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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGCTTCGGGGAACGGCAATAAAGGGTCACCTTTCGATGGTTCCTATAGATGCTGAACCTCAGCCAATAATTCTAGCATACATTGATCTTAATCTCCAGgtagaacatgcaaaaccactgttattaacaacattcttcctgcagcctttctttttttctttggtaaccaacattgttcggtcgttgtag

Basic information

species Zea mays
transcript GRMZM2G009849_T02
intron # 30
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G009849_T02 (Zea mays), 5'ss of exon 30
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 5'ss of exon 47
GAAGCTTCGGGGAACGGCAATAAAGGGTCACCTTTCGATGGTTCCTATAGATGCTGAACCTCAGCCAATAATTCTAGCATACATTGATCTTAATCTCCAGgtagaacatgcaaaaccact-gttatta-acaacattcttcctgcagcctttctttttttctttggtaaccaacattgttcggtcgttgtag
 |||||||| || || ||||| || ||||||||||| |||||||||||||||||||||||||||||||| ||| | |||||||||||||||||||| |||||| || |   | | ||  | ||| ||  ||||||  ||  |    | | | ||||||||  ||| || | |   |  |   |         
AAAGCTTCGTGGTACAGCAATCAAAGGTCACCTTTCAATGGTTCCTATAGATGCTGAACCTCAGCCAATCATTTTGGCATACATTGATCTTAATCTTCAGgtaaaaaaaatacatccttttgttgttccacaacaaactgtc-atggacatcctttttttaattgata-ctattgtgttctag---------

upper sequence: GRMZM2G009849_T02 (Zea mays), 5'ss of exon 30
lower sequence: GLYMA10G35140.1 (Glycine max), 5'ss of exon 50
GAAGCTTCGGGGAACGGCAATAAAGGGTCACCTTTCGATGGTTCCTATAGATGCTGAACCTCAGCCAATAATTCTAGCATACATTGATCTTAATCTCCAGgtagaacatgcaaaaccactgttattaacaacattcttcctgcagcctttctttttttctttggtaaccaacattgttcggtcgttgtag
 |||||||| ||  | |||||||||||||| ||||| ||||||||||| |||||| ||||||| || || || || || |||||||| ||||||||  ||||| ||     | || ||   | ||| |    |   | |  | || |||   ||| | || |  | |    || | ||   |  | |   
CAAGCTTCGTGGTGCAGCAATAAAGGGTCATCTTTCAATGGTTCCTATCGATGCTAAACCTCAACCCATCATCCTTGCCTACATTGAACTTAATCTTGAGgtataa---atagaaacaaattaatttattttaaggtactagtagactt--atttatactgtatttattctcacttttgtattttag---

upper sequence: GRMZM2G009849_T02 (Zea mays), 5'ss of exon 30
lower sequence: GLYMA20G32430.1 (Glycine max), 5'ss of exon 49
GAAGCTTCGGGGAACGGCAATAAAGGGTCACCTTTCGATGGTTCCTATAGATGCTGAACCTCAGCCAATAATTCTAGCATACATTGATCTTAATCTCCAGgtagaacatgcaaaaccactgttattaacaacattcttcctgcagcctttctttttttctttggtaaccaacattgttcggtcgttgtag
 |||||||| ||  | |||||||||||||| ||||| ||||||||||| |||||| ||||||| || || || || || |||||||| ||||||||  |||||    |     || ||   | ||| |    |   |    | || |||      ||| |  ||||   |   |   |      || |||
CAAGCTTCGTGGTGCAGCAATAAAGGGTCATCTTTCAATGGTTCCTATCGATGCTAAACCTCAACCCATCATCCTTGCCTACATTGAACTTAATCTTGAGgta---tacattgaaacagattaatttattttaaggtggtagtagactt-----atttatacggtatttattctcacttttgtattttag

upper sequence: GRMZM2G009849_T02 (Zea mays), 5'ss of exon 30
lower sequence: Vv00s0652g00030.t01 (Vitis vinifera), 5'ss of exon 19
GAAGCTTCGGGGAACGGCAATAAAGGGTCACCTTTCGATGGTTCCTATAGATGCTGAACCTCAGCCAATAATTCTAGCATACATTGATCTTAATCTCCAGgta--gaacatgcaaaaccactgttattaacaac------attcttcctg-----cagcctttctttttttctttggtaaccaacattgttcggtcgttgtag-----------
 |||||||| ||||| |||||||||||||||||||| ||||||||||||||    ||||| |||||||| || || || || ||||| |||||||| ||||||   |    |   ||  | |    | || | |      |||||| |||     ||   | | ||| ||||||   ||          ||   || || |             
TAAGCTTCGCGGAACTGCAATAAAGGGTCACCTTTCTATGGTTCCTATAGACATGGAACCCCAGCCAATTATCCTTGCCTATATTGACCTTAATCTTCAGgtattaattgagttcaagtatttacttaaatacctgttttattctttctggacatcaaattatttttctttcttctttatttttttcctttttttctttctccaaaccttacag

upper sequence: GRMZM2G009849_T02 (Zea mays), 5'ss of exon 30
lower sequence: EFJ15655 (Selaginella moellendorffii), 5'ss of exon 45
GAAGCTTCGGGGAACGGCAATAAAGGGTCACCTTTCGATGGTTCCTATAGATGCTGAACCTCAGCCAATAATTCTAGCATACATTGATCTTAATCTCCAGgtagaacatgcaaaaccactgttattaacaacattcttcctgcagcctttctttttttctttggtaaccaacattgttcggtcgttgtag
 |||||||| ||||| || || |||||||||||||| ||||| || || ||  | |||||||| || || ||||| || || |||||||| |||||||| ||| | | |||         ||| ||    | | | ||| | ||  || |                                        
AAAGCTTCGTGGAACAGCCATTAAGGGTCACCTTTCCATGGTGCCAATCGACACAGAACCTCAACCTATCATTCTTGCTTATATTGATCTCAATCTCCAAgta-agcttgc----ttgtggttgttgt--atagttttcttacaatctgttacag-----------------------------------

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|18450668|gb|BM428946.1|BM428946
EST:     ATGCTGAACCTCAGCCAATAATTCTAGCATACATTGATCTTAATCTCCAG                         ACCCTTGCTGCTGCTAGAATGTTGATGCCATCGGGACCTATGGGTCAAACT
genomic: ATGCTGAACCTCAGCCAATAATTCTAGCATACATTGATCTTAATCTCCAGgtagaacatg ... gtcgttgtagACCCTTGCTGCTGCTAGAATGTTGACGCCATCGGGACCTATGGGTCAAACT
EST: gi|67019308|gb|CO448057.1|CO448057
EST:     ATGCTGAACCTCAGCCAATAATTCTAGCATACATTGATCTTAATCTCCAG                         ACCCTTGCTGCTGCTAGAATGTTGACGCCATCGGGACCTATGGGTCAAACT
genomic: ATGCTGAACCTCAGCCAATAATTCTAGCATACATTGATCTTAATCTCCAGgtagaacatg ... gtcgttgtagACCCTTGCTGCTGCTAGAATGTTGACGCCATCGGGACCTATGGGTCAAACT
EST: gi|12045716|gb|BF727855.1|BF727855
EST:     ATGCTGAACCTCAGCCAATAATTCTAGCATACATTGATCTTAATCTCCAG                         ACCCTTGCTGCTGCTAGAATGTTGACGCCATCGGGACCTATGGGTCAAACT
genomic: ATGCTGAACCTCAGCCAATAATTCTAGCATACATTGATCTTAATCTCCAGgtagaacatg ... gtcgttgtagACCCTTGCTGCTGCTAGAATGTTGACGCCATCGGGACCTATGGGTCAAACT
EST: gi|67011174|gb|CO439923.1|CO439923
EST:     ATGCTGAACCTCAGCCAATAATTCTAGCATACATTGATCTTAATCTCCAG                         ACCCTTGCTGCTGCTAGAATGTTGACGCCATCGGGACCTATGGGTCAAACT
genomic: ATGCTGAACCTCAGCCAATAATTCTAGCATACATTGATCTTAATCTCCAGgtagaacatg ... gtcgttgtagACCCTTGCTGCTGCTAGAATGTTGACGCCATCGGGACCTATGGGTCAAACT
EST: gi|87152573|gb|DY397362.1|DY397362
EST:     ATGCTGAACCTCAGCCAATAATTCTAGCATACATTGATCTTAATCTCCAG                         ACCCTTGCTGCTGCTAGAATGTTGATGCCATCGGGACCTATGGGTCAAACT
genomic: ATGCTGAACCTCAGCCAATAATTCTAGCATACATTGATCTTAATCTCCAGgtagaacatg ... gtcgttgtagACCCTTGCTGCTGCTAGAATGTTGACGCCATCGGGACCTATGGGTCAAACT
EST: gi|78180940|gb|DV551313.1|DV551313
EST:     ATGCTGAACCTCAGCCAATAATTCTAGCATACATTGATCTTAATCTCCAG                         ACCCTTGCTGCTGCTAGAATGTTGACGCCATCGGGACCTATGGGTCAAACT
genomic: ATGCTGAACCTCAGCCAATAATTCTAGCATACATTGATCTTAATCTCCAGgtagaacatg ... gtcgttgtagACCCTTGCTGCTGCTAGAATGTTGACGCCATCGGGACCTATGGGTCAAACT
EST: gi|67035401|gb|CO463934.1|CO463934
EST:     TGCTGAACCTCAGCCCATA-TTCTAGCATACATTGATCTTAAATCTC-AG                         ACCCTTGCTGCTGCTAGAATGT
genomic: TGCTGAACCTCAGCCAATAATTCTAGCATACATTGATCTTAA-TCTCCAGgtagaacatg ... gtcgttgtagACCCTTGCTGCTGCTAGAATGT
EST: gi|22489973|gb|BU049896.1|BU049896
EST:     ATGCTGAACCTCAGCCAATAATTCTAGCATACATTGATCTTAATCTCCAG                         ACCCTTGCTGCTGCTAGAAT
genomic: ATGCTGAACCTCAGCCAATAATTCTAGCATACATTGATCTTAATCTCCAGgtagaacatg ... gtcgttgtagACCCTTGCTGCTGCTAGAAT
EST: gi|32851907|gb|CD991588.1|CD991588
EST:     ATGCTGAACCTCAGCCAATAATTCTAGCATACATTGATCTTAATCTCCAG                         ACCCTTGCTGCTGCTAGAATGTTGACGCCATCGGGACCTATGGGTCAAACT
genomic: ATGCTGAACCTCAGCCAATAATTCTAGCATACATTGATCTTAATCTCCAGgtagaacatg ... gtcgttgtagACCCTTGCTGCTGCTAGAATGTTGACGCCATCGGGACCTATGGGTCAAACT
EST: gi|19822797|gb|BQ048821.1|BQ048821
EST:     ATGCTGAACCTCAGCCAATAATTCTAGCATACATTGATCTTAATCTCCAG                         ACCCTTGCTGCTGCTAGAATGTTGATGCCATCGGGACCTATGGGTCAAACT
genomic: ATGCTGAACCTCAGCCAATAATTCTAGCATACATTGATCTTAATCTCCAGgtagaacatg ... gtcgttgtagACCCTTGCTGCTGCTAGAATGTTGACGCCATCGGGACCTATGGGTCAAACT
EST: gi|19822549|gb|BQ048573.1|BQ048573
EST:     ATGCTGAACCTCAGCCAATAATTCTAGCATACATTGATCTTAATCTCCAG                         ACCCTTGCTGCTGCTAGAATGTTGATGCCA
genomic: ATGCTGAACCTCAGCCAATAATTCTAGCATACATTGATCTTAATCTCCAGgtagaacatg ... gtcgttgtagACCCTTGCTGCTGCTAGAATGTTGACGCCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGCTTCGGGGAACGGCAATAAAGGGTCACCTTTCGATGGTTCCTATAGATGCTGAACCTCAGCCAATAATTCTAGCATACATTGATCTTAATCTCCAGgtagaacatgcaaaaccactgttattaacaacattcttcctgcagcctttctttttttctttggtaaccaacattgttcggtcgttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG