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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTGgtaagactcggtttattctgatttactttgtttggagtttggattttgtttatgtatgtggaatttgagaaatagatgttatttactgggttgaagggat...

Basic information

species Glycine max
transcript GLYMA06G34850.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G34850.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os09g21770.1 (Oryza sativa), 5'ss of exon 3
GTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTGgtaagactc---ggtttattctgattt-----actttgtttgga-gtttggattttgttt-atgtatgtggaatttgagaaatagatgttatttactgggttgaagggat
||| ||||| || |||||||| ||||||||||||||||| ||||| || || || || |||||||| ||||||  | |   ||   || || |  |     |||   | |||  |   | |   | ||| |||   ||  | ||| || |  |  | | ||  |||  ||         
GTACTGCAAGTGCGAGATGCCGTATAACCCGGATGATCTAATGGTGCAGTGCGAGGGATGCAAGGACTGgtaaatcacttggggacatccttacctttcatactgcatctggctgaccgaagggtatttcatgcccgtc-atttttaggaggaagtatcatagactcagt---------

upper sequence: GLYMA06G34850.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os08g32620.2 (Oryza sativa), 5'ss of exon 2
-------------------------------GTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTGgtaagactcggtttattctgatttactttgtttggagtttggattttgtttatgtatgtggaatttgagaaatagatgttatttactgggttga-agggat
                                || ||||| ||||||||||| || |||||||||||||||||||| || || || |  |||||||| ||||||  |      ||  | |  |   ||    || | ||  |  | | |   || ||||  | |   | |    | |   | | |     |||  |   ||
TGCTTGTGTTTTCTTTTTCGTTTTTCTGAAGATACTGCAAGTGTGAGATGCCATACAACCCGGATGATCTCATGGTGCAGTGCGATGACTGCAAGGACTGgtaattccattaataaaccgcctctgttatgatgcatttcagtctatata-gtgaatgtacactggaaaatcatggtaacaataatgaaattggcacccat

upper sequence: GLYMA06G34850.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os08g32620.1 (Oryza sativa), 5'ss of exon 3
GTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTGgtaagactcggtttattctgatttactttgtttggagtttggattttgtttatgtatgtggaatttgagaaatagatgttatttactgggttga-agggat
 || ||||| ||||||||||| || |||||||||||||||||||| || || || |  |||||||| ||||||  |      ||  | |  |   ||    || | ||  |  | | |   || ||||  | |   | |    | |   | | |     |||  |   ||
ATACTGCAAGTGTGAGATGCCATACAACCCGGATGATCTCATGGTGCAGTGCGATGACTGCAAGGACTGgtaattccattaataaaccgcctctgttatgatgcatttcagtctatata-gtgaatgtacactggaaaatcatggtaacaataatgaaattggcacccat

upper sequence: GLYMA06G34850.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G091265_T03 (Zea mays), 5'ss of exon 2
-------------------------------GTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTGgtaagactcggtttattctgatttactttgtttggagtttggattttgtttatgtatgtggaatttgagaaatagatgttatttactgggttgaagggat----
                                |||||||| ||||||||||| || ||||||||||| |||||||| || |||||||| |||||||| |||||| |  | ||  |  ||     |||||  |   | |   |  | | || |     ||  |  | |  ||||   ||| |   | ||| |  |     |    
TGATCTTATGTGACATTGTTTGTATGTGAAGATATTGCAAGTGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTGgtaaaatcctgtgaaaactc-cacacttttctcccattagtgcatgttttgagaggggtttatctagtaaaatcactgtga---aatggctccacattttgccc

upper sequence: GLYMA06G34850.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G091265_T05 (Zea mays), 5'ss of exon 3
GTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTGgtaagactcggtttattctgatttactttgtttggagtttggattttgtttatgtatgtggaatttgagaaatagatgttatttactgggttgaagggat----
 |||||||| ||||||||||| || ||||||||||| |||||||| || |||||||| |||||||| |||||| |  | ||  |  ||     |||||  |   | |   |  | | || |     ||  |  | |  ||||   ||| |   | ||| |  |     |    
ATATTGCAAGTGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTGgtaaaatcctgtgaaaactc-cacacttttctcccattagtgcatgttttgagaggggtttatctagtaaaatcactgtga---aatggctccacattttgccc

upper sequence: GLYMA06G34850.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G119357_T01 (Zea mays), 5'ss of exon 3
GTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTGgtaa----gactcggtttattctgatttactttgtttggagtttggattttgttta-tgtatgtggaatttgagaaatagatgttatttactgggttgaagggat
||||||||||||||||||||| || ||||||||||| |||||||| || || ||||  |||||||| |||||     | |||  |   ||   |||||| ||     ||  || |  |||||| | | ||| |     ||    ||   |  |  ||||      || |     
GTATTGCAAATGTGAGATGCCATACAACCCGGATGACCTCATGGTGCAGTGCGAAGCTTGCAAGGACTGgtacatttgtctcaatgattttcaatttacatttcactgatatttgcctttgttcagtctattttatgcttctacaaagcaaatgctttaaatctctgga-----

upper sequence: GLYMA06G34850.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G091265_T01 (Zea mays), 5'ss of exon 3
GTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTGgtaagactcggtttattctgatttactttgtttggagtttggattttgtttatgtatgtggaatttgagaaatagatgttatttactgggttgaagggat----
          ||||||||||| || ||||||||||| |||||||| || |||||||| |||||||| |||||| |  | ||  |  ||     |||||  |   | |   |  | | || |     ||  |  | |  ||||   ||| |   | ||| |  |     |    
----------TGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTGgtaaaatcctgtgaaaactc-cacacttttctcccattagtgcatgttttgagaggggtttatctagtaaaatcactgtga---aatggctccacattttgccc

upper sequence: GLYMA06G34850.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM5G871463_T02 (Zea mays), 5'ss of exon 3
GTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTGgtaagact----cggtttattctgatttactttgtttggagtttggattttgtt---tatgtatgtggaatttgagaaatagatgttatttactgggttgaagggat
||||||||||||||||||||| || ||||| ||||| |||||||| || || || |  |||||| | |||||    |    |  |   ||   |||||| ||     ||  || |  ||||||     | |||   |    ||   ||   ||||| || | |    |||      
GTATTGCAAATGTGAGATGCCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTGgtacatttgttacaatgatttgcaatttacatttcactgatatttgcctttgttccccgtctattatgtgactgtacaaagcatgtt-ttaaatctcctga------

upper sequence: GLYMA06G34850.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM5G871463_T01 (Zea mays), 5'ss of exon 1
-------------------------------GTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTGgtaagact----cggtttattctgatttactttgtttggagtttggattttgttt---atgtatgtggaatttgagaaatagatgttatttactgggttgaagggat
                               ||||||||||||||||||||| || ||||| ||||| |||||||| || || || |  |||||| | |||||    |    |  |   ||   |||||| ||     ||  || |  ||||||     | |||   |    ||   ||   ||||| || | |    |||      
GTGATGATTGGGTTGTCTATTTTCTCTCAAGGTATTGCAAATGTGAGATGCCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTGgtacatttgttacaatgatttgcaatttacatttcactgatatttgcctttgttccccgtctattatgtgactgtacaaagcatgtt-ttaaatctcctga------

upper sequence: GLYMA06G34850.1 (Glycine max), 5'ss of exon 2
lower sequence: AT4G22140.2 (Arabidopsis thaliana), 5'ss of exon 3
GTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTGgtaagactcggtttat-tctgatttactttgtttggagtttggattttgttta---------tgtatgtggaatttgagaaatagatgttatttactgggttgaagggat-------------------------
||| ||||||||||| |||||||| || || || ||||||||||| || |||||||| ||||| || ||||||   | | | | | |||  |||| |   ||      |||  |||               | |||||    ||| | |  ||  | || ||| |  ||    |  |||                         
GTACTGCAAATGTGAAATGCCTTACAATCCAGACGATCTCATGGTGCAGTGTGAAGGCTGCAAAGACTGgtaaatgttgatatttgtcttttttattaacttccttacttgtgtttcaacagaaaagagactatatgtctgtttttaaacttacgtattcttttccaggaattattgataataagcattaattcgctgttgtag

upper sequence: GLYMA06G34850.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv10s0116g00160.t01 (Vitis vinifera), 5'ss of exon 3
GTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTGgtaagactcggtttattctgatttactttgtttggagtttggattttgtttatgtatgtggaatttgagaaatagatgttatttactgggttgaagggat-----
|||||||||||| ||||||||||||||||| |||||||| ||||| || || || ||||||||||| ||||||    | | || |  |   ||  |||||| ||  |  || | |||||    | ||||  |||| ||   |  || | ||||  |      | || |      
GTATTGCAAATGCGAGATGCCTTATAACCCAGATGATCTTATGGTCCAGTGCGAGGGGTGCAAGGACTGgtaa---cctgcttttgtta--ttcttttgttgggtttccggttgttgttgtgttttgtgtcatttcagttttgtatctgattttgtaaaaacatggaaactcaa

upper sequence: GLYMA06G34850.1 (Glycine max), 5'ss of exon 2
lower sequence: PP1S307_14V6.1 (Physcomitrella patens), 5'ss of exon 3
GTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTGgtaagactcggtttattctgatttactttgtttggagtttggattttgtttatgtatgtggaatttgagaaatagatgttatttactgggttgaagggat---
|||||| |||||||||||||||||||| || |||||| | ||||| ||||||||    ||||| ||||||||||      |    ||    ||| || ||  | |  |||      | || | |   || | ||  |||   | ||  ||    |||  |    |       
GTATTGTAAATGTGAGATGCCTTATAATCCAGATGATTTGATGGTTCAATGTGAGACTTGCAAAGATTGgtaagttctcttcatctcatccttatttagtcagtatattgtgagcagcttgtct---tgtacttcaagaggcaaattgtagagtctgaatcactgaagcctt

upper sequence: GLYMA06G34850.1 (Glycine max), 5'ss of exon 2
lower sequence: EFJ26805 (Selaginella moellendorffii), 5'ss of exon 3
GTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTGgtaagactcggtttattctgatttactttgtttggagtttggattttgtttatgtatgtggaatttgagaaatagatgttatttactgggttgaagggat
||| ||||| || ||||||||||| |||||||||||||| ||||| || ||||| | |||||| || |||||||| || |||| |    | |      |  | |      |  |  | | |   |  ||| |                                     
GTACTGCAAGTGCGAGATGCCTTACAACCCGGATGATCTTATGGTGCAGTGTGAGGAGTGCAAAGACTGgtaagaatcagtttctctcaaatccaaaagccttgg---cagcctccgatgaaaaaaatggcag------------------------------------

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|208199612|gb|GD999909.1|GD999909
EST:     CATGGTACAATTGTTGTAAGGGTGTCAAGGATTG                         GTACCATCCTGCTTGCATGGGCATGACTATTGAAGAAGCTAAGAAACTAG
genomic: CATGGTACAA-TG-TG-AAGGGTG-CAAGGATTGgtaagactcg ... tttcttgtagGTACCATCCTGCTTGCATGGGCATGACTATTGAAGAAGCTAAGAAACTAG
EST: gi|208216064|gb|GE008972.1|GE008972
EST:     ACAATGTGAAGGGTGCAAGGATTG                         GTACCATCCTGCTTGCATGGGCATGATTATTGAAGAAGCTAAGAAACTAGA
genomic: ACAATGTGAAGGGTGCAAGGATTGgtaagactcg ... tttcttgtagGTACCATCCTGCTTGCATGGGCATGACTATTGAAGAAGCTAAGAAACTAGA
EST: gi|208169033|gb|GD971418.1|GD971418
EST:     TGGTACAATGTGAAGGGTGCAAGGATTG                         GTACCATCCTGCTTGCATGGGCATGACTATTGAAGAAGCTAAGAAACTAGA
genomic: TGGTACAATGTGAAGGGTGCAAGGATTGgtaagactcg ... tttcttgtagGTACCATCCTGCTTGCATGGGCATGACTATTGAAGAAGCTAAGAAACTAGA
EST: gi|207806317|gb|GD778794.1|GD778794
EST:     CCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTG                         GTACCATCCTGCTTGCATGGGCATGACTATTGAAGAAGCTAAGAAACTAGA
genomic: CCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTGgtaagactcg ... tttcttgtagGTACCATCCTGCTTGCATGGGCATGACTATTGAAGAAGCTAAGAAACTAGA
EST: gi|193635788|gb|FK579359.1|FK579359
EST:     GTACAATGTGAAGGGTGCAAGGATTG                         GTACCATCCTGCTTGCATGGGCATGACTATTGAAGAAGCTAAGAAACTAGA
genomic: GTACAATGTGAAGGGTGCAAGGATTGgtaagactcg ... tttcttgtagGTACCATCCTGCTTGCATGGGCATGACTATTGAAGAAGCTAAGAAACTAGA
EST: gi|151393735|gb|EV263610.1|EV263610
EST:     CCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTG                         GTACCATCCTGCTTGCATGGGCATGACTATTGAAGAAGCTAAGAAACTAGA
genomic: CCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTGgtaagactcg ... tttcttgtagGTACCATCCTGCTTGCATGGGCATGACTATTGAAGAAGCTAAGAAACTAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTGgtaagactcggtttattctgatttactttgtttggagtttggattttgtttatgtatgtggaatttgagaaatagatgttatttactgggttgaagggat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaataga