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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACTACAGATTCCAACACTAGCATTACCTTTCTTCCAGAACCACATGAAGATGAAATACAATTTATATTGGATGCCATCTCTGATTACCTTAATGTTAAAgtatgatattcttgccaacacaggcaatttttaagcacaatagttttccttttctttctgcctttaaatgcagaaattaaatgatcccatgcttattaca...

Basic information

species Glycine max
transcript GLYMA02G28000.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G28000.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os04g14790.1 (Oryza sativa), 5'ss of exon 3
AACTACAGATTCCAACACTAGCATTACCTTTCTTCCAGAACCACATGAAGATGAAATACAATTTATATTGGATGCCATCTCTGATTACCTTAATGTTAAAgtatgatattcttgccaacacaggcaatttttaagcacaatagttttccttttctttctgcctttaaatgcagaaattaaatgatcccatgcttattaca---------
 || || || || |  ||    || ||  | ||||| ||||||||||| ||||| ||||| || ||||| ||||| |||| |||||| ||||| ||| | || || | |  ||||  |   | | |||      | ||| || |||   |     |   |     ||||    || ||      ||  |    || |            
TACAACCGACTCTAGTACAGCAATAACAATGCTTCCTGAACCACATGAGGATGAGATACAGTTCATATTAGATGCTATCTGTGATTATCTTAACGTTCAGgtttg-tgtgtttgc--atttatgtaat------gtacagtaatttatttgacgctgtcgaaaaaaaatagtaaagtttttctttctgaaatatagtgtttttcatgtt

upper sequence: GLYMA02G28000.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G446108_T03 (Zea mays), 5'ss of exon 3
AACTACAGATTCCAACACTAGCATTACCTTTCTTCCAGAACCACATGAAGATGAAATACAATTTATATTGGATGCCATCTCTGATTACCTTAATGTTAAAgtatgatattcttgccaacacaggcaatttttaagcacaatagttttccttt----tctttctgcctttaaatgcagaaattaaatgatcccatgct-tattaca
||| || ||||| |||||    || ||  | ||||| |||||||| || ||||||||||| || ||||||||||| |||||||| || ||||||||| | || || | | | |     || |  |  |||  |    |   | |  |    |    |  || |||  ||  |        | | ||  |  |||  | ||||   
AACAACTGATTCTAACACAGCAATAACAATGCTTCCTGAACCACACGAGGATGAAATACAGTTCATATTGGATGCAATCTCTGACTATCTTAATGTTCAGgtgtgtt-tgcatatatgca-atcctttttccacatgctgaaataatgtcgtaaagttcttatgctattgtagtgttgtttcacatattttcatcttgtatt---

upper sequence: GLYMA02G28000.1 (Glycine max), 5'ss of exon 3
lower sequence: AT3G10370.1 (Arabidopsis thaliana), 5'ss of exon 3
AACTACAGATTCCAACACTAGCATTACCTTTCTTCCAGAACCACATGAAGATGAAATACAATTTATATTGGATGCCATCTCTGATTACCTTAATGTTAAAgtatgatattcttgccaacacaggcaatttttaagcacaatagttttcctttt--ctttctgcc--tttaaatgcagaaattaaatgatcccatgcttattaca-
 |||||||| || || |||   || || |  ||||||||||| ||||||||||| || ||||||||| |||| || |||   || || |||||  |||| ||||       ||   |  |  |   | |  | |   | ||  ||  ||   |  || |||  |  || |  ||  ||  |||    |||| |    |  || | 
CACTACAGACTCTAATACTTCAATCACTTCACTTCCAGAACCTCATGAAGATGAGATTCAATTTATACTGGACGCAATCAGCGACTATCTTAACATTAAGgtatatccagattcagattaatgaggaataatcaattctatttttgacccaatagctctctaacaattcagttgatgatgttatgc-atcctaaatcttatatag

upper sequence: GLYMA02G28000.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv13s0019g04730.t01 (Vitis vinifera), 5'ss of exon 3
AACTACAGATTCCAACACTAGCATTACCTTTCTTCCAGAACCACATGAAGATGAAATACAATTTATATTGGATGCCATCTCTGATTACCTTAATGTTAAAgtatgatattcttgccaacacaggcaatttttaagcacaatagttttccttttctttctgcctttaaatgcagaaattaaatgatcccatgcttattaca-----
 ||||| ||||||||||||||||| ||  | ||||||||||| ||||| ||||| || ||||||||| | ||||| |||  |||||||||||||||||| ||  | |  | |  | |||  |  |  ||  |    |  | |   ||  | ||  ||  |    || ||||    | |  || ||  || | || ||  |     
CACTACTGATTCCAACACTAGCATCACAATGCTTCCAGAACCGCATGAGGATGAGATCCAATTTATACTCGATGCTATCAGTGATTACCTTAATGTTAAGgttggttgatttctctaactaaatctcttgatttttattacatgctttatcttactttaggaactatatgct---actgtatcat--caagatttttggaattgc

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|26268161|gb|CA819224.1|CA819224
EST:     AAATACAATTTATATTGGATGCCATCTCTGATTACCTTAATGTTAAA                         GTCCGCCGCACTGATGTTCTTTCTGCCTGGAGTGGCATTCGCCCATTAGCG
genomic: AAATACAATTTATATTGGATGCCATCTCTGATTACCTTAATGTTAAAgtatgatatt ... gaaaatttagGTCCGCCGCACTGATGTTCTTTCTGCCTGGAGTGGCATTCGCCCATTAGCG
EST: gi|7691586|gb|AW759711.1|AW759711
EST:     ATGAAATACAATTTATATTGGATGCCATCTCTGATTACCTTAATGTTAAA                         GTCCGCCGCACTGATGTTCTTTCTGCCTGGAGTGGCATTCGCCCATTAACG
genomic: ATGAAATACAATTTATATTGGATGCCATCTCTGATTACCTTAATGTTAAAgtatgatatt ... gaaaatttagGTCCGCCGCACTGATGTTCTTTCTGCCTGGAGTGGCATTCGCCCATTAGCG
EST: gi|151403213|gb|EV273023.1|EV273023
EST:     ATGAAATACAATTTATATTGGATGCCATCTCTGATTACCTTAATGTTAAA                         GTCCGCCGCACTGATGTTCTTTCTGCCTGGAGTGGCATTCGCCCATTAGCG
genomic: ATGAAATACAATTTATATTGGATGCCATCTCTGATTACCTTAATGTTAAAgtatgatatt ... gaaaatttagGTCCGCCGCACTGATGTTCTTTCTGCCTGGAGTGGCATTCGCCCATTAGCG
EST: gi|10844622|gb|BF067792.1|BF067792
EST:     ATGAAATACAATTTATATTGGATGCCATCTCTGATTACCTTAATGTTAAA                         GTCCGCCGCACTGATGTTCTTTCTGCCTGGAGTGGCATTCGCCCATTAGCG
genomic: ATGAAATACAATTTATATTGGATGCCATCTCTGATTACCTTAATGTTAAAgtatgatatt ... gaaaatttagGTCCGCCGCACTGATGTTCTTTCTGCCTGGAGTGGCATTCGCCCATTAGCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACTACAGATTCCAACACTAGCATTACCTTTCTTCCAGAACCACATGAAGATGAAATACAATTTATATTGGATGCCATCTCTGATTACCTTAATGTTAAAgtatgatattcttgccaacacaggcaatttttaagcacaatagttttccttttctttctgcctttaaatgcagaaattaaatgatcccatgcttattaca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaattaaa