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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGGTTGCTACAAAGTACCCTGGAATCAAGTATAACGAAATTATTGTGGATAACTGCTGTATGCAGCTTGTTTCAAAGCCTGAACAGTTTGATGTCATGgtatgtgtatttacatttcaatcctggcttgcagctatttatgcacttatgtaatttgtctaatgtatttgtgcagtaacccccccgccccccgcccccc...

Basic information

species Glycine max
transcript GLYMA02G04780.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G04780.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os02g38200.1 (Oryza sativa), 5'ss of exon 2
AGAGGTTGCTACAAAGTACCCTGGAATCAAGTATAACGAAATTATTGTGGATAACTGCTGTATGCAGCTTGTTTCAAAGCCTGAACAGTTTGATGTCATGgtatgtgtatttacatttcaatcctggct-tgcagct--atttatgcact---tatgtaatttgtctaatgtatttgtgcagtaacccccccgccccccgcccccc
 |||||||| |||||||| ||||||||  | ||||| ||||| || ||||| ||||| ||||||||||||||| | ||||||||||| |||||||| |||||| || | ||   | ||| ||| |  || |||| ||  |   ||||| |   | |||||  |  | |   | | |   ||   ||    |    |      |   
TGAGGTTGCAACAAAGTATCCTGGAATTCAATATAATGAAATCATCGTGGACAACTGTTGTATGCAGCTTGTTGCTAAGCCTGAACAATTTGATGTTATGgtaagtatgtt---agttctatcattactatgcatcttaacaaatgcattctgtttgtaacgtcaccatattctatactcacctactgatctatgcttttatc---

upper sequence: GLYMA02G04780.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os04g40310.2 (Oryza sativa), 5'ss of exon 2
AGAGGTTGCTACAAAGTACCCTGGAATCAAGTATAACGAAATTATTGTGGATAACTGCTGTATGCAGCTTGTTTCAAAGCCTGAACAGTTTGATGTCATGgtatgtgtatttacatttca-atcctggcttgcagctatttatgcacttatgtaatttg--tctaatgtatttg---tgcagtaacccccccgccccccgcccccc
 ||||||||  ||||||| ||||| ||  ||||||| || || ||||| || |||||||||||||| |||||| |||||||||| || |||||||||||||||||  | ||||| |   | || ||  || |    |   | |    | | ||| ||||   ||    | ||||   |||| | |    |    |    ||     
TGAGGTTGCCTCAAAGTATCCTGGTATTCAGTATAATGAGATCATTGTCGACAACTGCTGTATGCAACTTGTTGCAAAGCCTGAGCAATTTGATGTCATGgtatgc-tctttacttcatacattctatctggagcatcactgtctgttca-gtactttggagctgccttgtttgaactgcactgagtttctttgcgtgtgct----

upper sequence: GLYMA02G04780.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G006672_T02 (Zea mays), 5'ss of exon 2
AGAGGTTGCTACAAAGTACCCTGGAATCAAGTATAACGAAATTATTGTGGATAACTGCTGTATGCAGCTTGTTTCAAAGCCTGAACAGTTTGATGTCATGgtatgtgtatttacatttcaatcctggcttgcagctatttatgcacttatgtaattt---gtctaatgtatttgtgcagtaacccccccgccccccgcccccc
 |||||||| |  |||||||||||||| || ||||| ||||| |||||||| ||||| ||||||||||||||| ||||||||||||| |||||||| |||||| || |||| || | | |   ||    | | ||  ||| | ||| || |  || |    | |  | |  ||   |   ||       |  |  |  |    
TGAGGTTGCAAAGAAGTACCCTGGAATTAAATATAATGAAATCATTGTGGACAACTGTTGTATGCAGCTTGTTGCAAAGCCTGAACAATTTGATGTTATGgtacgtatattcac-tcttatcacttatatac-gcagtttct-cacctaggagatgttggatgtggttttcttactctacaaaggagaaggacaacaactttt

upper sequence: GLYMA02G04780.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G025366_T02 (Zea mays), 5'ss of exon 2
AGAGGTTGCTACAAAGTACCCTGGAATCAAGTATAACGAAATTATTGTGGATAACTGCTGTATGCAGCTTGTTTCAAAGCCTGAACAGTTTGATGTCATGgtatgtgtatttacatttcaatcctggcttgcagctatttatgcacttatgtaatttgtctaatgtatttgtgcagtaacccccccgccccccgcccccc--
 || |||||| |||| || ||||| ||  |||| || ||||| ||||| || ||||||| |||||| |||||||||||||||||||| |||||||||||||||||| | |  |  | |      |    ||    || | ||  | || || || ||  ||  | | ||    ||            |    | |    |  
TGAAGTTGCTTCAAAATATCCTGGTATTCAGTACAATGAAATGATTGTTGACAACTGCTCTATGCAACTTGTTTCAAAGCCTGAACAATTTGATGTCATGgtatgtatctaaatttctgggcatttttctgtgtatact-atttaatt-tggaactttacttttttgttcaaacaaaccttggattacatttctctgttcta

upper sequence: GLYMA02G04780.1 (Glycine max), 5'ss of exon 2
lower sequence: AT4G35650.1 (Arabidopsis thaliana), 5'ss of exon 2
AGAGGTTGCTACAAAGTACCCTGGAATCAAGTATAACGAAATTATTGTGGATAACTGCTGTATGCAGCTTGTTTCAAAGCCTGAACAGTTTGATGTCATGgtatgtgtatttacatttcaatcctggcttgcagctatttatgcacttatgtaatt--tgtctaatgtatttgtgcagtaacccccccgccccccgcccccc---------------------
||||||||||| | | ||  | || || |  || || ||||| || || || || |||||||||||||||||  | |||||||| || |||||||||||||||    | ||    |   | |      |   |   | | ||      |||| |     |   ||   ||   ||  ||         | | | |                            
AGAGGTTGCTAAACATTATTCGGGGATTACTTACAATGAAATAATCGTAGACAATTGCTGTATGCAGCTTGTCGCCAAGCCTGAGCAATTTGATGTCATGgtaatgctcttcttttcctagttacaaatcaaaatgagtcattttgaaatgtgacagacgatgaaaccatcattgatgttgttttgatgtctctcatggatattttttgttggtttgtttcag

upper sequence: GLYMA02G04780.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv04s0210g00180.t01 (Vitis vinifera), 5'ss of exon 2
AGAGGTTGCTACAAAGTACCCTGGAATCAAGTATAACGAAATTATTGTGGATAACTGCTGTATGCAGCTTGTTTCAAAGCCTGAACAGTTTGATGTCATGgtatgtgtatttacatttcaatcctggcttg-cagctatttatgc-acttatgtaatttgtctaatgtatttgtgcagtaacccccccgccccccgcccccc
||||||||| ||||| || |||||||||||||| |  |||||||||||||| || ||||| ||||||||||||||||||||||| |||||||||||||||||||||| || |||  ||  ||      ||    |  ||  |     |||    ||| | | | |||| | |||  | ||  |         || |    | 
AGAGGTTGCAACAAAATATCCTGGAATCAAGTACAGTGAAATTATTGTGGACAATTGCTGCATGCAGCTTGTTTCAAAGCCTGAGCAGTTTGATGTCATGgtatgtgaatatactattgtatagcactttaattgagatgcaaattgcttggtcaatgtttgtcatgt-tctgta-attattcttaagatttcctgatagca

upper sequence: GLYMA02G04780.1 (Glycine max), 5'ss of exon 2
lower sequence: PP1S212_85V6.2 (Physcomitrella patens), 5'ss of exon 3
AGAGGTTGCTACAAAGTACCCTGGAATCAAGTATAACGAAATTATTGTGGATAACTGCTGTATGCAGCTTGTTTCAAAGCCTGAACAGTTTGATGTCATGgtatgtgtatttacatttcaatcctggcttgcagctatttatgcacttatgtaatttgtctaatgtatttgtgcagtaacccccccgccccccgcccccc---
 ||||| || | ||| ||||| || ||||| || |||||  | ||||||||||||||||||||||| ||||| || |||||  | |||||||| || ||||||  |    ||| | | |  || |   ||  |  | |   |    |||| | | ||| |  | | |||   ||||   || |  | |          ||   
TGAGGTGGCCAAAAACTACCCAGGCATCAAATACAACGAGGTCATTGTGGATAACTGCTGTATGCAACTTGTGTCTAAGCCCCAGCAGTTTGACGTGATGgta-attctcttagactgctctcattaatt-tatttctccgttttattattttaattg-ccgacggattgcagcaggtgcctcaaccctagagatgatcccgt

upper sequence: GLYMA02G04780.1 (Glycine max), 5'ss of exon 2
lower sequence: PP1S101_151V6.1 (Physcomitrella patens), 5'ss of exon 2
AGAGGTTGCTACAAAGTACCCTGGAATCAAGTATAACGAAATTATTGTGGATAACTGCTGTATGCAGCTTGTTTCAAAGCCTGAACAGTTTGATGTCATGgtatgtgtatttacatttcaatcctggcttgcagctatttatgcacttatgtaatt-tgtctaatgtatttgtgca-gtaacccccccgccccccgcccccc-
 ||||| |||| ||| || || || ||||| || |||||  ||||||||||||||||||||||||||||||| || |||||  | |||||||| ||||||||| ||   | ||| |  ||   |||   |  | || ||| |  | ||  | |||  || |   ||  |     || | ||    || |   |  |   |   
TGAGGTAGCTAAAAACTATCCAGGTATCAAATACAACGAGGTTATTGTGGATAACTGCTGTATGCAGCTTGTGTCGAAGCCCCAGCAGTTTGACGTCATGgtaagtt--tctac-tcgcatctctgtgatttatctgtttgttaattttaggaatcgtggccgttgcttgcactcaagaaatggtcctgtgtctggtggcttt

upper sequence: GLYMA02G04780.1 (Glycine max), 5'ss of exon 2
lower sequence: PP1S152_81V6.1 (Physcomitrella patens), 5'ss of exon 2
AGAGGTTGCTACAAAGTACCCTGGAATCAAGTATAACGAAATTATTGTGGATAACTGCTGTATGCAGCTTGTTTCAAAGCCTGAACAGTTTGATGTCATGgtatgt----gtatttacatttcaatcct----ggcttgcagctatttat-gcacttatgtaatttgtctaatgtatttgtgcagtaaccc----ccccgccccccgcccccc---------------------------------
 ||||| || | |||||| || |  ||||||||||||||  | ||||||||||| ||||||||||||||||| || |||||| |||| ||||||||||||||| ||    |||| |     |||||  |    | |||  || ||||    |   |||||  | |    | ||||   ||||   | | |     | | |   |  |                                       
TGAGGTGGCCAAAAAGTATCCCGCCATCAAGTATAACGAGGTCATTGTGGATAATTGCTGTATGCAGCTTGTGTCGAAGCCTCAACAATTTGATGTCATGgtaagttctcgtatgtcaggctcaattttctccgacttttagttattggcagtgtttatgctaatgacttgatgttactgtgacatcagctggaactctgattcaagttgtttgccttggtgctattgtgtgtatttttcccccag

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|20498379|gb|BQ273309.1|BQ273309
EST:     ATAACTGCTGTATGCAGCTTGTTTCAAAGCCTGAACAGTTTGATGTCATG                         GTGACCCCAAATCTTTATGGAAATCTAGTTGCAAACACTGCAGCAGGCATT
genomic: ATAACTGCTGTATGCAGCTTGTTTCAAAGCCTGAACAGTTTGATGTCATGgtatgtgtat ... ctcttgctagGTGACCCCAAATCTTTATGGAAATCTAGTTGCAAACACTGCAGCAGGCATT
EST: gi|4313507|gb|AI460626.1|AI460626
EST:     ATAACTGCTGTATGCAGCTTGTTTCAAAGCCTGAACAGTTTGATGTCATG                         GT-ACCCCAAATCTTTATGGAAATCTAGTTGCAAACACTGCAGCAGGCATT
genomic: ATAACTGCTGTATGCAGCTTGTTTCAAAGCCTGAACAGTTTGATGTCATGgtatgtgtat ... ctcttgctagGTGACCCCAAATCTTTATGGAAATCTAGTTGCAAACACTGCAGCAGGCATT
EST: gi|31307171|gb|CD392374.1|CD392374
EST:     ATAACTGCTGTATGCAGCTTGTTTCAAAGCCTGAACAGTTTGATGTCATG                         GTGACCCCAAATCTTTATGGAAATCTAGTTGCAAACACTGCAGCAGGCATT
genomic: ATAACTGCTGTATGCAGCTTGTTTCAAAGCCTGAACAGTTTGATGTCATGgtatgtgtat ... ctcttgctagGTGACCCCAAATCTTTATGGAAATCTAGTTGCAAACACTGCAGCAGGCATT
EST: gi|12774307|gb|BG239234.1|BG239234
EST:     ATAACTGCTGTATGCAGCTTGTTTCAAAGCCTGAACAGTTTGATGTCATG                         GTGACCCCAAATCTTTATGGAAATCTAGTTGCAAACACTGCAGCAGGCATT
genomic: ATAACTGCTGTATGCAGCTTGTTTCAAAGCCTGAACAGTTTGATGTCATGgtatgtgtat ... ctcttgctagGTGACCCCAAATCTTTATGGAAATCTAGTTGCAAACACTGCAGCAGGCATT
EST: gi|15285790|gb|BI469681.1|BI469681
EST:     ATAACTGCTGTATGCAGCTTGTTTCAAAGCCTGAACAGTTTGATGTCATG                         GTGACCCCAAATCTTTATGGAAATCTAGTTGCAAACACTGCAGCANGCATT
genomic: ATAACTGCTGTATGCAGCTTGTTTCAAAGCCTGAACAGTTTGATGTCATGgtatgtgtat ... ctcttgctagGTGACCCCAAATCTTTATGGAAATCTAGTTGCAAACACTGCAGCAGGCATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGGTTGCTACAAAGTACCCTGGAATCAAGTATAACGAAATTATTGTGGATAACTGCTGTATGCAGCTTGTTTCAAAGCCTGAACAGTTTGATGTCATGgtatgtgtatttacatttcaatcctggcttgcagctatttatgcacttatgtaatttgtctaatgtatttgtgcagtaacccccccgccccccgcccccc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccccccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cgccccc