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

gtgttgtctctaaaccctaattgcttccctgtttggatttttgtgtgtttatcgctgaaacatattcgatttttctacagTTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCTGAAGCT

Basic information

species Glycine max
transcript GLYMA07G31840.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G31840.2 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os03g27260.1 (Oryza sativa), 3'ss of exon 1
------------------------------------------gtgttgtctctaaacc-ctaattgcttccctgtttggatttttgtgtgtttatcgctgaaacatattcgat-ttttctacagTTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCTGAAGCT
                                          || | |   |    |  ||  ||| |||       |   |||  | || || | |  |   |      ||| ||||   ||||||||||| || || || ||||| ||||||||||||||||| || ||||||||||||| ||||||
gtacccatttctcctcctcccctccccgcgggcgacgtggtcgtctcgatccggtccggctggttgtttcttgtagcgcggtttgatctgatt-ttgtggtcgccctgatgatgttttgcgcagTTCAACATCGCCAACCCGACCACCGGGTGCCAGAAGAAGCTCGAGATCGATGACGACCAGAAGCT

upper sequence: GLYMA07G31840.2 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os07g42950.1 (Oryza sativa), 3'ss of exon 1
--------------------------gtgttgtctctaaaccctaattgcttccctgt----ttggatttttgtgt----gtttatcgctgaaacata-----ttcgatttt-tctacagTTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCTGAAGCT
                          |  |   |   |    |||     ||    ||    || ||||||| | |    | |     ||||  | |      | ||  ||  | | ||||||||||| || || || ||||| ||||||||||||||||| || ||||||||||||| ||||||
gtaagacgctcctcgtcgccgttgctggatcccccagatgagctagggattttatggtagggttagatttttttttcgtgggtggcttctgattcgtgtggtttccgccttcgttttcagTTCAACATCGCGAACCCGACCACCGGGTGCCAGAAGAAGCTCGAGATCGATGACGACCAGAAGCT

upper sequence: GLYMA07G31840.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G054136_T02 (Zea mays), 3'ss of exon 1
gtgttgtctctaaaccctaattgcttccctgtttgga--tttttgtgtgtttatcgc-tgaaacatattcgatttttctacagTTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCTGAAGCT
     ||     |  ||    |  | ||  | | |||  | |||||| |  ||| |  |   |  | | ||   ||||  ||||||||||| || || ||  |||| |||||||| ||||||||||||||||||||||||| ||||||
-----gtaagctactcccggcttttcccacgataggaggtgtttgtgggaatatagtatctgatctgtgcgcactttc--cagTTCAACATCGCGAACCCTTCCACCGGGTGCCAAAAGAAGCTGGAAATCGATGACGACCAGAAGCT

upper sequence: GLYMA07G31840.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G054136_T01 (Zea mays), 3'ss of exon 1
gtgttgtctctaaaccctaattgcttccctgtttg--gatttttgtgtgtttatcgc-tgaaacatattcgatttttctacagTTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCTGAAGCT
     ||     |  ||       | ||  | | |  | | |||||| |  | | |  |   |  | | ||   ||||  ||||||||||| || || ||  |||| |||||||| ||||||||||||||||||||||||| ||||||
-----gtaagctactcccggcctttcccgcgataggcggtgtttgtgggaatctagtatctgatctgtgcgcactttc--cagTTCAACATCGCGAACCCTTCCACCGGGTGCCAAAAGAAGCTGGAAATCGATGACGACCAGAAGCT

upper sequence: GLYMA07G31840.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G054136_T03 (Zea mays), 3'ss of exon 1
----------gtgttgtctctaaacc---ctaattgcttccctgtttggatttttgtgtgtttatcgctgaaacatattcgattt-------ttctacagTTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCTGAAGCT
            |    |   ||      ||| |  |  || |    |   |     |||||| | |        |||  ||| |        | | ||||||||||| || || ||  |||| |||||||| ||||||||||||||||||||||||| ||||||
gcgcgccgcaacgccaccatgaaggtaagctactcccggcctttcccgcgataggcggtgtttgtgggaatctagtatctgatctgtgcgcactttccagTTCAACATCGCGAACCCTTCCACCGGGTGCCAAAAGAAGCTGGAAATCGATGACGACCAGAAGCT

upper sequence: GLYMA07G31840.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM5G851698_T02 (Zea mays), 3'ss of exon 1
----gtgttgtctctaaaccctaattgcttccctgtttggatttttgtgtgtttatcg-ctgaaacatattcgatttttc---tacagTTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCTGAAGCT
    |  |   |||    |  |||    |     | | |  ||| || |  | || || ||||    |   |  ||  |    | ||||||||||| || || ||  | || |||||||||||||||||||||||||||||||||| ||| ||
gtaagcttatcctccgcgctgtaaca--tcgataggtggtgtttgtgggaatctagcgtctgatctgtgcccttttcgttgcttccagTTCAACATCGCGAACCCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACT

upper sequence: GLYMA07G31840.2 (Glycine max), 3'ss of exon 1
lower sequence: AT4G31700.1 (Arabidopsis thaliana), 3'ss of exon 1
gtgt-tgtctctaaaccctaattgcttccctgtttggatttttgtgtgtttatcgctgaaacatattcgatttttctac-----agTTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCTGAAGCT
|||  || |    ||  | ||| |  ||    ||||    | |  | ||||        ||| | ||  || ||||| |     |||||||| |||| ||||| || ||||| |||||||||||||| || ||||| || |||| ||| ||
gtgcgtgacggcgaaatcgaatagactctacatttgctcgtattcgagtttcctttgctaacctttttcatgtttcttcgtttcagTTCAACGTTGCGAATCCAACTACTGGATGCCAGAAGAAGCTCGAGATCGACGATGACCAGAAACT

upper sequence: GLYMA07G31840.2 (Glycine max), 3'ss of exon 1
lower sequence: PP1S31_322V6.1 (Physcomitrella patens), 3'ss of exon 1
-----------------------------------------------gtgttgtctctaaaccctaattgcttc---cctgtttggatttttgtgtgtttatcgctgaaacatattcgatttttctacagTTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCTGAAGCT
                                                ||  ||  |        ||||  ||    | || ||| ||||    |||||          |  |  | | || ||   ||| |||| || || ||||||||||| ||||||||||||||| | || ||||||||||||   |||||
gtgtgctgtacgctccgcatattctctctcgtacaatgctgctgatgttgccgttccaggggtggaattattttggacgtgcttgcatttgca-gtgttggagaggactaactgcttgcttcttgcgcagCTCAATATCGCTAATCCCACCACAGGGTGCCAGAAGAAGGTCGAGATCGATGACGACGCTAAGCT

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|193711766|gb|FK647865.1|FK647865
EST:     AGGCGCGGCGGGATCAGCACAAGATTGCAAAATGAAG                         TTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGAT
genomic: AGGCGCGGCGGGATCAGCACAAGATTGCAAAATGAAGgtgttgtctc ... ttttctacagTTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGAT
EST: gi|298167911|gb|HO013174.1|HO013174
EST:     AGGCGCGGCGGGATCAGCACAAGATTGCAAAATGTAG                         TTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGAT
genomic: AGGCGCGGCGGGATCAGCACAAGATTGCAAAATGAAGgtgttgtctc ... ttttctacagTTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGAT
EST: gi|298189754|gb|HO038157.1|HO038157
EST:     AGGCGCGGCGGGATCGGCACAAGATTGCAAAATGAAG                         TTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGAT
genomic: AGGCGCGGCGGGATCAGCACAAGATTGCAAAATGAAGgtgttgtctc ... ttttctacagTTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGAT
EST: gi|298164705|gb|HO014350.1|HO014350
EST:     AGGCGCGGCGGGATCAGCACAAGATTGCAAAATGAAG                         TTCAACATTGCAAATCCCACCACTGGGTGCCGGAAGAAGCTGGAAATCGAT
genomic: AGGCGCGGCGGGATCAGCACAAGATTGCAAAATGAAGgtgttgtctc ... ttttctacagTTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGAT
EST: gi|208041564|gb|GD843014.1|GD843014
EST:     CGGCGGGATCAGCACAAGATTGCAAAATGAAG                         TTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGAT
genomic: CGGCGGGATCAGCACAAGATTGCAAAATGAAGgtgttgtctc ... ttttctacagTTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGAT
EST: gi|298166233|gb|HO009204.1|HO009204
EST:     CGGGATCAGCACAAGATTGCAAAATGAAG                         TTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGAT
genomic: CGGGATCAGCACAAGATTGCAAAATGAAGgtgttgtctc ... ttttctacagTTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGAT
EST: gi|208190348|gb|GD994524.1|GD994524
EST:     CGCGGCGGGATCAGCACAAGATTGCGAAATGAAG                         TTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGAT
genomic: CGCGGCGGGATCAGCACAAGATTGCAAAATGAAGgtgttgtctc ... ttttctacagTTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGAT
EST: gi|19346568|gb|BM891448.1|BM891448
EST:     CACAAGATTGCAAAATGAAG                         TTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGAT
genomic: CACAAGATTGCAAAATGAAGgtgttgtctc ... ttttctacagTTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGAT
EST: gi|213601378|gb|DB956684.1|DB956684
EST:     AGGCGCGGCGGGATCAGCACAAGATTGCAAAATGAAG                         TTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGAT
genomic: AGGCGCGGCGGGATCAGCACAAGATTGCAAAATGAAGgtgttgtctc ... ttttctacagTTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGAT
EST: gi|298164434|gb|HO014079.1|HO014079
EST:     GCGCGGCGGGATCAGCACAAGATTGCAAAATGAAG                         TTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCAAT
genomic: GCGCGGCGGGATCAGCACAAGATTGCAAAATGAAGgtgttgtctc ... ttttctacagTTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGAT
EST: gi|208231930|gb|GE030885.1|GE030885
EST:     GCGGCGGGATCAGCACAAGATTGCAAAATGAAG                         TTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGAT
genomic: GCGGCGGGATCAGCACAAGATTGCAAAATGAAGgtgttgtctc ... ttttctacagTTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGAT
EST: gi|298188012|gb|HO031969.1|HO031969
EST:     AGGCGCGGCGGGATCAGCACAAGATTGCAAAATGAAG                         TTCAACATTGCAAATCCCACCACTGGGTGGCCAGAAGAAGCTGGAAATCGA
genomic: AGGCGCGGCGGGATCAGCACAAGATTGCAAAATGAAGgtgttgtctc ... ttttctacagTTCAACATTGCAAATCCCACCACTGGGT-GCCAGAAGAAGCTGGAAATCGA
EST: gi|193447979|gb|FK414118.1|FK414118
EST:     AGGCGCGGCGGGATCAGCACAAGATTGCAAAATGAAG                         TTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGAT
genomic: AGGCGCGGCGGGATCAGCACAAGATTGCAAAATGAAGgtgttgtctc ... ttttctacagTTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGAT
EST: gi|16347870|gb|BI973465.1|BI973465
EST:     CAAGATTGCAAAATGAAG                         TTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGAT
genomic: CAAGATTGCAAAATGAAGgtgttgtctc ... ttttctacagTTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGAT
EST: gi|298187978|gb|HO031935.1|HO031935
EST:     AGGCGCGGCGGGATCAGCACAAGATTGCAAAATGAAG                         TTCAACATTGCAAATCCCACCACTGGGTGGCCAGAAGAAGCTGGAAATCGA
genomic: AGGCGCGGCGGGATCAGCACAAGATTGCAAAATGAAGgtgttgtctc ... ttttctacagTTCAACATTGCAAATCCCACCACTGGGT-GCCAGAAGAAGCTGGAAATCGA
EST: gi|9259173|gb|BE347320.1|BE347320
EST:     GGGATCAGCACAAGATTGCAAAATGAAG                         TTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGAT
genomic: GGGATCAGCACAAGATTGCAAAATGAAGgtgttgtctc ... ttttctacagTTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGAT
EST: gi|208156915|gb|GD956343.1|GD956343
EST:     AGGCGCGGCGGGATCAGCACAAGATTGCAAAATGAAG                         TTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGAT
genomic: AGGCGCGGCGGGATCAGCACAAGATTGCAAAATGAAGgtgttgtctc ... ttttctacagTTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGAT
EST: gi|298190488|gb|HO032609.1|HO032609
EST:     AGGCGCGGCGGGATCAGCACAAGATTGCAAAATGAAG                         TTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGAT
genomic: AGGCGCGGCGGGATCAGCACAAGATTGCAAAATGAAGgtgttgtctc ... ttttctacagTTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGAT
EST: gi|298171661|gb|HO021253.1|HO021253
EST:     AGGCGCGGCGGGATCAGCACAAGATTGCAAAATGAAG                         TTCAACATTGCAAATCCCACCACTGGGTGGCCAGAAGAAGCTGGAAATCGA
genomic: AGGCGCGGCGGGATCAGCACAAGATTGCAAAATGAAGgtgttgtctc ... ttttctacagTTCAACATTGCAAATCCCACCACTGGGT-GCCAGAAGAAGCTGGAAATCGA
EST: gi|10847435|gb|BF070122.1|BF070122
EST:     CAAGATTGCAAAATGAAG                         TTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGAT
genomic: CAAGATTGCAAAATGAAGgtgttgtctc ... ttttctacagTTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGAT
EST: gi|298170108|gb|HO018732.1|HO018732
EST:     AGGCGCGGCGGGATCAGCACAAGATTGCAAAATGAAG                         TTCAACATTGCAAATCCCACCACTGGGTGGCCAGAAGAAGCTGGAAATCGA
genomic: AGGCGCGGCGGGATCAGCACAAGATTGCAAAATGAAGgtgttgtctc ... ttttctacagTTCAACATTGCAAATCCCACCACTGGGT-GCCAGAAGAAGCTGGAAATCGA
EST: gi|207696549|gb|GD678670.1|GD678670
EST:     AGGCGCGGCGGGATCAGCACAAGATTGCAAAATGAAG                         TTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGAT
genomic: AGGCGCGGCGGGATCAGCACAAGATTGCAAAATGAAGgtgttgtctc ... ttttctacagTTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGAT
EST: gi|298170056|gb|HO018680.1|HO018680
EST:     AGGCGCGGCGGGATCAGCACAAGATTGCAAAATGAAG                         TTCAACATTGCAAATCCCACCACTGGGTGGCCAGAAGAAGCTGGAAATCGA
genomic: AGGCGCGGCGGGATCAGCACAAGATTGCAAAATGAAGgtgttgtctc ... ttttctacagTTCAACATTGCAAATCCCACCACTGGGT-GCCAGAAGAAGCTGGAAATCGA
EST: gi|298168528|gb|HO009458.1|HO009458
EST:     CACGCAGCGAGTTAGGCGCGGCGGGATCAGCACAAGATTGCAAAATGAAG                         TTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGAT
genomic: CACGCAGCGAGTTAGGCGCGGCGGGATCAGCACAAGATTGCAAAATGAAGgtgttgtctc ... ttttctacagTTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGAT
EST: gi|193324144|gb|FK292592.1|FK292592
EST:     AGGCGCGGCGGGATCAGCACAAGATTGCAAAATGAAG                         TTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGAT
genomic: AGGCGCGGCGGGATCAGCACAAGATTGCAAAATGAAGgtgttgtctc ... ttttctacagTTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGAT
EST: gi|298168505|gb|HO009435.1|HO009435
EST:     AGGCGCGGCGGGATCAGCACAAGATTGCAAAATGAAG                         TTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGAT
genomic: AGGCGCGGCGGGATCAGCACAAGATTGCAAAATGAAGgtgttgtctc ... ttttctacagTTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGAT
EST: gi|208209117|gb|GE003527.1|GE003527
EST:     AGGCGCGGCGGGATCAGCACAAGATTGCAAAATGAAG                         TTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGAT
genomic: AGGCGCGGCGGGATCAGCACAAGATTGCAAAATGAAGgtgttgtctc ... ttttctacagTTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGAT
EST: gi|193703199|gb|FK639673.1|FK639673
EST:     CGGCGGGATCAGCACAAGATTGCAAAATGAAG                         TTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGAT
genomic: CGGCGGGATCAGCACAAGATTGCAAAATGAAGgtgttgtctc ... ttttctacagTTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccctgtttggatttttgtgtgtttatcgctgaaacatattcgatttttctacagTTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCTGAAGCT
                                            tttttctac  CT-rich tract
                                aaacatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgttgtctctaaaccctaattgcttccctgtttggatttttgtgtgtttatcgctgaaacatattcgatttttctacagTTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCTGAAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC