Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctcgttagctggaaatcttattatatctgtgtctgttcctattttttgtggagcattaagaaatgatctattaacctctataactttgccactgaagGAGTTTAAAGGATATGTTTTCAAAATCACCGGTGGGTGTGACAAACAAGGATTCCCTATGAAGCAGGGAGTGCTGACCCCTGGTCGTGTTCGACTTTTGC

Basic information

species Glycine max
transcript GLYMA07G31840.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G31840.3 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os07g42950.1 (Oryza sativa), 3'ss of exon 3
gtatgctcgttagctggaaatcttattatatctgtgtctgttcctattttttgtggagcattaagaaatgatctattaacctctataactttgccactgaagGAGTTTAAAGGATATGTTTTCAAAATCACCGGTGGGTGTGACAAACAAGGATTCCCTATGAAGCAGGGAGTGCTGACCCCTGGTCGTGTTCGACTTTTGC
                | ||| |  | |   || ||    |||||| ||  |||     |   ||   | |  | ||||| | | |  ||          |||| || || || ||||| ||||| ||||  || || |||||||| || || ||||||||||||||||||||||| ||  |||| ||||| || ||| | |
----------------gtaatatcgtgaggcctctgatgtttcctaattactgt----tacctagtcttaagatgttaacatatctctctcctttttctcagGAATTCAAGGGCTATGTCTTCAAGATCATGGGGGGTTGTGACAAGCAGGGTTTCCCTATGAAGCAGGGAGTGCTCACTGCTGGACGTGTCCGCCTTCTTC

upper sequence: GLYMA07G31840.3 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G851698_T02 (Zea mays), 3'ss of exon 3
gtatgctcgttagctggaaatcttattatatctgtgtctgttcctattttttgtggagcattaagaaatgatctattaacctctataactttgccactgaagGAGTTTAAAGGATATGTTTTCAAAATCACCGGTGGGTGTGACAAACAAGGATTCCCTATGAAGCAGGGAGTGCTGACCCCTGGTCGTGTTCGACTTTTGC
        || |  |       || |||| |||   ||  | ||   | ||  ||    |||    | | |  |||     |       ||      || |||||||||| || ||||| ||||| ||||  ||||| |||||||||||||| ||||| |||||||| ||||| |||||  |||||||||| || ||| |||
--------gtaaattttctgctttcttatttcttgatccatgccccctattgctg----atttcatacttaattataggtgtgatgtgtttcttttttgcagGAGTTTAAGGGTTATGTCTTCAAGATCATGGGTGGATGTGACAAACAAGGCTTCCCAATGAAGCAAGGAGTTCTGACTTCTGGTCGTGTCCGCCTTCTGC

upper sequence: GLYMA07G31840.3 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G054136_T09 (Zea mays), 3'ss of exon 3
gtatgctcgttagctggaaatcttattatatctgtgtctgttcctattttttgtggagcattaagaaatgatctattaacctctataactttgccactgaagGAGTTTAAAGGATATGTTTTCAAAATCACCGGTGGGTGTGACAAACAAGGATTCCCTATGAAGCAGGGAGTGCTGACCCCTGGTCGTGTTCGACTTTTGC
|||  ||  || |   ||  | ||  |  |||  || || || ||  |||      |   ||||  |  | | |  ||   |   |   |||||      ||||||| || || ||||| ||||| ||||  ||||| |||||||| ||||| ||||| |||||||| |||||  ||||  ||||||||||||| ||| |||
gtaaact--ttgggatgacttatttcttgatccatgactcttgctgatttc-----atacttaaatataggtgtgatatgtttctttgttttgc------agGAGTTCAAGGGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGCTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGC

upper sequence: GLYMA07G31840.3 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G054136_T08 (Zea mays), 3'ss of exon 3
-------gt-atgctc-gttagctggaaatctta-------ttatatctgtgtctgttcctattttttgtggagcattaagaaatgatctattaacctctataactttgccactgaagGAGTTTAAAGGATATGTTTTCAAAATCACCGGTGGGTGTGACAAACAAGGATTCCCTATGAAGCAGGGAGTGCTGACCCCTGGTCGTGTTCGACTTTTGC
       || |||||| |   |  | |||  ||        |||| |||   ||  |  || ||  |  |     | | | ||||       | |  | | |  |||||    || ||||||| || || ||||| ||||| ||||  ||||| |||||||| ||||| ||||| |||||||| |||||  ||||  ||||||||||||| ||| |||
gtcagtggtgatgctctgggtgaggtaaactttggggtgacttatttcttgatccatgactcttgctgatttcatacttaaaaatataggtgtgatatgttt--ctttgtt-ttgcagGAGTTCAAGGGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGCTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGC

upper sequence: GLYMA07G31840.3 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G054136_T05 (Zea mays), 3'ss of exon 3
--gtatgctcgttagctggaaatcttattatatctgtgtctgttcctattttttgtggagcattaagaaatgatctattaacctctataactttgccactgaagGAGTTTAAAGGATATGTTTTCAAAATCACCGGTGGGTGTGACAAACAAGGATTCCCTATGAAGCAGGGAGTGCTGACCCCTGGTCGTGTTCGACTTTTGC
  |  ||   || | ||          |||| |||   ||  |  || ||  |  |     | | | ||||       | |  | | |  |||||    || ||||||| || || ||||| ||||| ||||  ||||| |||||||| ||||| ||||| |||||||| |||||  ||||  ||||||||||||| ||| |||
ctgggtgag-gtaaactttggggtgacttatttcttgatccatgactcttgctgatttcatacttaaaaatataggtgtgatatgttt--ctttgtt-ttgcagGAGTTCAAGGGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGCTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGC

upper sequence: GLYMA07G31840.3 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G040600_T01 (Zea mays), 3'ss of exon 5
---gtatgctcgttagctggaaatcttattatatctgtgtctgttcctattttttgtggagcattaagaaat-gatctattaacctctataactttgccactgaagGAGTTTAAAGGATATGTTTTCAAAATCACCGGTGGGTGTGACAAACAAGGATTCCCTATGAAGCAGGGAGTGCTGACCCCTGGTCGTGTTCGACTTTTGC
    |    |    | ||          |||| |||   ||  |  || ||  |  ||    | | | | || | | |  ||   ||  |   |||||      ||||||| || || ||||| ||||| ||||  ||||| |||||||| ||||| ||||| |||||||| |||||  ||||  ||||||||||||| ||| |||
gagttgaatttacaaactttgggatgacttatttcttgatccatgactcttgctgatgtcatacttaaatataggtgtgatatgttcctttgttttgc------agGAGTTCAAGGGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGGTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGCCTTCTGC

upper sequence: GLYMA07G31840.3 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G054136_T01 (Zea mays), 3'ss of exon 3
gtatgctcgttagctggaaatcttattatatctgtgtctgttcctattttttgtggagcattaagaaatgatctattaacctctataactttgccactgaagGAGTTTAAAGGATATGTTTTCAAAATCACCGGTGGGTGTGACAAACAAGGATTCCCTATGAAGCAGGGAGTGCTGACCCCTGGTCGTGTTCGACTTTTGC
        || | ||          |||| |||   ||  |  || ||  |  |     | | | ||||       | |  | | |  |||||    || ||||||| || || ||||| ||||| ||||  ||||| |||||||| ||||| ||||| |||||||| |||||  ||||  ||||||||||||| ||| |||
--------gtaaactttggggtgacttatttcttgatccatgactcttgctgatttcatacttaaaaatataggtgtgatatgttt--ctttgtt-ttgcagGAGTTCAAGGGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGCTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGC

upper sequence: GLYMA07G31840.3 (Glycine max), 3'ss of exon 2
lower sequence: AT4G31700.1 (Arabidopsis thaliana), 3'ss of exon 3
--gtatgctcgttagctggaaatcttattatatctgtgtctgttcctattttttgtggagcattaagaaatgatctattaacctctataactttgccactgaagGAGTTTAAAGGATATGTTTTCAAAATCACCGGTGGGTGTGACAAACAAGGATTCCCTATGAAGCAGGGAGTGCTGACCCCTGGTCGTGTTCGACTTTTGC
    |   ||  |   |   | | | ||   ||  ||||           ||| |  |      |    ||||| | ||    | |  |   |||  | || ||||||| |||||||| |||||||| ||||  ||||| || || || ||||| ||||| ||||||||||||||  |||| || || |||||||| |||||||
gtacagattccatttttcttactttgatctaatgagtgtgaagattagcatttcgaag-----cagatgatgatgt-tttgtttatgaattgttgttattgcagGAGTTCAAAGGATACGTTTTCAAGATCAAGGGTGGTTGCGATAAGCAAGGTTTCCCAATGAAGCAGGGAGTTTTGACTCCAGGCCGTGTTCGCCTTTTGC

upper sequence: GLYMA07G31840.3 (Glycine max), 3'ss of exon 2
lower sequence: AT4G31700.2 (Arabidopsis thaliana), 3'ss of exon 1
----gtatgctcgttagctggaaatcttattatatctgtgtctgttcctattttttgtggagcattaagaaatgatctattaacctctataactttgccactgaagGAGTTTAAAGGATATGTTTTCAAAATCACCGGTGGGTGTGACAAACAAGGATTCCCTATGAAGCAGGGAGTGCTGACCCCTGGTCGTGTTCGACTTTTGC
      |   ||  |   |   | | | ||   ||  ||||           ||| |  |      |    ||||| | ||    | |  |   |||  | || ||||||| |||||||| |||||||| ||||  ||||| || || || ||||| ||||| ||||||||||||||  |||| || || |||||||| |||||||
aggtacagattccatttttcttactttgatctaatgagtgtgaagattagcatttcgaag-----cagatgatgatgt-tttgtttatgaattgttgttattgcagGAGTTCAAAGGATACGTTTTCAAGATCAAGGGTGGTTGCGATAAGCAAGGTTTCCCAATGAAGCAGGGAGTTTTGACTCCAGGCCGTGTTCGCCTTTTGC

upper sequence: GLYMA07G31840.3 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0001g06290.t01 (Vitis vinifera), 3'ss of exon 3
gtatgctcgttagctggaaatcttattatatctgtgtctgt-tcctattttttgtggagcattaagaaatgatctattaacctctataactttgccactgaagGAGTTTAAAGGATATGTTTTCAAAATCACCGGTGGGTGTGACAAACAAGGATTCCCTATGAAGCAGGGAGTGCTGACCCCTGGTCGTGTTCGACTTTTGC
        || |||    |   || ||||  |  || |    | ||| | |  |   || ||| | | |  || ||||    | | |   ||||       |||| ||||| || ||||| ||||||||||  || || |||||||| ||||| ||||| ||||||||||||||| | || |||||||||||| | || ||||
--------gtaagcatttaccattgttatg-caatgccaaaattctactatcagactag-atttatataacatttatttttgtttgtttgtttgt-gtgacagGAATTTAATGGCTATGTATTCAAAATCATGGGAGGCTGTGACAAGCAAGGGTTCCCAATGAAGCAGGGAGTGTTAACTCCTGGTCGTGTTAGTCTCTTGC

upper sequence: GLYMA07G31840.3 (Glycine max), 3'ss of exon 2
lower sequence: Vv07s0191g00060.t01 (Vitis vinifera), 3'ss of exon 3
gtatgctcgttagctggaaatcttattatatctgtgtctgttcctattttttgtggagcattaagaaatgatctattaacctctataactttgccactgaagGAGTTTAAAGGATATGTTTTCAAAATCACCGGTGGGTGTGACAAACAAGGATTCCCTATGAAGCAGGGAGTGCTGACCCCTGGTCGTGTTCGACTTTTGC
                   ||  | || |  || |   | ||   ||   |||       ||| ||| |||| |||| |  | | | |            ||||||| || || ||||| |||||||| |  || || |||||||| ||||| || || |||||||||||||| |||||||| || || || | |||| |||
-----------------gtatgattttgttactattcttcttaggataacttgccctttgttaggaa-tgatttattgatgtatcttaagcgtgtttgacagGAGTTCAAGGGTTATGTATTCAAAATAATGGGAGGCTGTGACAAGCAAGGTTTTCCAATGAAGCAGGGAGTACTGACCCCAGGCCGAGTCCAACTTCTGC

upper sequence: GLYMA07G31840.3 (Glycine max), 3'ss of exon 2
lower sequence: Vv03s0017g01350.t01 (Vitis vinifera), 3'ss of exon 3
gtatgctcgttagctggaaatcttattatatctgtgtctgttcctattttttgtggagcattaagaaatgatctattaacctctataactttgccactgaagGAGTTTAAAGGATATGTTTTCAAAATCACCGGTGGGTGTGACAAACAAGGATTCCCTATGAAGCAGGGAGTGCTGACCCCTGGTCGTGTTCGACTTTTGC
               | |   ||| |    |||    |   |  | | | |  |   |  | |   | | |||    ||    | | | | |||  |   ||||||| || || ||||||||||| ||||  ||||| |||||||| ||||| || || |||||||||||||| ||||| ||||| |||||| | |||||||
---------------gtatgccttttctgctcttctcccacttatttatctcatattgtttgatctactaatcatacaaaacatgtca-tctgcttc-acagGAGTTCAAGGGCTATGTTTTCAAGATCATGGGTGGTTGTGACAAGCAAGGGTTTCCCATGAAGCAGGGAGTACTGACTCCTGGCCGTGTTAGTCTTTTGC

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|7684901|gb|AW755549.1|AW755549
EST:     TTTGGGACAAGAGGATCTCCCAGGAGGTTCTTGGTGATGCTCTGGGTGAG                         GAGTTTAAAGGATATGTTTTCAAAATCACCGGTGGGTGTGACAAACAAGGA
genomic: TTTGGGACAAGAGGATCTCCCAGGAGGTTCTTGGTGATGCTCTGGGTGAGgtatgctcgt ... gccactgaagGAGTTTAAAGGATATGTTTTCAAAATCACCGGTGGGTGTGACAAACAAGGA
EST: gi|208239627|gb|GE036697.1|GE036697
EST:     TTTGGGACAAGAGGATCTCCCAGGAGGTTCTTGGTGATGCTCTGGGTGAG                         GAGTTTAAAGGATATGTTTTCAAAATCACCGGTGGGTGTGACAAACAAGGA
genomic: TTTGGGACAAGAGGATCTCCCAGGAGGTTCTTGGTGATGCTCTGGGTGAGgtatgctcgt ... gccactgaagGAGTTTAAAGGATATGTTTTCAAAATCACCGGTGGGTGTGACAAACAAGGA
EST: gi|7692658|gb|AW760759.1|AW760759
EST:     CTTGGTGATGCTCTGGGTGAG                         GAGTTTAAAGGATATGTTTTCAAAATCACCGGTGGGTGTGACAAACAAGGA
genomic: CTTGGTGATGCTCTGGGTGAGgtatgctcgt ... gccactgaagGAGTTTAAAGGATATGTTTTCAAAATCACCGGTGGGTGTGACAAACAAGGA
EST: gi|6916434|gb|AW397964.1|AW397964
EST:     TTTGGGACAAGAGGATCTCCCAGGAGGTTCTTGGTGATGCTCTGGGTGAG                         GAGTTTAAAGGATATGTTTTCAAAATCACCGGTGGGTGTGACAAACAAGGA
genomic: TTTGGGACAAGAGGATCTCCCAGGAGGTTCTTGGTGATGCTCTGGGTGAGgtatgctcgt ... gccactgaagGAGTTTAAAGGATATGTTTTCAAAATCACCGGTGGGTGTGACAAACAAGGA
EST: gi|208284798|gb|GE085612.1|GE085612
EST:     TTTGGGACAAGAGGATCTCCCAGGAGGTTCTTGGTGATGCTCTGGGTGAG                         GAGTTTAAAGGATATGTTTTCAAAATCACCGGTGGGTGTGACAAACAGGGA
genomic: TTTGGGACAAGAGGATCTCCCAGGAGGTTCTTGGTGATGCTCTGGGTGAGgtatgctcgt ... gccactgaagGAGTTTAAAGGATATGTTTTCAAAATCACCGGTGGGTGTGACAAACAAGGA
EST: gi|151395160|gb|EV265031.1|EV265031
EST:     ATGCTCTGGGTGAG                         GAGTTTAAAGGATATGTTTTCAAAATCACCGGTGGGTGTGACAAACAAGGA
genomic: ATGCTCTGGGTGAGgtatgctcgt ... gccactgaagGAGTTTAAAGGATATGTTTTCAAAATCACCGGTGGGTGTGACAAACAAGGA
EST: gi|16997201|gb|BM086573.1|BM086573
EST:     TTGGTGATGCTCTGGGTGAG                         GAGTTTAAAGGATATGTTTTCAAAATCACCGGTGGGTGTGACAAACAAGGA
genomic: TTGGTGATGCTCTGGGTGAGgtatgctcgt ... gccactgaagGAGTTTAAAGGATATGTTTTCAAAATCACCGGTGGGTGTGACAAACAAGGA
EST: gi|8825892|gb|BE209622.1|BE209622
EST:     TTTGGGACAAGAGGATCTCCCAGGAGGTTCTTGGTGATGCTCTGGGTGAG                         GAGTTTAAAGGATATGTTTTCAAAATCACCGGTGGGTGTGACAAACAAGGA
genomic: TTTGGGACAAGAGGATCTCCCAGGAGGTTCTTGGTGATGCTCTGGGTGAGgtatgctcgt ... gccactgaagGAGTTTAAAGGATATGTTTTCAAAATCACCGGTGGGTGTGACAAACAAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttgtggagcattaagaaatgatctattaacctctataactttgccactgaagGAGTTTAAAGGATATGTTTTCAAAATCACCGGTGGGTGTGACAAACAAGGATTCCCTATGAAGCAGGGAGTGCTGACCCCTGGTCGTGTTCGACTTTTGC
                                         ctttgcc  CT-rich tract
                  aaatgatctattaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctcgttagctggaaatcttattatatctgtgtctgttcctattttttgtggagcattaagaaatgatctattaacctctataactttgccactgaagGAGTTTAAAGGATATGTTTTCAAAATCACCGGTGGGTGTGACAAACAAGGATTCCCTATGAAGCAGGGAGTGCTGACCCCTGGTCGTGTTCGACTTTTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC