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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAAGGCTGATGTTTTCCATTTGTTGTCTGGTATGTGGAAAACACCTGCTGAGAGGTGTTTTTTGTGGCTTGGTGGTTTTCGGTCATCTGAACTCCTCAAGgtcaggttttgctgatccttttcattctggtttcatggtttagaaaatgggttttctagagcagtaattgggccattttgtttaaatttttttaagaaaa...

Basic information

species Glycine max
transcript GLYMA15G37220.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G37220.1 (Glycine max), 5'ss of exon 6
lower sequence: LOC_Os03g20310.3 (Oryza sativa), 5'ss of exon 7
TAAGGCTGATGTTTTCCATTTGTTGTCTGGTATGTGGAAAACACCTGCTGAGAGGTGTTTTTTGTGGCTTGGTGGTTTTCGGTCATCTGAACTCCTCAAGgt---caggttttgctgatcctttt-----cattctggtttcatggtttagaaa-atgggttttctagagcagtaattgggcca---ttttgtttaaat---ttttttaagaaaa------------------------------
 ||||||||||| || ||| |  | || || |||||||||||||||||||| ||||| || ||||||||||| |||||||| || ||||| || || |||||    | |   || || | | | |      ||| |     ||    | ||  | |      | ||| || |  || |   | |   | |||||| |||   | ||  |    ||                              
AAAGGCTGATGTGTTTCATATACTTTCAGGCATGTGGAAAACACCTGCTGAAAGGTGCTTCTTGTGGCTTGGGGGTTTTCGTTCCTCTGAGCTTCTAAAGgtgcataagccgtg-tgctgcatataagaaaattataaaagcacacctcagggatactttagtcctaaagaaaaaagtcatctaatatcttgttttaatgggtattgcatcgtaacactaatttcaatctcctgtaaaatttcag

upper sequence: GLYMA15G37220.1 (Glycine max), 5'ss of exon 6
lower sequence: LOC_Os01g59350.1 (Oryza sativa), 5'ss of exon 9
TAAGGCTGATGTTTTCCATTTGTTGTCTGGTATGTGGAAAACACCTGCTGAGAGGTGTTTTTTGTGGCTTGGTGGTTTTCGGTCATCTGAACTCCTCAAGgtcaggttttgctgatccttttcattctggtttcatggtttagaa----aatgggttttctagagcagtaattgggccattttgtttaaatttttttaagaaaa
 || || || ||||| ||| || |||| || ||||||||||| |||||||||||||| ||  ||||||| ||||| || || |||||||| || || ||||| ||  | | ||  |  | |  |||  |  | | |  |||  |     |   ||      |  || |   |      || || ||| ||||  |  || |   
CAAAGCAGACGTTTTTCATGTGCTGTCGGGAATGTGGAAAACCCCTGCTGAGAGGTGCTTCATGTGGCTAGGTGGCTTCCGATCATCTGAGCTTCTTAAGgtaagaatatactattattat--attgcgcctacttattttgaagcctcacccggaggcaaaatgctgacctgaatatatattattttaattgatccaatat--

upper sequence: GLYMA15G37220.1 (Glycine max), 5'ss of exon 6
lower sequence: LOC_Os01g17260.1 (Oryza sativa), 5'ss of exon 8
TAAGGCTGATGTTTTCCATTTGTTGTCTGGTATGTGGAAAACACCTGCTGAGAGGTGTTTTTTGTGGCTTGGTGGTTTTCGGTCATCTGAACTCCTCAAGgtcaggttttgctgatccttttcattctggtttcatggtttaga-aaatgggttttctagagcagtaattgggccatttt--gtttaaatttttttaagaaaa------
 || || ||||| || ||| |||| || || |||||||| ||||| |||||||||||||| |||||||| || || || ||  |||| || ||  | ||||||      ||   |  |||   ||   | | |  | |||||    |       |||||  |||         | |||         ||| ||| ||  | ||      
CAAAGCAGATGTCTTTCATGTGTTATCAGGCATGTGGAAGACACCAGCTGAGAGGTGTTTCTTGTGGCTAGGAGGATTCCGACCATCCGAGCTTTTAAAGgtc------tgtaaagtcttacgat---gttcttgttgtttatttgagccatccttctattgcaaagcccctcctattaccaaaaccaatgtttctaccataatattat

upper sequence: GLYMA15G37220.1 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G174284_T01 (Zea mays), 5'ss of exon 8
TAAGGCTGATGTTTTCCATTTGTTGTCTGGTATGTGGAAAACACCTGCTGAGAGGTGTTTTTTGTGGCTTGGTGGTTTTCGGTCATCTGAACTCCTCAAGgt-caggttttgctgatccttttcattctggtttcatggtttagaaaatgggttttctagagcagtaattgggccattttgtttaaatttttttaagaaaa
 ||||||||||| |||||| |  | || || |||||||||||||||||||| ||||| || ||||||||||| ||||| || || ||||| || || ||||| || |  |     ||   |   ||| |  |  ||  |  |   |  |    |   |  || |           ||   |   |  | |    |  | ||
AAAGGCTGATGTGTTCCATATACTTTCAGGCATGTGGAAAACACCTGCTGAAAGGTGCTTCTTGTGGCTTGGGGGTTTCCGTTCGTCTGAGCTTCTAAAGgtgcatgcatatgatatagatcaaattata-tcacaccgcctttgatttcaaatagttctagtacctgcctcaaaatgacggacacctgtacacaccacaa

upper sequence: GLYMA15G37220.1 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G056099_T01 (Zea mays), 5'ss of exon 8
TAAGGCTGATGTTTTCCATTTGTTGTCTGGTATGTGGAAAACACCTGCTGAGAGGTGTTTTTTGTGGCTTGGTGGTTTTCGGTCATCTGAACTCCTCAAGgtcaggttttgctgatccttttcattctggtttcatggtttagaaaatgggttttctagagc---agtaattgggccattttgtttaaatttttttaagaaaa---
 ||||||||||| |||||| |  | || || |||||||||||| ||||||| ||||| || ||||||||||| ||||| || || ||||| || || |||||       |||  ||  | |  || |  |||  |||      |   | | |||   | ||     |||  ||   ||   ||  | |        |    |    
AAAGGCTGATGTGTTCCATATACTTTCAGGCATGTGGAAAACATCTGCTGAAAGGTGCTTCTTGTGGCTTGGGGGTTTCCGTTCGTCTGAGCTTCTAAAGgtgca----tgcatatgatatagat-caagttatatgaaacc-acctttgatttcaaatagtcttggtacctgcctcaaaatgactgacaccccacacaccataat

upper sequence: GLYMA15G37220.1 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G030280_T02 (Zea mays), 5'ss of exon 7
TAAGGCTGATGTTTTCCATTTGTTGTCTGGTATGTGGAAAACACCTGCTGAGAGGTGTTTTTTGTGGCTTGGTGGTTTTCGGTCATCTGAACTCCTCAAGgt-caggttttgctgatccttttcattctggtttcatggtttagaaaatgggttttctagagcagtaattgggccattttgttt--aaatttttttaagaaaa---------------------------------
 ||||| |||||||| ||  | || ||||| |||||||| ||||| || |||||||||||||||||||| || ||||| ||  |||||||  |  | |||||  | |   || || |  || ||  |  ||||  |  |       ||||   ||| |        |    |    |||| |||  ||    |  | |    |                                 
CAAGGCAGATGTTTTTCACGTCTTATCTGGCATGTGGAAGACACCGGCGGAGAGGTGTTTTTTGTGGCTAGGAGGTTTCCGACCATCTGAGGTTTTAAAGgtatatgcaatg-tgtttattatctcttgggttctactggagtagcaatgcactttttgttaatacatgaagtttgttttctttccaagcactggtgatttcattgttgggttgctgataaaatatgcaactgcag

upper sequence: GLYMA15G37220.1 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G125243_T02 (Zea mays), 5'ss of exon 11
TAAGGCTGATGTTTTCCATTTGTTGTCTGGTATGTGGAAAACACCTGCTGAGAGGTGTTTTTTGTGGCTTGGTGGTTTTCGGTCATCTGAACTCCTCAAGgtcaggttttgctgatccttttcattctggtttcatggtttagaaaatgggttttctagagcagtaattgggccattttgtttaaatttttttaagaaaa---------
||| || |||||||| ||| || ||||||| |||||||| || ||||||||||| |||||  ||||| | ||||| || || |||||||| || || |||||     | |  || |    ||  || ||  | ||   || |     | |   |  | |  |     |||  ||         |  |    ||| |  |          
TAAAGCAGATGTTTTTCATGTGCTGTCTGGGATGTGGAAGACCCCTGCTGAGAGATGTTTCATGTGGTTAGGTGGCTTCCGATCATCTGAGCTTCTTAAGgtagtaatctaatggt----tttgttttgaatgcacaattaaatttcttgacctcttggctc-----ttgcccctgaactccaaggtccccttatgggagttttcattc

upper sequence: GLYMA15G37220.1 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G019907_T01 (Zea mays), 5'ss of exon 5
TAAGGCTGATGTTTTCCATTTGTTGTCTGGTATGTGGAAAACACCTGCTGAGAGGTGTTTTTTGTGGCTTGGTGGTTTTCGGTCATCTGAACTCCTCAAGgtcaggttttgctgatccttttcattctggtttcatggtttagaaaatgggttttctagagcagtaattgggccattttgtttaaatttttttaagaaaa---------
||   | |||||||| ||| || ||||||| |||||||| || ||||||||||| |||||  ||||| | ||||| || || ||||||||  | || |||||     | |  || |    ||  || ||  | ||   || |     | |   |  | |  |     |||  |    |     |  |    ||| |  |          
TAGATCAGATGTTTTTCATGTGCTGTCTGGGATGTGGAAGACCCCTGCTGAGAGATGTTTCATGTGGTTAGGTGGCTTCCGATCATCTGAGGTTCTTAAGgtagtaatctaatggt----tttgttttgaatgcacaattaaatttgttgacctcttggctc-----ttgccctcgatctccaaggtccccttatgggagttttcgttc

upper sequence: GLYMA15G37220.1 (Glycine max), 5'ss of exon 6
lower sequence: AT5G06950.3 (Arabidopsis thaliana), 5'ss of exon 8
TAAGGCTGATGTTTTCCATTTGTTGTCTGGTATGTGGAAAACACCTGCTGAGAGGTGTTTTTTGTGGCTTGGTGGTTTTCGGTCATCTGAACTCCTCAAGgtcaggttttgctgatccttttcattctggtttcatggtttagaaaatgggttttc-tagagcagtaattgggccatttt-gtttaaatttttttaagaaaa
||||  |||||| || || ||| | ||||| |||||||||||||| |||||||| ||||| |||||||| ||||| ||||| ||||| ||||| || ||||| ||||            ||||| | ||  ||||  | || | |  ||  | | | |||| ||  ||  |     |  | |   ||| | | || | | | 
TAAGAATGATGTCTTTCACTTGCTATCTGGCATGTGGAAAACACCAGCTGAGAGATGTTTCTTGTGGCTCGGTGGATTTCGTTCATCCGAACTTCTAAAGgtgaggtcaaa--------tttcactttgtcttcaccgatt-gcatctgtttctacatagaacataaaaagaatggtcatagggaaaaatgtgttgaaacag

upper sequence: GLYMA15G37220.1 (Glycine max), 5'ss of exon 6
lower sequence: AT3G12250.5 (Arabidopsis thaliana), 5'ss of exon 8
TAAGGCTGATGTTTTCCATTTGTTGTCTGGTATGTGGAAAACACCTGCTGAGAGGTGTTTTTTGTGGCTTGGTGGTTTTCGGTCATCTGAACTCCTCAAGgtcaggttttgctgatccttttcat---tctggtttcatggtttagaaaatgggttttctagagcagtaattgggccattttgtttaaatttttttaagaaaa
||||  |||||| ||||| ||||| ||||| |||||||||||||| |||||| | ||||| ||||||||||| || || || ||||| ||||| |||||||| || | || |  |  |  |  |    | | | |  |  |   |   |||| ||        |||||  ||   | |                         
TAAGAATGATGTCTTCCACTTGTTATCTGGAATGTGGAAAACACCAGCTGAGCGATGTTTCTTGTGGCTTGGCGGGTTCCGCTCATCCGAACTTCTCAAGgtaagctctttccaagtccatagagagattttgatgaacagccaacttaatgagtc-------gcagtgttttcacaacag----------------------

upper sequence: GLYMA15G37220.1 (Glycine max), 5'ss of exon 6
lower sequence: AT5G06960.1 (Arabidopsis thaliana), 5'ss of exon 7
TAAGGCTGATGTTTTCCATTTGTTGTCTGGTATGTGGAAAACACCTGCTGAGAGGTGTTTTTTGTGGCTTGGTGGTTTTCGGTCATCTGAACTCCTCAAGgtcaggttttgctgatccttttcattctggtttcatggtttagaaaatgggttttctagagcagtaattgggccattttgtttaaatttttttaagaaaa
||||  |||||| |||||||| || || || ||||||||||| || |||||||| ||||| |||||||| || ||||| || ||||| ||||| |||||||| |         || |   |||  | |  |||  |   ||    |    |||| | | |    | | |   | | |                       
TAAGAGTGATGTCTTCCATTTATTATCAGGGATGTGGAAAACCCCAGCTGAGAGATGTTTCTTGTGGCTCGGCGGTTTCCGTTCATCAGAACTTCTCAAGgtaaaaaacacacgaccaggttcggttta-tttggtctcttcactagcaagtttcc-aaactttttacttctctactacag-------------------

upper sequence: GLYMA15G37220.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv13s0084g00660.t01 (Vitis vinifera), 5'ss of exon 10
TAAGGCTGATGTTTTCCATTTGTTGTCTGGTATGTGGAAAACACCTGCTGAGAGGTGTTTTTTGTGGCTTGGTGGTTTTCGGTCATCTGAACTCCTCAAGgtcaggttttgctgatccttttcattctggtttcatggtttagaaaatgggttttc---tagagcagtaattgggccattttgtttaaatttttttaagaaaa
 |||||||||||||||||||| || || || ||||||||||||||||| ||||||||||||||||||||||||||||| || |||||||||||||| |||||  |    |  | | | |||| ||  |    |  || |   | |    |    ||     ||  | |||| ||   | ||  | |  || |   |       
CAAGGCTGATGTTTTCCATTTATTATCAGGCATGTGGAAAACACCTGCAGAGAGGTGTTTTTTGTGGCTTGGTGGTTTCCGTTCATCTGAACTCCTAAAGgtatgaccct-tttaccattttgatggtttccttctgttggggtattcagaccctcaccctgacaaataataggaagacttcatctccatatccatttctt--

upper sequence: GLYMA15G37220.1 (Glycine max), 5'ss of exon 6
lower sequence: EFJ18699 (Selaginella moellendorffii), 5'ss of exon 1
TAAGGCTGATGTTTTCCATTTGTTGTCTGGTATGTGGAAAACACCTGCTGAGAGGTGTTTTTTGTGGCTTGGTGGTTTTCGGTCATCTGAACTCCTCAAGgt--caggttttgctgatccttttcattctggtttcatggtttagaaaatgggttttctagagcagtaattgggccattttgtttaaatttttttaagaaaa
 || || ||||| |||||  |  | ||||| ||||||||||| || || |||||||||||| ||||| | ||||| ||  || |||| ||||| ||||||||    ||| || | | |  |||     || |  || | ||||  |      |||||| | |  | | || |     ||||||||     | |  |      
GAAAGCCGATGTCTTCCACCTCGTCTCTGGGATGTGGAAAACTCCCGCCGAGAGGTGTTTTATGTGGATGGGTGGCTTCAGGCCATCAGAACTTCTCAAGgtacttggtctttcagtttttttcttagcttgagtcttcgtttccatc----gttttccata-tactgatcga-tggttttgtttg----tctccag-----

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|31464913|gb|CD406941.1|CD406941
EST:     GCTTGGTGGTTTTCGGTCATCTGAACTCCTCAAG                         CTGCTGGTTAGTCAATTGGAGCCTCTCACAGAGCAGCAGCTGATGGGTATT
genomic: GCTTGGTGGTTTTCGGTCATCTGAACTCCTCAAGgtcaggtttt ... tgcattgcagCTGCTGGTTAGTCAATTGGAGCCTCTCACAGAGCAGCAGCTGATGGGTATT
EST: gi|5820488|gb|AI988694.1|AI988694
EST:     AGAGGTGTTTTTTGCGGCTTGGTGGCTTTCGCTCATCTGAACTCCTCAAG                         CTGCTGGTTAGTCAATTGGAGCCTCTCACAGAGCAGCAGCTGATGGGTATT
genomic: AGAGGTGTTTTTTGTGGCTTGGTGGTTTTCGGTCATCTGAACTCCTCAAGgtcaggtttt ... tgcattgcagCTGCTGGTTAGTCAATTGGAGCCTCTCACAGAGCAGCAGCTGATGGGTATT
EST: gi|15287325|gb|BI471216.1|BI471216
EST:     AGAGGTGTTTTTTGTGGCTTGGTGGTTTTCGGTCATCTGAACTCCTCAAG                         CTGCTGGTTAGTCAATTGGAGCCTCTCACAGAGCAGCAGCTGATGGGTATT
genomic: AGAGGTGTTTTTTGTGGCTTGGTGGTTTTCGGTCATCTGAACTCCTCAAGgtcaggtttt ... tgcattgcagCTGCTGGTTAGTCAATTGGAGCCTCTCACAGAGCAGCAGCTGATGGGTATT
EST: gi|18717081|gb|BM522915.1|BM522915
EST:     AGAGGTGTTTTTTGTGGCTTGGTGGTTTTCGGTCATCTGAACTCCTCAAG                         CTGCTGGTTAGTCAATTGGAGCCTCTCACAGAGCAGCAGCTGATGGGTATT
genomic: AGAGGTGTTTTTTGTGGCTTGGTGGTTTTCGGTCATCTGAACTCCTCAAGgtcaggtttt ... tgcattgcagCTGCTGGTTAGTCAATTGGAGCCTCTCACAGAGCAGCAGCTGATGGGTATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAAGGCTGATGTTTTCCATTTGTTGTCTGGTATGTGGAAAACACCTGCTGAGAGGTGTTTTTTGTGGCTTGGTGGTTTTCGGTCATCTGAACTCCTCAAGgtcaggttttgctgatccttttcattctggtttcatggtttagaaaatgggttttctagagcagtaattgggccattttgtttaaatttttttaagaaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC