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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caatacaaagtaacatgcgctaaattggctgacaattgacccattgtatcacttttttgcacttaatcctttgggtttgttgactttgttgttggtttagATTATATTGGAAGATCAAGTATGTAAGCCGGCTTCAGTACCTTTGGGATGACATAAAGAAAGGAGAGATTGAGATACCGGATTTTGTGAAAAGTCATGAT

Basic information

species Glycine max
transcript GLYMA03G28460.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G28460.2 (Glycine max), 3'ss of exon 3
lower sequence: AT3G10210.1 (Arabidopsis thaliana), 3'ss of exon 2
caatacaaagtaacatgcgctaa--attggctgacaattgacccattgtatcacttttttgcacttaatcctttgggtttgttga---ctttgttgttggtttagATTATATTGGAAGATCAAGTATGTAAGCCGGCTTCAGTACCTTTGGGATGACATAAAGAAAGGAGAGATTGAGATACCGGATTTTGTGAAAAGTCATGAT
    |    ||||| ||        || || |    |||     |   |   ||   | || ||||||   ||| |        |   || | |      |  ||| | || |||||||| ||||| || ||| || | |||||||||||||| |||||||||||||| ||| | || || || || |||||||| |  ||||| 
----agcttgtaacttgaaacggttatgggatctagattactttagaat-caacaactgtggacttaactgttttgtcaaaacaatatctctttcaacattgcagACTGTACTGGAAGATTAAGTACGTGAGCAGGTTGCAGTACCTTTGGGAGGACATAAAGAAAGGCGAGGTGGAAATTCCCGACTTTGTGAAGAACCATGAC

upper sequence: GLYMA03G28460.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv08s0007g05700.t01 (Vitis vinifera), 3'ss of exon 2
---caatacaaagtaacatgcgctaaattggctgac--aattgacccattgtatcacttttttgcacttaatcctttgggtttgttgactttgttgttggtttagATTATATTGGAAGATCAAGTATGTAAGCCGGCTTCAGTACCTTTGGGATGACATAAAGAAAGGAGAGATTGAGATACCGGATTTTGTGAAAAGTCATGAT
    | | |   || | | | | ||||     |  |  | |||    ||||  | |     |      | ||  |   | | ||||| |||   |||      || ||||| ||||| ||||||||||| ||||| || |||||||||||||| ||  ||||||| |||||| | ||||| || || |||||| |||| ||||||
gaatagttcctggtgataagtgataaacccattctcttatttgcattattgagttaacaagtc-tgtgtcatgatcaagatgtgttgccttctctgtg----cagCTTATACTGGAAAATCAAGTATGTCAGCCGCCTGCAGTACCTTTGGGAAGATGTAAAGAAGGGAGAGGTCGAGATTCCTGAATTTGTGCAAAGCCATGAT
















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|193595199|gb|FK553932.1|FK553932
EST:     CGGTCCCGGCTAGTCATCGCTACTCTTGGCCGCTTTTTCTTGAGTGGAGG                         ATTATATTGGAAGATCAAGTATGTAAGCCGGCTTCAGTACCTTTGGGATGA
genomic: CGGTCCCGGCTAGTCATCGCTACTCTTGGCCGCTTTTTCTTGAGTGGAGGgtaactcatc ... gttggtttagATTATATTGGAAGATCAAGTATGTAAGCCGGCTTCAGTACCTTTGGGATGA
EST: gi|208195491|gb|GD989908.1|GD989908
EST:     CGGTCCCGGCTAGTCATCGCTACTCTTGGCCGCTTTTTCTTGAGTGGAGG                         ATTATATTGGAAGATCAAGTATGTAAGCCGG
genomic: CGGTCCCGGCTAGTCATCGCTACTCTTGGCCGCTTTTTCTTGAGTGGAGGgtaactcatc ... gttggtttagATTATATTGGAAGATCAAGTATGTAAGCCGG
EST: gi|207710486|gb|GD690722.1|GD690722
EST:     CGGTCCCGGCTAGTCATCGCTACTCTTGGCCGCTTTTTCTTGAGTGGAGG                         ATTATATTGGAAGATCAAGTATGTAAGCCGGCTTCAGTACCTTTGGGATGA
genomic: CGGTCCCGGCTAGTCATCGCTACTCTTGGCCGCTTTTTCTTGAGTGGAGGgtaactcatc ... gttggtttagATTATATTGGAAGATCAAGTATGTAAGCCGGCTTCAGTACCTTTGGGATGA
EST: gi|209707267|gb|BW670586.1|BW670586
EST:     CGGTCCCGGCTAGTCATCGCTACTCTTGGCCGCTTTTTCTTGAGTGGAGG                         ATTATATTGGAAGATCAAGTATGTAAGCCGGCTTCAGTACCTTTGGGATGA
genomic: CGGTCCCGGCTAGTCATCGCTACTCTTGGCCGCTTTTTCTTGAGTGGAGGgtaactcatc ... gttggtttagATTATATTGGAAGATCAAGTATGTAAGCCGGCTTCAGTACCTTTGGGATGA
EST: gi|24205443|gb|BU964696.1|BU964696
EST:     CGGTCCCGGCTAGTCATCGCTACTCTTGGCCGCTTTTTCTTGAGTGGAGG                         ATTATATTGGAAGATCAAGTATGTAAGCCGGCTTCAGTACCTTTGGGATGA
genomic: CGGTCCCGGCTAGTCATCGCTACTCTTGGCCGCTTTTTCTTGAGTGGAGGgtaactcatc ... gttggtttagATTATATTGGAAGATCAAGTATGTAAGCCGGCTTCAGTACCTTTGGGATGA
EST: gi|11273682|gb|BF324140.1|BF324140
EST:     CGGTCCCGGCTAGTCATCGCTACTCTTGGCCGCTTTTTCTTGAGTGGAGG                         ATTATATTGGAAGATCAAGTATGTAAGCCGGCTTCAGTACCTTTGGGATGA
genomic: CGGTCCCGGCTAGTCATCGCTACTCTTGGCCGCTTTTTCTTGAGTGGAGGgtaactcatc ... gttggtttagATTATATTGGAAGATCAAGTATGTAAGCCGGCTTCAGTACCTTTGGGATGA
EST: gi|208195719|gb|GD989968.1|GD989968
EST:     CGGTCCCGGCTAGTCATCGCTACTCTTGGCCGCTTTTTCTTGAGTGGAGG                         ATTATATTGGAAGATCAAGTATGTAAGCCGGCTTCAGTACCTTTG
genomic: CGGTCCCGGCTAGTCATCGCTACTCTTGGCCGCTTTTTCTTGAGTGGAGGgtaactcatc ... gttggtttagATTATATTGGAAGATCAAGTATGTAAGCCGGCTTCAGTACCTTTG
EST: gi|193300009|gb|FK266266.1|FK266266
EST:     CGGTCCCGGCTAGTCATCGCTACTCTTGGCCGCTTTT-CTTGAGTGGAGG                         ATTATATTGGAAGATCAAGTATGTAAGCCGGCTTCAGTACCTT
genomic: CGGTCCCGGCTAGTCATCGCTACTCTTGGCCGCTTTTTCTTGAGTGGAGGgtaactcatc ... gttggtttagATTATATTGGAAGATCAAGTATGTAAGCCGGCTTCAGTACCTT
EST: gi|207738071|gb|GD715079.1|GD715079
EST:     CGGTCCCGGCTAGTCATCGCTACTCTTGGCCGCTTTTTCTTGAGTGGAGG                         ATTTATATTTGGAAG
genomic: CGGTCCCGGCTAGTCATCGCTACTCTTGGCCGCTTTTTCTTGAGTGGAGGgtaactcatc ... gttggtttagATT-ATATT-GGAAG
EST: gi|192314396|gb|FK008394.1|FK008394
EST:     TTTTTCTTGAGTGGAGG                         ATTATATTGGAAGATCAAGTATGTAAGCCGGCTTCAGTACCTTTGGGATGA
genomic: TTTTTCTTGAGTGGAGGgtaactcatc ... gttggtttagATTATATTGGAAGATCAAGTATGTAAGCCGGCTTCAGTACCTTTGGGATGA
EST: gi|193375524|gb|FK341665.1|FK341665
EST:     CGGTCCCGGCTAGTCATCGCTACTCTTGGCCGCTTTTTCTTGAGTGGAGG                         ATTATATTGGAAGATCAA
genomic: CGGTCCCGGCTAGTCATCGCTACTCTTGGCCGCTTTTTCTTGAGTGGAGGgtaactcatc ... gttggtttagATTATATTGGAAGATCAA
EST: gi|209728759|gb|BW666809.1|BW666809
EST:     CGGTCCCGGCTAGTCATCGCTACTCTTGGCCGCTTTTTCTTGAGTGGAGG                         ATTATATTGGAAGATCAAGTATGTAAGCCGGCTTCAGTACCTTTGGGATGA
genomic: CGGTCCCGGCTAGTCATCGCTACTCTTGGCCGCTTTTTCTTGAGTGGAGGgtaactcatc ... gttggtttagATTATATTGGAAGATCAAGTATGTAAGCCGGCTTCAGTACCTTTGGGATGA
EST: gi|207698363|gb|GD680602.1|GD680602
EST:     CGGTCCCGGCTAGTCATCGCTACTCTTGGCCGCTTTTTCTTGAGTGGAGG                         ATTATATTGGAAGATCAAGTATGTAAGCCGGCTTCAGTACCTTTGGGATGA
genomic: CGGTCCCGGCTAGTCATCGCTACTCTTGGCCGCTTTTTCTTGAGTGGAGGgtaactcatc ... gttggtttagATTATATTGGAAGATCAAGTATGTAAGCCGGCTTCAGTACCTTTGGGATGA
EST: gi|207801461|gb|GD773853.1|GD773853
EST:     CGGTCCCGGCTAGTCATCGCTACTCTTGGCCGTTTTTTCTTGAGTGGAGG                         ATTATATTGGAAGATCAAGTATGTAAGCCGGCTTCAGTACCTTTGGGATGA
genomic: CGGTCCCGGCTAGTCATCGCTACTCTTGGCCGCTTTTTCTTGAGTGGAGGgtaactcatc ... gttggtttagATTATATTGGAAGATCAAGTATGTAAGCCGGCTTCAGTACCTTTGGGATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatcacttttttgcacttaatcctttgggtttgttgactttgttgttggtttagATTATATTGGAAGATCAAGTATGTAAGCCGGCTTCAGTACCTTTGGGATGACATAAAGAAAGGAGAGATTGAGATACCGGATTTTGTGAAAAGTCATGAT
                                tgttgac  putative branch site (score: 3)
     actttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caatacaaagtaacatgcgctaaattggctgacaattgacccattgtatcacttttttgcacttaatcctttgggtttgttgactttgttgttggtttagATTATATTGGAAGATCAAGTATGTAAGCCGGCTTCAGTACCTTTGGGATGACATAAAGAAAGGAGAGATTGAGATACCGGATTTTGTGAAAAGTCATGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA