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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGTTTGAGAACAAAAGATAAAGAGCGTATACTTGTTCTTGCTGCTACAAATAGACCTTTTGATCTTGATGAGGCTGTTATTAGGAGACTTCCACGAAGgtaaactcgttatgtttgatgttaacttcttttatttcgtgttttacaaatgagatctatgctaattcgtgttctttgttgaaaaatattgtag

Basic information

species Glycine max
transcript GLYMA02G17400.1
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G17400.1 (Glycine max), 5'ss of exon 20
lower sequence: LOC_Os03g22420.1 (Oryza sativa), 5'ss of exon 24
ATGGTTTGAGAACAAAAGATAAAGAGCGTATACTTGTTCTTGCTGCTACAAATAGACCTTTTGATCTTGATGAGGCTGTTATTAGGAGACTTCCACGAAGgtaaactcgttatgttt------------gatgttaacttc---ttttatttcgtgttttacaaatgagatctatgctaattcgtgttctttgttgaaaaatattg--tag
||||| | ||||||||||||||||||||| || | || |||||||| || ||||| || ||||| ||||||||||||||| ||||||| |||||  |  ||| |      ||| |||            ||| | ||||       | ||||  || |||  | || |      ||   || | |||  |||| | | |  |||||  |||
ATGGTCTAAGAACAAAAGATAAAGAGCGTGTATTAGTACTTGCTGCAACTAATAGGCCATTTGACCTTGATGAGGCTGTTGTTAGGAGGCTTCCTAGGCGgtgagtatcatatttttcattcattttaagatttgaactgtggtgctaattttatgatttttagataattgacttgactatgcatgtgttttggt-atatgtattgcttag

upper sequence: GLYMA02G17400.1 (Glycine max), 5'ss of exon 20
lower sequence: LOC_Os07g47530.1 (Oryza sativa), 5'ss of exon 24
ATGGTTTGAGAACAAAAGATAAAGAGCGTATACTTGTTCTTGCTGCTACAAATAGACCTTTTGATCTTGATGAGGCTGTTATTAGGAGACTTCCACGAAGgtaaactcgttatgtttgatgtta-acttcttttatttcgtgttttacaaatgagatctatgctaat--tcgtgttctttgttgaaaaatattgtag
||||| ||||||||||||||||||| ||  || | || |||||||| || |||||||| |||||||||||||| |||||| ||||||| || ||  | ||||||  |  ||    | | |||   | | |||||||||      |||||| ||| ||    ||||||  | |  | | |  |   | |  | | |||
ATGGTCTGAGAACAAAAGATAAAGAACGCGTATTAGTACTTGCTGCCACCAATAGACCATTTGATCTTGATGAAGCTGTTGTTAGGAGGCTCCCCAGGAGgtaactttttttacatcgctgtggtattccttttattt------ttacaa-tgaaat----gctaatggttgcttgcctgatcacatatcaatttag

upper sequence: GLYMA02G17400.1 (Glycine max), 5'ss of exon 20
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 5'ss of exon 24
ATGGTTTGAGAACAAAAGATAAAGAGCGTATACTTGTTCTTGCTGCTACAAATAGACCTTTTGATCTTGATGAGGCTGTTATTAGGAGACTTCCACGAAGgtaaactcgttatgtttgatgttaacttcttttatttcgtgttttacaaatgagatctatgctaattcgtgttctttgttgaaaaatattgtag
|||| ||  | || ||||||||||| ||| |||| ||||||| ||| |||||||| ||||| || || ||||||||||| ||||||||  | || || |||| |   |  ||   |||   |    ||    || |      ||      ||   |  ||    |  | | ||  | ||| |  | || |||||
ATGGATTACGCACTAAAGATAAAGAACGTGTACTGGTTCTTGGTGCCACAAATAGGCCTTTCGACCTGGATGAGGCTGTCATTAGGAGGTTCCCGCGCAGgtgacagctataaccttgtgttggggttgggataatgaaaaattgctgtttg---ttgatttctaaccat-ttggtcgttaattactactgtag

upper sequence: GLYMA02G17400.1 (Glycine max), 5'ss of exon 20
lower sequence: GRMZM2G354532_T01 (Zea mays), 5'ss of exon 3
ATGGTTTGAGAACAAAAGATAAAGAGCGTATACTTGTTCTTGCTGCTACAAATAGACCTTTTGATCTTGATGAGGCTGTTATTAGGAGACTTCCACGAAGgtaaac-tcgttatgtttgatg--------ttaacttcttttatttc-gtgttttacaaatgagatctatgctaat----tcgtgttctttgttgaaaaatattgtag-----------------------------------------------------------------------
|||| ||| | || |||||||| |||||| | |||||||||| ||||||||||||||||||||| || || |||||||| ||||||||  | || || |||||||  | |||   ||   ||        ||| |   ||  ||  | ||  |||     || |  | ||| | ||    ||||    ||||   |  |||| | | |                                                                       
ATGGGTTGCGCACTAAAGATAAGGAGCGTGTGCTTGTTCTTGGTGCTACAAATAGACCTTTTGACCTGGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtaaatgttgtttcattcagtgggactggattacccagttgcataactgtagttttgttctgtgggccatggttatctaatcgttgcttttgggtagcaatagttttgtttggttgggtgggactatcaaatcgctgctgctggttccatattcatcaccatcttactcattgtttcag

upper sequence: GLYMA02G17400.1 (Glycine max), 5'ss of exon 20
lower sequence: GRMZM2G052403_T01 (Zea mays), 5'ss of exon 15
ATGGTTTGAGAACAAAAGATAAAGAGCGTATACTTGTTCTTGCTGCTACAAATAGACCTTTTGATCTTGATGAGGCTGTTATTAGGAGACTTCCACGAAGgtaaac-tcgttatgtt---tgatgttaacttcttttatttcgtgttttacaaatgagatcta---tgctaattcgtgttctttgttgaaaaatattgtag
||||  || | || |||||||| |||||| | |||||||||| ||||||||||||||||||||| || || |||||||| ||||||||  | || || |||| ||  |  || | ||   || |||    |       ||  || | |    | ||     |      ||||||  || | || | |   ||   || |  
ATGGACTGCGCACTAAAGATAAGGAGCGTGTGCTTGTTCTTGGTGCTACAAATAGACCTTTTGACCTGGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtgaatataattttattcaatggtgtgggatgacccggttgggtatctgttcagtggcccatggttctctaattgttgctgttgggtagcaatagttttg-

upper sequence: GLYMA02G17400.1 (Glycine max), 5'ss of exon 20
lower sequence: GRMZM2G126453_T02 (Zea mays), 5'ss of exon 9
ATGGTTTGAGAACAAAAGATAAAGAGCGTATACTTGTTCTTGCTGCTACAAATAGACCTTTTGATCTTGATGAGGCTGTTATTAGGAGACTTCCACGAAGgtaaac-tcgttatgtttgatg--------ttaacttcttttatttc-gtgttttacaaatgagatctatgctaat----tcgtgttctttgttgaaaaatattgtag-----------------------------------
|||| ||| | || |||||||| |||||| | |||||||||| |||||||||||| |||||||| || || |||||||| ||||||||  | || || |||||||  | |||   ||   ||        ||| |   || |||  | ||  |||      | |  | ||| | ||    ||||    ||||   |  |||| | | |                                   
ATGGGTTGCGCACTAAAGATAAGGAGCGTGTGCTTGTTCTTGGTGCTACAAATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtaaatgttgtttcattcagtgggactggattacccagttgtataactgtagttttgttcggtgggccatgattatctaatcgttgcttttgggtagcaatagtttggttccatattcatcaccatcttactcattgtttcag

upper sequence: GLYMA02G17400.1 (Glycine max), 5'ss of exon 20
lower sequence: GRMZM2G042074_T02 (Zea mays), 5'ss of exon 19
ATGGTTTGAGAACAAAAGATAAAGAGCGTATACTTGTTCTTGCTGCTACAAATAGACCTTTTGATCTTGATGAGGCTGTTATTAGGAGACTTCCACGAAGgtaaactcgttatgtttgatgttaacttcttttatttcgtgtt--ttacaaatgagatctatgctaattcgtgttctttgttgaaaaatattgtag
||||| |||||||||| || ||||| ||| || | || |||||||| || || || || ||||||||||||||||||||||||||| | |||||| | |||| |  |  ||  ||||| |  || | |  |        |||   |     ||       |  ||  |  ||||||| |                 
ATGGTCTGAGAACAAAGGAGAAAGAACGTGTATTAGTACTTGCTGCAACTAACAGGCCATTTGATCTTGATGAGGCTGTTATTAGGCGGCTTCCAAGGAGgtga-tttatt--gtttgtttatagcctaatacgacatctgtcaatagtttattgacctcagtcttgtgtgtgttctctag---------------

upper sequence: GLYMA02G17400.1 (Glycine max), 5'ss of exon 20
lower sequence: GRMZM2G409190_T01 (Zea mays), 5'ss of exon 2
ATGGTTTGAGAACAAAAGATAAAGAGCGTATACTTGTTCTTGCTGCTACAAATAGACCTTTTGATCTTGATGAGGCTGTTATTAGGAGACTTCCACGAAGgtaaactcgttatgtttgatgttaacttcttttatttcgtgttttacaaatgagatctatgctaattcgtgttctttgttgaaaaatattgtag
||||| |||||||||  || ||||| ||| || | || |||||||| || ||||| || ||||||||||||||||||||| ||||| | |||||| | |||| |  |  |   ||||| |  || | |  |  |     |||      ||||   | |   |   |  || || |  |   | || |  | |||
ATGGTCTGAGAACAAGGGAGAAAGAACGTGTATTAGTACTTGCTGCAACTAATAGGCCATTTGATCTTGATGAGGCTGTTGTTAGGCGGCTTCCAAGGAGgtga-tttatc--gtttgtttatagcctaatacaacatctgtc-----aatggttttttgacc--tcagtcttatggggcaataatttctttag

upper sequence: GLYMA02G17400.1 (Glycine max), 5'ss of exon 20
lower sequence: GRMZM2G435582_T01 (Zea mays), 5'ss of exon 4
ATGGTTTGAGAACAAAAGATAAAGAGCGTATACTTGTTCTTGCTGCTACAAATAGACCTTTTGATCTTGATGAGGCTGTTATTAGGAGACTTCCACGAAGgtaaac-tcgttatgtttgatg--------ttaacttcttttatttc-gtgttttacaaatgagatctatg-----ctaattcgtgttctttgttgaaaaatattgtag-----------------------------------------------------------------------
|||| |||   || |||||||| ||| || |  ||||||||| || |||||||||||||||||| || || |||||||| ||||||||  | || || |||||||  | |||   ||   ||        ||| |   ||  ||  | ||  |||     || |  | |||     ||||||  || | || | | |  |||| | | |                                                                       
ATGGGTTGCACACTAAAGATAAGGAGTGTGTGGTTGTTCTTGGTGTTACAAATAGACCTTTTGACCTGGACGAGGCTGTGATTAGGAGGTTCCCCCGTAGgtaaatgttgtttcattcagtgggactggattacccagttgcataactgtagttttgttctgtgggccatggttatctaattgttgcttttgggt-agcaatagtttcgtttggttgggtgggactatcaaatcgctgctgctggttccatattcatcaccatcttactcattgtttcag

upper sequence: GLYMA02G17400.1 (Glycine max), 5'ss of exon 20
lower sequence: GRMZM2G370521_T01 (Zea mays), 5'ss of exon 2
ATGGTTTGAGAACAAAAGATAAAGAGCGTATACTTGTTCTTGCTGCTACAAATAGACCTTTTGATCTTGATGAGGCTGTTATTAGGAGACTTCCACGAAGgtaaactcgttatgtttgatgttaacttcttttatttcgtgttttacaaatgagatctatgctaattcgtgttctttgttgaaaaatattgtag
||||| |||||||||  || ||||| ||| || | || |||||||| || || || || ||||||||||||||||||||| ||||| | |||||| | |||| |  |  |   ||||| |  || | |  |  |     |||      ||||   | |   |   |  || || |  |   | || |  | |||
ATGGTCTGAGAACAAGGGAGAAAGAACGTGTATTAGTACTTGCTGCAACTAACAGGCCATTTGATCTTGATGAGGCTGTTGTTAGGCGGCTTCCAAGGAGgtga-tttatc--gtttgtttatagcctaatacagcatctgtc-----aatggttttttgacc--tcagtcttatggggcaataatttctttag

upper sequence: GLYMA02G17400.1 (Glycine max), 5'ss of exon 20
lower sequence: GRMZM2G168228_T01 (Zea mays), 5'ss of exon 3
ATGGTTTGAGAACAAAAGATAAAGAGCGTATACTTGTTCTTGCTGCTACAAATAGACCTTTTGATCTTGATGAGGCTGTTATTAGGAGACTTCCACGAAGgtaaactcgttatgtttgatgttaacttcttttatttcgtgttttacaaatgagatctatgctaattcgtgttctttgttgaaaaatattgtag
||||| |||||||||  || ||||| ||| || | || |||||||| || || || || ||||||||||||||||||||| ||||| | |||||| | |||| |  |  |   ||||| |  || | |  |  |     |||      ||||   | |   |   |  || || |  |   |  | |  | |||
ATGGTCTGAGAACAAGGGAGAAAGAACGTGTATTAGTACTTGCTGCAACTAACAGGCCATTTGATCTTGATGAGGCTGTTGTTAGGCGGCTTCCAAGGAGgtga-tttatc--gtttgtttatagcctaatacaacatctgtc-----aatggttttttgacc--tcagtcttatggggcaatgatttctttag

upper sequence: GLYMA02G17400.1 (Glycine max), 5'ss of exon 20
lower sequence: GRMZM2G157621_T03 (Zea mays), 5'ss of exon 24
ATGGTTTGAGAACAAAAGATAAAGAGCGTATACTTGTTCTTGCTGCTACAAATAGACCTTTTGATCTTGATGAGGCTGTTATTAGGAGACTTCCACGAAGgtaaact-cgttatgt-ttgatgttaacttcttttatttcgtgttttacaaatgag-atctatgctaattcgtgttctttgttgaaaaatattgtag
||||| | || |||||||| ||||| ||| | || || |||||||| || ||||| || ||||||||||| ||||||||| | ||||| || ||  | ||||||| | |  |  || || ||| ||  ||  ||      |||   |    || |  | |   || |   | | |  |  |                
ATGGTCTTAGGACAAAAGACAAAGAACGTGTTCTGGTACTTGCTGCCACTAATAGGCCATTTGATCTTGACGAGGCTGTTGTCAGGAGGCTCCCCAGGAGgtaaattgcactccgtatttatgctacttttcttccaactgtgacatggttataaataacccggccacaacttctcttcag----------------

upper sequence: GLYMA02G17400.1 (Glycine max), 5'ss of exon 20
lower sequence: Vv07s0005g00200.t01 (Vitis vinifera), 5'ss of exon 23
ATGGTTTGAGAACAAAAGATAAAGAGCGTATACTTGTTCTTGCTGCTACAAATAGACCTTTTGATCTTGATGAGGCTGTTATTAGGAGACTTCCACGAAGgtaaactcgttatgtttgatgttaacttcttttatttcgt----gtttta--caaatgagatctatgctaattcgtgttctttgt-tgaaaaatattgtag-
||||  |  | ||||| |||||||| ||| || | || ||||| || || ||||| |||||||| ||||||||||||||||||||||| || ||  | ||||||||    |||| || ||  |  |||  ||| ||  ||    || |||  |||   |||   |   ||||||   | || ||| ||  || |        
ATGGCCTACGTACAAAGGATAAAGAACGTGTATTGGTACTTGCCGCCACCAATAGGCCTTTTGACCTTGATGAGGCTGTTATTAGGAGGCTACCCAGGAGgtaaacatcatatgatt-ataatcccttgatttgttgtgtatgagtattagtcaacccagaaaaaccttaattc-cctactatgtatgttaactgccaacac

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|13312558|gb|BG406209.1|BG406209
EST:     CTTTTGATCTTGATGAGGCTGTTATTAGGAGACTTCCACGAAG                         ATTGATGGTTAATTTGCCAGATGCTCCAAATAGAGGAAAAATTGTCAGAGT
genomic: CTTTTGATCTTGATGAGGCTGTTATTAGGAGACTTCCACGAAGgtaaactcgt ... aatattgtagATTGATGGTTAATTTGCCAGATGCTCCAAATAGAGGAAAAATTGTCAGAGT
EST: gi|6667763|gb|AW279214.1|AW279214
EST:     AATAGACCTTTTGATCTTGATGAAGCTGTTATTAAGAGACTTCCACGAAG                         ATTGATGGTTAATTTGCCAGATGCTCCAAATAGAAGAAAAATTGTCAGAGT
genomic: AATAGACCTTTTGATCTTGATGAGGCTGTTATTAGGAGACTTCCACGAAGgtaaactcgt ... aatattgtagATTGATGGTTAATTTGCCAGATGCTCCAAATAGAGGAAAAATTGTCAGAGT
EST: gi|254341441|gb|GR850654.1|GR850654
EST:     GGCTGTTATTAGGAGACTTCCACGAAG                         ATTGATGGTTAATTTGCCAGATGCTCCAAATAGAGGAAAAATTGTCAGAGT
genomic: GGCTGTTATTAGGAGACTTCCACGAAGgtaaactcgt ... aatattgtagATTGATGGTTAATTTGCCAGATGCTCCAAATAGAGGAAAAATTGTCAGAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGGTTTGAGAACAAAAGATAAAGAGCGTATACTTGTTCTTGCTGCTACAAATAGACCTTTTGATCTTGATGAGGCTGTTATTAGGAGACTTCCACGAAGgtaaactcgttatgtttgatgttaacttcttttatttcgtgttttacaaatgagatctatgctaattcgtgttctttgttgaaaaatattgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA