Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcctatatctttattatgaaattgggtttattattcaattctgggtgttgaattcaattgggcatgtctaattttcagGTGGCTATGGAACTTTGGGCAAGATGGGCTCATAGAGCTCTTTGGCATGCTTCCTTGTGGCACATGCACGAG

Basic information

species Glycine max
transcript GLYMA20G30230.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G30230.2 (Glycine max), 3'ss of exon 2
lower sequence: AT4G25700.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaagtcctatatctttattatgaaattgggtttattattcaattctgggtgttgaattcaattgggcatgtctaatt-ttcagGTGGCTATGGAACTTTGGGCAAGATGGGCTCATAGAGCTCTTTGGCATGCTTCCTTGTGGCACATGCACGAG
||||||   | | ||| ||     ||||   ||| | |||||             | ||    || |  | |   ||| ||||||| | ||||||| | |||||||||||||||||||||||||| ||||| |||||  | ||| | ||||| |||
gtaagtttcaaaacttcatccc--aatt---tttctgattca---taaacaaaaaagtttggctgagatttttggattattcagGTTGGTATGGAATTCTGGGCAAGATGGGCTCATAGAGCTCTGTGGCACGCTTCTCTATGGAATATGCATGAG

upper sequence: GLYMA20G30230.2 (Glycine max), 3'ss of exon 2
lower sequence: AT5G52570.1 (Arabidopsis thaliana), 3'ss of exon 2
--------gtaagtcctatatctttattatg--aaattg----ggtttattattcaattctgggt--gttgaatt-caattgggcatgtctaattttcagGTGGCTATGGAACTTTGGGCAAGATGGGCTCATAGAGCTCTTTGGCATGCTTCCTTGTGGCACATGCACGAG
          |||| | ||| |   |  | |  |||  |         | | | ||    |       || | ||  | ||  | || | | | ||| |||| |  |||||  |||||||||||||||||||||||||||||||||||| ||| || ||| ||||||| |||
gaaaaaaacgaagttcaataaccagaacaagttaaaccgtaaaaagccaatgtccatgcttattccgattcatttatattttcgtatatttgaattttagGTTGGGATGGAGTTTTGGGCAAGATGGGCTCATAGAGCTCTTTGGCATGATTCTTTATGGAACATGCATGAG

upper sequence: GLYMA20G30230.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv16s0050g01090.t01 (Vitis vinifera), 3'ss of exon 2
----------------------------------gtaagtcctatatctttattatgaaattgggtttattattcaattctgggtgttgaattcaattgggcatgtctaattttcagGTGGCTATGGAACTTTGGGCAAGATGGGCTCATAGAGCTCTTTGGCATGCTTCCTTGTGGCACATGCACGAG
                                     ||| | | ||| |  ||  |||  |||||||   |  | |||    | |||||||  || | || || | | ||| |||||| |  |||||  | ||||| ||||||||||| | |||||| ||||| || ||||| |||||||||||||||
gtaagtgcctttttcccttcattttccttcggtttctagttccaaatcatgtttgcgaagctgggtttg--aggcgatt----gcgttgaatcgaaataggtattttttattctcagGTAGGCATGGAGTTCTGGGCGAGATGGGCTCACAAAGCTCTCTGGCACGCCTCCTTATGGCACATGCACGAG

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|11412630|gb|BF424641.1|BF424641
EST:     TTCCTTGGTCTGAAATGCTAGGCACATTTTCCCTCTCCGTCGGTGCTGCT                         GTGGCTATGGAACTTTGGGCAAGATGGGCTCATAGAGCTCTTTGGCATGCT
genomic: TTCCTTGGTCTGAAATGCTAGGCACATTTTCCCTCTCCGTCGGTGCTGCTgtaagtccta ... taattttcagGTGGCTATGGAACTTTGGGCAAGATGGGCTCATAGAGCTCTTTGGCATGCT
EST: gi|120492766|gb|EH220933.1|EH220933
EST:     TTCCTTGGTCTGAAATGCTAGGCACATTTTCCCTCTCCGTCGGTGCTGCT                         GTGGCTATGGAACTTTGGGCAAGATGGGCTCATAGAGCTCTTTGGCATGCT
genomic: TTCCTTGGTCTGAAATGCTAGGCACATTTTCCCTCTCCGTCGGTGCTGCTgtaagtccta ... taattttcagGTGGCTATGGAACTTTGGGCAAGATGGGCTCATAGAGCTCTTTGGCATGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggtttattattcaattctgggtgttgaattcaattgggcatgtctaattttcagGTGGCTATGGAACTTTGGGCAAGATGGGCTCATAGAGCTCTTTGGCATGCTTCCTTGTGGCACATGCACGAG
                                          gtctaat  putative branch site (score: 3)
                                                ttttc  CT-rich tract
     tattattcaattct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcctatatctttattatgaaattgggtttattattcaattctgggtgttgaattcaattgggcatgtctaattttcagGTGGCTATGGAACTTTGGGCAAGATGGGCTCATAGAGCTCTTTGGCATGCTTCCTTGTGGCACATGCACGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT