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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTTTTGGTGCGACAACCAATCCAAACCCAAACAGGGCGCTGCTTGGGGTACCTCTCTTCGCAAGGTCTACACCTTCGACACCGTTGAAGAGTTCTGGTGgtataaattttctcttcctcctccttttttctgttccacaattttcatttttctaatttcagaaaaagggaatctaagcatgcaatctcaaatcttatta...

Basic information

species Glycine max
transcript GLYMA20G21510.2
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G21510.2 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os10g32970.1 (Oryza sativa), 5'ss of exon 1
CGTTTTGGTGCGACAACCAATCCAAACCCAAACAGGGCGCTGCTTGGGGTACCTCTCTTCGCAAGGTCTACACCTTCGACACCGTTGAAGAGTTCTGGTGgtataaattttctcttcctcctccttttttctgttccacaattttcatttttctaatttcagaaaaagggaatctaagcatgcaatctcaaatcttatta
|||| |||| ||||| ||| ||||| ||||| |  ||||| || ||||| ||||| || ||||||| |||||||||||||||||| || ||||||||| ||||             |  |||      ||        |  ||  |  | |||  || | |   |       | |    || |  |||   | || ||  
CGTTCTGGTACGACATCCAGTCCAAGCCCAAGCCCGGCGCCGCGTGGGGGACCTCGCTCCGCAAGGCCTACACCTTCGACACCGTCGAGGAGTTCTGGGGgtacgtgccgatgaagcgccctaagcccttgcccgatccgtttcccggtcttcggatctgatctactttctgtgttttgatcctgtctggtagctcatat

upper sequence: GLYMA20G21510.2 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G022019_T01 (Zea mays), 5'ss of exon 1
CGTTTTGGTGCGACAACCAATCCAAACCCAAACAGGGCGCTGCTTGGGGTACCTCTCTTCGCAAGGTCTACACCTTCGACACCGTTGAAGAGTTCTGGTGgtataaattttctcttcctcctccttttttctgttccacaattttcatttttctaatttcagaaaaagggaatctaagcatgcaatctcaaatcttatta---
| || |||| ||||| |||  | ||  ||||    || ||||| ||||| ||||| ||    |||| ||||||||||||||||||||| ||||||||| ||||    ||  |  | |  |       ||  ||  ||       |    |    | |  |      |     |||       |    |    |||   ||   
CCTTCTGGTACGACATCCAGACGAAGACCAAGTCCGGGGCTGCGTGGGGCACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAGgtacg--ttggcgatgcgccggataccttcatggcccggttccctttcctgatcactcccgttctgatctggtctggatgc-cgtggtggtttctgggtagtg

upper sequence: GLYMA20G21510.2 (Glycine max), 5'ss of exon 1
lower sequence: Vv05s0049g01770.t01 (Vitis vinifera), 5'ss of exon 1
CGTTTTGGTGCGACAACCAATCCAAACCCAAACAGGGCGCTGCTTGGGGTACCTCTCTTCGCAAGGTCTACACCTTCGACACCGTTGAAGAGTTCTGGTGgtataaatttt-ctc-ttcctcctccttttttctgttccacaattttcatttt-tctaatt--tcagaaaaagggaatctaagcatgcaatctcaaatcttatta
| || |||| ||| ||||| ||||| ||||| || ||||| |||||||| ||||||||||||||||  ||||||||||| ||||| ||||| || |||||||||   | |  ||| ||  | ||    | ||  ||| |  | ||||  || | | |  ||  || |||||   | |   ||| |    | ||  ||| |     
CCTTCTGGTTCGATAACCAGTCCAAGCCCAAGCAAGGCGCGGCTTGGGGGACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTGgtatctctctcgctcgttatttctttaatctttggtttcgaattttttcttctgtttggttgatcggaaaacacgcaggaaagtagtggaactttaattt-----

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|10709400|gb|BF009124.1|BF009124
EST:     ACCTCTCTTCGCAAGGTCTACACCTTCGACACCGTTGAAGAGTTCTGGTG                         TTTGTATGATCAGGTATTCAAGCCCAGCAAGTTGCAAATCAATGCGGATTT
genomic: ACCTCTCTTCGCAAGGTCTACACCTTCGACACCGTTGAAGAGTTCTGGTGgtataaattt ... gctggtatagTTTGTATGATCAGGTATTCAAGCCCAGCAAGTTGCAAATCAATGCGGATTT
EST: gi|298192521|gb|HO036603.1|HO036603
EST:     ACCTCTCTTCGCAAGGTCTACACCTTCGACACCGTTGAAGAGTTCTGGTG                         TTTGTATGATCAGGTATTCAAGCCCAGCAAGTTGCAAATCAATGCGGATTT
genomic: ACCTCTCTTCGCAAGGTCTACACCTTCGACACCGTTGAAGAGTTCTGGTGgtataaattt ... gctggtatagTTTGTATGATCAGGTATTCAAGCCCAGCAAGTTGCAAATCAATGCGGATTT
EST: gi|192325421|gb|FK018377.1|FK018377
EST:     ACCTCTCTTCGCAAGGTCTACACCTTCGACACCGTTGAAGAGTTCTGGTG                         TTTGTATGATCAGGTATTCAAGCCCAGCAAGTTGCAAATCAATGCGGATTT
genomic: ACCTCTCTTCGCAAGGTCTACACCTTCGACACCGTTGAAGAGTTCTGGTGgtataaattt ... gctggtatagTTTGTATGATCAGGTATTCAAGCCCAGCAAGTTGCAAATCAATGCGGATTT
EST: gi|14999254|gb|BI320281.1|BI320281
EST:     ACCTCTCTTCGCAAGGTCTACACCTTCGACACCGTTGAAGAGTTCTGGTG                         TTTGTATGATCAGGTATTCAAGCCCAGCAAGTTGCAAATCAATGCGGATTT
genomic: ACCTCTCTTCGCAAGGTCTACACCTTCGACACCGTTGAAGAGTTCTGGTGgtataaattt ... gctggtatagTTTGTATGATCAGGTATTCAAGCCCAGCAAGTTGCAAATCAATGCGGATTT
EST: gi|209724913|gb|BW669602.1|BW669602
EST:     ACCTCTCTTCGCAAGGTCTACACCTTCGACACCGTTGAAGAGTTCTGGTG                         TTTGTATGATCAGGTATTCAAGCCCAGCAAGTTGCAAATCAATGCGGATTT
genomic: ACCTCTCTTCGCAAGGTCTACACCTTCGACACCGTTGAAGAGTTCTGGTGgtataaattt ... gctggtatagTTTGTATGATCAGGTATTCAAGCCCAGCAAGTTGCAAATCAATGCGGATTT
EST: gi|254320358|gb|GR831166.1|GR831166
EST:     ACCTCTCTTCGCAAGGTCTACACCTTCGACACCGTTGAAGAGTTCTGGTG                         TTTGTATGATCAGGTATTCAAGCCCAGCAAGTTGCAAATCAATGCGGATTT
genomic: ACCTCTCTTCGCAAGGTCTACACCTTCGACACCGTTGAAGAGTTCTGGTGgtataaattt ... gctggtatagTTTGTATGATCAGGTATTCAAGCCCAGCAAGTTGCAAATCAATGCGGATTT
EST: gi|13791212|gb|BG653803.1|BG653803
EST:     ACCTCTCTTCGCAAGGTCTACACCTTCGACACCGTTGAAGAGTTCTGGTG                         TTTGTATGATCAGGTATTCAAGCCCAGCAAGTTGCAAATCAATGCGGATTT
genomic: ACCTCTCTTCGCAAGGTCTACACCTTCGACACCGTTGAAGAGTTCTGGTGgtataaattt ... gctggtatagTTTGTATGATCAGGTATTCAAGCCCAGCAAGTTGCAAATCAATGCGGATTT
EST: gi|298197400|gb|HO044879.1|HO044879
EST:     ACCTCTCTTCGCAAGGTCTACACCTTCGACACCGTTGAAGAGTTCTGGTG                         TTTGTATGATCAGGTATTCAAGCCCAGCAAGTTGCAAATCAATGCGGATTT
genomic: ACCTCTCTTCGCAAGGTCTACACCTTCGACACCGTTGAAGAGTTCTGGTGgtataaattt ... gctggtatagTTTGTATGATCAGGTATTCAAGCCCAGCAAGTTGCAAATCAATGCGGATTT
EST: gi|298176097|gb|HO015502.1|HO015502
EST:     ACCTCTCTTCGCAAGGTCTACACCTTCGACACCGTTGAAGAGTTCTGGTG                         TTTGTATGATCAGGTATTCAAGCCCAGCAAGTTGCAAATCAATGCGGATTT
genomic: ACCTCTCTTCGCAAGGTCTACACCTTCGACACCGTTGAAGAGTTCTGGTGgtataaattt ... gctggtatagTTTGTATGATCAGGTATTCAAGCCCAGCAAGTTGCAAATCAATGCGGATTT
EST: gi|298177677|gb|HO023696.1|HO023696
EST:     ACCTCTCTTCGCAAGGTCTACACCTTCGACACCGTTGAAGAGTTCTGGTG                         TTTGTATGATCAGGTATTCAAGCCCAGCAAGTTGCAAATCAATGCGGATTT
genomic: ACCTCTCTTCGCAAGGTCTACACCTTCGACACCGTTGAAGAGTTCTGGTGgtataaattt ... gctggtatagTTTGTATGATCAGGTATTCAAGCCCAGCAAGTTGCAAATCAATGCGGATTT
EST: gi|120532041|gb|EH260174.1|EH260174
EST:     ACCTCTCTTCGCAAGGTCTACACCTTCGACACCGTTGAAGAGTTCTGGTG                         TTTGTATGATCAGGTATTCAAGCCCAGCAAGTTGCAAATCAATGCGGATTT
genomic: ACCTCTCTTCGCAAGGTCTACACCTTCGACACCGTTGAAGAGTTCTGGTGgtataaattt ... gctggtatagTTTGTATGATCAGGTATTCAAGCCCAGCAAGTTGCAAATCAATGCGGATTT
EST: gi|209700394|gb|BW664407.1|BW664407
EST:     ACCTCTCTTCGCAAGGTCTACACCTTCGACACCGTTGAAGAGTTCTGGTG                         TTTGTATGATCAGGTATTCAAGCCCAGCAAGTTGCAAATCAATGCGGATTT
genomic: ACCTCTCTTCGCAAGGTCTACACCTTCGACACCGTTGAAGAGTTCTGGTGgtataaattt ... gctggtatagTTTGTATGATCAGGTATTCAAGCCCAGCAAGTTGCAAATCAATGCGGATTT
EST: gi|192310624|gb|FG999591.1|FG999591
EST:     ACCTCTCTTCGCAAGGTCTACACCTTCGACACCGTTGAAGAGTTCTGGTG                         TTTGTATGATCAGGTATTCAAGCCCAGCAAGTTGCAAATCAATGCGGATTT
genomic: ACCTCTCTTCGCAAGGTCTACACCTTCGACACCGTTGAAGAGTTCTGGTGgtataaattt ... gctggtatagTTTGTATGATCAGGTATTCAAGCCCAGCAAGTTGCAAATCAATGCGGATTT
EST: gi|7685617|gb|AW756265.1|AW756265
EST:     ACCTCTCTTCGCAAGGTCTACACCTTCGACACCGTTGAAGAGTTCTGGTG                         TTTGTATGATCAGGTATTCAAGCCCAGCAAGTTGCAAATCAATGCGGATTT
genomic: ACCTCTCTTCGCAAGGTCTACACCTTCGACACCGTTGAAGAGTTCTGGTGgtataaattt ... gctggtatagTTTGTATGATCAGGTATTCAAGCCCAGCAAGTTGCAAATCAATGCGGATTT
EST: gi|120533215|gb|EH261348.1|EH261348
EST:     ACCTCTCTTCGCAAGGTCTACACCTTCGACACCGTTGAAGAGTTCTGGTG                         TTTGTATGATCAGGTATTCAAGCCCAGCAAGTTGCAAATCAATGCGGATTT
genomic: ACCTCTCTTCGCAAGGTCTACACCTTCGACACCGTTGAAGAGTTCTGGTGgtataaattt ... gctggtatagTTTGTATGATCAGGTATTCAAGCCCAGCAAGTTGCAAATCAATGCGGATTT
EST: gi|298177406|gb|HO027187.1|HO027187
EST:     ACCTCTCTTCGCAAGGTCTACACCTTCGACACCGTTGAATAGTTCTGGTG                         TTTGTATGATCAGGTATTCAAGCTCAGCAAGTGGCAAATCAACGCGGATTT
genomic: ACCTCTCTTCGCAAGGTCTACACCTTCGACACCGTTGAAGAGTTCTGGTGgtataaattt ... gctggtatagTTTGTATGATCAGGTATTCAAGCCCAGCAAGTTGCAAATCAATGCGGATTT
EST: gi|23733803|gb|BU765115.1|BU765115
EST:     ACCTCTCTTCGCAAGGTCTACACCTTCGACACCGTTGAAGAGTTCTGGTG                         TTTGTATGATCAGGTATTCAAGCCCAGCAAGTTGCAAATCAATGCGGATTT
genomic: ACCTCTCTTCGCAAGGTCTACACCTTCGACACCGTTGAAGAGTTCTGGTGgtataaattt ... gctggtatagTTTGTATGATCAGGTATTCAAGCCCAGCAAGTTGCAAATCAATGCGGATTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGTTTTGGTGCGACAACCAATCCAAACCCAAACAGGGCGCTGCTTGGGGTACCTCTCTTCGCAAGGTCTACACCTTCGACACCGTTGAAGAGTTCTGGTGgtataaattttctcttcctcctccttttttctgttccacaattttcatttttctaatttcagaaaaagggaatctaagcatgcaatctcaaatcttatta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaaagg