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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGACAAGTCAATTAAAATTGCTGACTTTGGAGTTGCCCGTATTGAGGTGCAAACTGAAGGAATGACACCTGAGACTGGAACATACCGTTGGATGGCTCCgtaagatcttttgctgttctctctttttatatttatatagttttatatgcattctagcttcatttttggaatgatttttggagagcttctctattatggt...

Basic information

species Glycine max
transcript GLYMA05G36540.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G36540.2 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os06g45300.1 (Oryza sativa), 5'ss of exon 2
GTGACAAGTCAATTAAAATTGCTGACTTTGGAGTTGCCCGTATTGAGGTGCAAACTGAAGGAATGACACCTGAGACTGGAACATACCGTTGGATGGCTCCgtaagatcttttgctgttctctctttttatatttatatagttttatatgcattctagcttcatttttggaatgatttttggagagcttctctattatggt-
  ||||| || || || || ||||||||||||||||| || |||||||| |||||||| |||||||| || ||||| ||||| |||||||||||||| |||||||   |  |   |   || |  |   |   ||      ||||  |   || ||  |   | |     ||| || |         |  | || |||   
CAGACAAATCCATCAAGATAGCTGACTTTGGAGTTGCTCGAATTGAGGTACAAACTGAGGGAATGACCCCAGAGACAGGAACCTACCGTTGGATGGCACCgtaagtcataatcacgcattcacgctcattgcctactg---tttacct---ttttaaatctctgtcaaatatgcttatc--------ttgccatcatgcag

upper sequence: GLYMA05G36540.2 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os08g12750.1 (Oryza sativa), 5'ss of exon 2
GTGACAAGTCAATTAAAATTGCTGACTTTGGAGTTGCCCGTATTGAGGTGCAAACTGAAGGAATGACACCTGAGACTGGAACATACCGTTGGATGGCTCCgtaagatcttttgctgttctctctttttatatttatatagttttatatgcattctagcttcatttttggaatgatttttggagagcttctctattatggt---
| ||||| || || || ||||||||||||||||| ||  | ||||| ||| | ||||| |||||||||||||| || ||||| ||||| |||||||||||||||| |    | |  | |||| | | | |  |||| |   |   ||   ||   |  ||| | ||  ||      | |       ||||  | |  ||    
GAGACAAATCTATCAAGATTGCTGACTTTGGAGTGGCTAGGATTGAAGTGAAGACTGAGGGAATGACACCTGAAACAGGAACTTACCGCTGGATGGCTCCgtaagttggcatac-atgctctttatct-tgcttattttaatcagtaattatctcaaattcgtattaagacaatgctgttttatttttcttcact-cggcatt

upper sequence: GLYMA05G36540.2 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os02g07790.1 (Oryza sativa), 5'ss of exon 2
GTGACAAGTCAATTAAAATTGCTGACTTTGGAGTTGCCCGTATTGAGGTGCAAACTGAAGGAATGACACCTGAGACTGGAACATACCGTTGGATGGCTCCgtaagatct-tttgctgttctctctttttatatttatatagttttatatgcattctagcttcatttttggaatgatttttggagagcttctctattatggt-
  || || || ||||| ||||||||||||||||| || || || || ||  ||||||| || |||||||| ||||| ||||| ||||| |||||||| ||||||| | | | | |   | | | ||||| | |   | | ||| | | |  || | | || ||| | | |  |     ||| |  |  |     |||   | 
CAGATAAATCCATTAAGATTGCTGACTTTGGAGTGGCTCGCATCGAAGTAAAAACTGAGGGTATGACACCAGAGACAGGAACCTACCGCTGGATGGCACCgtaagttatatattcccctgtttatttttttctccctgt-gttatttgtatatgccaact-catgtatagcttatcacttgcaaggacttcactttagaatg

upper sequence: GLYMA05G36540.2 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os04g51950.1 (Oryza sativa), 5'ss of exon 2
GTGACAAGTCAATTAAAATTGCTGACTTTGGAGTTGCCCGTATTGAGGTGCAAACTGAAGGAATGACACCTGAGACTGGAACATACCGTTGGATGGCTCCgtaagatcttttgctgttctctcttttta-tatttatatagttttatatgcattctagcttcatttttggaatgatttttggagagcttctctattatggt
| || || || ||||| || || ||||||||||||||| | ||||| ||  |||| || || ||||||||||| || ||||| || ||||||||||| ||||||| |   |       ||   ||  || ||||||     || | | |   |||||||  | |        | ||||| |   ||    | |  | ||| 
GCGATAAATCGATTAAGATAGCAGACTTTGGAGTTGCCAGGATTGAAGTCAAAACCGAGGGGATGACACCTGAAACAGGAACCTATCGTTGGATGGCCCCgtaagttgaataaaacaactacattaatactatttaccatattatctgttagttctagccgcgtgcaacactttattttagttaagagaattttgtttgg-

upper sequence: GLYMA05G36540.2 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G140612_T03 (Zea mays), 5'ss of exon 2
GTGACAAGTCAATTAAAATTGCTGACTTTGGAGTTGCCCGTATTGAGGTGCAAACTGAAGGAATGACACCTGAGACTGGAACATACCGTTGGATGGCTCCgtaagatcttttgctgttctctctttttatatttatatagttttatatgcattctagcttcatttttggaatgatttttgga--gagcttctctattatggt
|||| ||||| ||||| ||||||||||||||||| ||  | ||||| ||  | ||||| || ||||||||||| |||||||||||||| |||||||||||||||| |  |      | |||| | |   | ||||| |   |   |   ||| |||     ||      |||   ||||  |  ||| |  |   || ||  
GTGATAAGTCCATTAAGATTGCTGACTTTGGAGTGGCTAGGATTGAAGTCAAGACTGAGGGGATGACACCTGAAACTGGAACATACCGCTGGATGGCTCCgtaagttgatcaaacatgctctttgtcc-tgtttatttcaatcagtcatcatgctattccaataaggcaaatctgttttaaattgagttatttctttttgc-

upper sequence: GLYMA05G36540.2 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G156013_T01 (Zea mays), 5'ss of exon 2
GTGACAAGTCAATTAAAATTGCTGACTTTGGAGTTGCCCGTATTGAGGTGCAAACTGAAGGAATGACACCTGAGACTGGAACATACCGTTGGATGGCTCCgtaagatct-tttgctgttctctctttttatatttatatagttttatatgcattctagcttcatttttggaatgatttttggagagcttctctattatggt
|||| || || || || || |||||||||||||| || || ||||| ||  ||||||| || ||||||||||| || ||||| |||||||||||||| ||||||| |       |||   ||  |  || |  ||| | |  ||  ||  ||  | |  || |||      || | |           |   ||| |  | 
GTGATAAATCTATCAAGATAGCTGACTTTGGAGTAGCTCGCATTGAAGTAAAAACTGAGGGGATGACACCTGAAACGGGAACCTACCGTTGGATGGCACCgtaagttgaacactctgacatcattagttctgcttacagatcttgttagccacacgatattaattaaaattataagtcacatctcatattagtatgaaag-

upper sequence: GLYMA05G36540.2 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G102088_T02 (Zea mays), 5'ss of exon 2
GTGACAAGTCAATTAAAATTGCTGACTTTGGAGTTGCCCGTATTGAGGTGCAAACTGAAGGAATGACACCTGAGACTGGAACATACCGTTGGATGGCTCCgtaagatcttttgctgttctctctttttatatttatatagttttatatgcattctagcttcatttttggaatgatttttggagagcttctctattatggt--------
|||| || || || || || |||||||||||||| || || ||||| ||  ||||||| || ||||||||||| || ||||| || ||||||||||| ||||||| |      |||   |  ||  |  || |||| ||   ||| | |     |  | |||| | | |||  |||| ||   | |     ||  |   |        
GTGATAAATCTATCAAGATAGCTGACTTTGGAGTAGCTCGGATTGAAGTAAAAACTGAGGGGATGACACCTGAAACGGGAACCTATCGTTGGATGGCACCgtaag-ttgaacactgacattgctggtgttacttat-taaaattagaag-----tcacatcatatattgaac-atttatgtcaatcaatagtacaaaaatgtgggtca

upper sequence: GLYMA05G36540.2 (Glycine max), 5'ss of exon 2
lower sequence: Vv11s0065g00140.t01 (Vitis vinifera), 5'ss of exon 1
GTGACAAGTCAATTAAAATTGCTGACTTTGGAGTTGCCCGTATTGAGGTGCAAACTGAAGGAATGACACCTGAGACTGGAACATACCGTTGGATGGCTCCgtaagatcttttgctgttctctctttttatatttatat--agttttatatgcattctagcttcatttttggaatgatttttggagagcttctctattatggt
  |||||||| || |||||||| |||||||| ||||| || || ||||||||||| |||||||||||||| ||||| || |||||||| |||||||| |||||||  |||||| |  | |  || | || |||| | |  ||||||  ||  | |||   || |  ||      |||  || |  | ||  |   || ||||
CAGACAAGTCCATCAAAATTGCAGACTTTGGGGTTGCTCGAATAGAGGTGCAAACAGAAGGAATGACACCAGAGACAGGGACATACCGCTGGATGGCCCCgtaag-ccttttgattcttttcctgtctagatttgtctttagtttttcat-tactctcttttaaaattcactgggatgctttgcaatctcttgatttgtggt

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|192328960|gb|FK019687.1|FK019687
EST:     CAAACTGAAGGAATGACACCTGAGACTGGAACATACCGTTGGATGGCTCC                         GGAGATGATCCAGCATAG-CCTTACACACAAAAAGTGGATGTATATAGCTT
genomic: CAAACTGAAGGAATGACACCTGAGACTGGAACATACCGTTGGATGGCTCCgtaagatctt ... tctactgcagGGAGATGATCCAGCATAGGCCTTACACACAAAAAGTGGATGTATATAGCTT
EST: gi|151400181|gb|EV269995.1|EV269995
EST:     CAAACTGAAGGAATGACACCTGAGACTGGAACATACCGTTGGATGGCTCC                         GGAGATGATCCAGCATAGGCCTTACACA-AAAA-GTGGATGTATATAGCTT
genomic: CAAACTGAAGGAATGACACCTGAGACTGGAACATACCGTTGGATGGCTCCgtaagatctt ... tctactgcagGGAGATGATCCAGCATAGGCCTTACACACAAAAAGTGGATGTATATAGCTT
EST: gi|209728008|gb|BW666730.1|BW666730
EST:     CAAACTGAAGGAATGACACCTGAGACTGGAACATACCGTTGGATGGCTCC                         GGAGATGATCCAGCATAGGCCTTACACACAAAAAGTGGATGTATATAGCTT
genomic: CAAACTGAAGGAATGACACCTGAGACTGGAACATACCGTTGGATGGCTCCgtaagatctt ... tctactgcagGGAGATGATCCAGCATAGGCCTTACACACAAAAAGTGGATGTATATAGCTT
EST: gi|192315798|gb|FK008508.1|FK008508
EST:     CAAACTGAAGGAATGACACCTGAGACTGGAACATACCGTTGGATGGCTCC                         GGAGATGATCCAGCATAGGCCTTACACACAAAAAGTGGATGTATATAGCTT
genomic: CAAACTGAAGGAATGACACCTGAGACTGGAACATACCGTTGGATGGCTCCgtaagatctt ... tctactgcagGGAGATGATCCAGCATAGGCCTTACACACAAAAAGTGGATGTATATAGCTT
EST: gi|193396736|gb|FK362308.1|FK362308
EST:     CAAACTGAAGGAATGACACCTGAGACTGGAACATACCGTTGGATGGCTCC                         GGAGATGATCCAGCATAGGCCTTACACACAAAAAGTGGATGTATATAGCTT
genomic: CAAACTGAAGGAATGACACCTGAGACTGGAACATACCGTTGGATGGCTCCgtaagatctt ... tctactgcagGGAGATGATCCAGCATAGGCCTTACACACAAAAAGTGGATGTATATAGCTT
EST: gi|58020855|gb|CX707597.1|CX707597
EST:     CAAACTGAAGGAATGACACCTGAGACTGGAACATACCGTTGGATGGCTCC                         GGAGATGATCCAGCATAGGCCTTACACACAAAAAGTGGATGTATATAGCTT
genomic: CAAACTGAAGGAATGACACCTGAGACTGGAACATACCGTTGGATGGCTCCgtaagatctt ... tctactgcagGGAGATGATCCAGCATAGGCCTTACACACAAAAAGTGGATGTATATAGCTT
EST: gi|16348555|gb|BI974150.1|BI974150
EST:     CAAACTGAAGGAATGACACCTGAGACTGGAACATACCGTTGGATGGCTCC                         GGAGATGATCCAGCATAGGCCTTACACACAAAAAGTGGATGTATATAGCTT
genomic: CAAACTGAAGGAATGACACCTGAGACTGGAACATACCGTTGGATGGCTCCgtaagatctt ... tctactgcagGGAGATGATCCAGCATAGGCCTTACACACAAAAAGTGGATGTATATAGCTT
EST: gi|58020683|gb|CX707425.1|CX707425
EST:     CAAACTGAAGGAATGACACCTGAGACTGGAACATACCGTTGGATGGCTCC                         GGAGATGATCCAGCATAGGCCTTACACACAAAAAGTGGATGTATATAGCTT
genomic: CAAACTGAAGGAATGACACCTGAGACTGGAACATACCGTTGGATGGCTCCgtaagatctt ... tctactgcagGGAGATGATCCAGCATAGGCCTTACACACAAAAAGTGGATGTATATAGCTT
EST: gi|7588676|gb|AW704466.1|AW704466
EST:     CAATCTGAAGGAATGACACCTGAGACTGGAACATACCGTTGGATGGCTCC                         GGAGATGATCCAGCATATGTCTTACACACAAATAGTGGATGTATATAGATT
genomic: CAAACTGAAGGAATGACACCTGAGACTGGAACATACCGTTGGATGGCTCCgtaagatctt ... tctactgcagGGAGATGATCCAGCATAGGCCTTACACACAAAAAGTGGATGTATATAGCTT
EST: gi|254327838|gb|GR834803.1|GR834803
EST:     CAAACTGAAGGAATGACACCTGAGACTGGAACATACCGTTGGATGGCTCCC                         GGAGATGATCCAGCATAGGCCTTACACACAAAAAGTGGATGTATATAGCT
genomic: CAAACTGAAGGAATGACACCTGAGACTGGAACATACCGTTGGATGGCT-CCgtaagatctt ... tctactgcagGGAGATGATCCAGCATAGGCCTTACACACAAAAAGTGGATGTATATAGCT
EST: gi|192315799|gb|FK008509.1|FK008509
EST:     CAAACTGAAGGAATGACACCTGAGACTGGAACATACCGTTGGATGGCTCC                         GGAGATGATCCAGCATAGGCCTTACACACAAAAAGTGGATGTATATAGCTT
genomic: CAAACTGAAGGAATGACACCTGAGACTGGAACATACCGTTGGATGGCTCCgtaagatctt ... tctactgcagGGAGATGATCCAGCATAGGCCTTACACACAAAAAGTGGATGTATATAGCTT
EST: gi|58020514|gb|CX707256.1|CX707256
EST:     CAAACTGAAGGAATGACACCTGAGACTGGAACATACCGTTGGATGGCTCC                         GGAGATGATCCAGCATAGGCCTTACACACAAAAAGTGGATGTATATAGCTT
genomic: CAAACTGAAGGAATGACACCTGAGACTGGAACATACCGTTGGATGGCTCCgtaagatctt ... tctactgcagGGAGATGATCCAGCATAGGCCTTACACACAAAAAGTGGATGTATATAGCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGACAAGTCAATTAAAATTGCTGACTTTGGAGTTGCCCGTATTGAGGTGCAAACTGAAGGAATGACACCTGAGACTGGAACATACCGTTGGATGGCTCCgtaagatcttttgctgttctctctttttatatttatatagttttatatgcattctagcttcatttttggaatgatttttggagagcttctctattatggt

- - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA