729|gb|BG842667.2|BG842667
EST:     ATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTG                         GAGACGGTTTTCTTTGATGTCCTGTTCATTATCCAACACTACGTG-TGTAC
genomic: ATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTGgtgagcacag ... gtttttttagGAGACGGTTTTCTTTGATGTCCTGTTCATTATCCAACACTACGTGTTGTAC
EST: gi|14208276|gb|BG841954.1|BG841954
EST:     ATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTG                         GAGACGGTTTTCTTTGATGTCCTGTTCATTATCCAACACTACGTG-TGTAC
genomic: ATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTGgtgagcacag ... gtttttttagGAGACGGTTTTCTTTGATGTCCTGTTCATTATCCAACACTACGTGTTGTAC
EST: gi|5919428|gb|AW054525.1|AW054525
EST:     ATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTG                         GAGACGGTTTTCTTTGATGTCCTGTTCATTATCCAACACTACGTGTTGTAC
genomic: ATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTGgtgagcacag ... gtttttttagGAGACGGTTTTCTTTGATGTCCTGTTCATTATCCAACACTACGTGTTGTAC
EST: gi|78084875|gb|DV513268.1|DV513268
EST:     ATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTG                         NAGACGGTTTTCTTTGATGTCCTGTTCATTATCCAACACTACGTGTTGTAC
genomic: ATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTGgtgagcacag ... gtttttttagGAGACGGTTTTCTTTGATGTCCTGTTCATTATCCAACACTACGTGTTGTAC
EST: gi|213191208|gb|FM187518.1|FM187518
EST:     ATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTG                         GAGACGGTTTTCTTTGATGTCCTGTTCATTATCCAACACTACGTGTTGTAC
genomic: ATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTGgtgagcacag ... gtttttttagGAGACGGTTTTCTTTGATGTCCTGTTCATTATCCAACACTACGTGTTGTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagaaattactcatgctgcttgcagaacgttaaaatattctctttgtttttttagGAGACGGTTTTCTTTGATGTCCTGTTCATTATCCAACACTACGTGTTGTACCCTGTCAAGAAGGACGAGAATGGTAAGGCAATCATTTCTGAAAGGGTAG
                                   tattctctttgttttt  CT-rich tract
                             ttaaaatattctcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcacagcatccatccagtgccagcaatatattctttatcttttgacaacgcatcgttatctgtgcagaaattactcatgctgcttgcagaacgttaaaatattctctttgtttttttagGAGACGGTTTTCTTTGATGTCCTGTTCATTATCCAACACTACGTGTTGTACCCTGTCAAGAAGGACGAGAATGGTAAGGCAATCATTTCTGAAAGGGTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG