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

gtgagtgctgccatcaattacttctctttttcatgtgaggattatttatttggtggctctgtgtttgatatgtttgttcggttttctttgaatgacagATGGGAGAGCTTAAAAGGCTGGTCCAAGAGGGAAAAATAAGGTACATAGGATTGTCGGAAGCTAGCCCTGACACAATTAGGAGGGCACATGCTGTTCATC

Basic information

species Glycine max
transcript GLYMA03G40680.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G40680.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv14s0030g02050.t01 (Vitis vinifera), 3'ss of exon 3
---------------------------gtgagtgctgccatcaattacttctctttttcatgtgaggattatttatttggtggctctgtgtttgatatgtttgttcggt--tttctttgaatg------------------acagATGGGAGAGCTTAAAAGGCTGGTCCAAGAGGGAAAAATAAGGTACATAGGATTGTCGGAAGCTAGCCCTGACACAATTAGGAGGGCACATGCTGTTCATC
                            ||| | ||   ||    | |  |||  | |   |   ||| | ||  |||    |||    ||||    | |||     ||   |||||| || |                  | ||||||| |||||||| | | ||||  ||||||||||||| | |||||| ||||| || ||||||||||| |||||||| |||||||| |||||||||||||
gtaagtgttacatttttactctttttaatgaattcttaaattttcttcaactccatgttcagaatggacttttctttttactgcttcaagtttacattattttactagtaccttctttaaaagtcttttttgtgcaataacatagATGGGGGAGCTTAAGAAGTTGGTTGAAGAGGGAAAAATTAAGTACATTGGATTATCTGAAGCTAGCCCAGACACAATAAGGAGGGCTCATGCTGTTCATC
















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|192325845|gb|FK018067.1|FK018067
EST:     ATCTCTATTATCAGCACCGTGTTGACACAACTGTACCCATTGAAGACACC                         ATGGGAGAGCTTAAAAGGCTGGTCCAAGAGGGAAAAATAAGGTACATAGGA
genomic: ATCTCTATTATCAGCACCGTGTTGACACAACTGTACCCATTGAAGACACCgtgagtgctg ... tgaatgacagATGGGAGAGCTTAAAAGGCTGGTCCAAGAGGGAAAAATAAGGTACATAGGA
EST: gi|192332295|gb|FK025960.1|FK025960
EST:     ATCTCTATTATCAGCACCGTGTTGACACAACTGTACCCATTGAAGACACC                         ATGGGAGAGCTTAAAAGGCTGGTCCAAGAGGGAAAAATAAGGTACATAGGA
genomic: ATCTCTATTATCAGCACCGTGTTGACACAACTGTACCCATTGAAGACACCgtgagtgctg ... tgaatgacagATGGGAGAGCTTAAAAGGCTGGTCCAAGAGGGAAAAATAAGGTACATAGGA
EST: gi|4396672|gb|AI495669.1|AI495669
EST:     ATCTCTATTATCAGCACCGTGTTGACACAACTGTACCCATTGAAGACACC                         ATGNGAGAGCTTAAAAG
genomic: ATCTCTATTATCAGCACCGTGTTGACACAACTGTACCCATTGAAGACACCgtgagtgctg ... tgaatgacagATGGGAGAGCTTAAAAG
EST: gi|298168820|gb|HO009750.1|HO009750
EST:     ATCTCTATTATCAGCACCGTGTTGACACAACTGTACCCATTGAAGACACC                         ATGGGAGAGCTTAAAAGGCTGGTCCAAGAGGGAAAAATAAGGTACATAGGA
genomic: ATCTCTATTATCAGCACCGTGTTGACACAACTGTACCCATTGAAGACACCgtgagtgctg ... tgaatgacagATGGGAGAGCTTAAAAGGCTGGTCCAAGAGGGAAAAATAAGGTACATAGGA
EST: gi|192334362|gb|FK025539.1|FK025539
EST:     ATCTCTATTATCAGCACCGTGTTGACACAACTGTACCCATTGAAGACACC                         ATGGGAGAGCTTAAAA
genomic: ATCTCTATTATCAGCACCGTGTTGACACAACTGTACCCATTGAAGACACCgtgagtgctg ... tgaatgacagATGGGAGAGCTTAAAA
EST: gi|151410675|gb|EV280490.1|EV280490
EST:     ATCTCTATTATCAGCACCGTGTTGACACAACTGTACCCATTGAAGACACC                         ATGGGAGAGCTTAAAAGGCTGGTCCAAGAGGGAAAAATAAGGTACATAGGA
genomic: ATCTCTATTATCAGCACCGTGTTGACACAACTGTACCCATTGAAGACACCgtgagtgctg ... tgaatgacagATGGGAGAGCTTAAAAGGCTGGTCCAAGAGGGAAAAATAAGGTACATAGGA
EST: gi|192314627|gb|FK006385.1|FK006385
EST:     ATCTCTATTATCAGCACCGTGTTGACACAACTGTACCCATTGAAGACACC                         ATGGGAGAGCTTAAAAGGCTGGTCCAAGAGGGAAAAATAAGGTACATAGGA
genomic: ATCTCTATTATCAGCACCGTGTTGACACAACTGTACCCATTGAAGACACCgtgagtgctg ... tgaatgacagATGGGAGAGCTTAAAAGGCTGGTCCAAGAGGGAAAAATAAGGTACATAGGA
EST: gi|38192837|gb|CF922043.1|CF922043
EST:     ATCTCTATTATCAGCACCGTGTTGACACAACTGTACCCATTGAAGACACC                         ATGGGAGAGCTTAAAAGGCTGGTCCAAGAGGGAAAAATAAG
genomic: ATCTCTATTATCAGCACCGTGTTGACACAACTGTACCCATTGAAGACACCgtgagtgctg ... tgaatgacagATGGGAGAGCTTAAAAGGCTGGTCCAAGAGGGAAAAATAAG
EST: gi|298165604|gb|HO011653.1|HO011653
EST:     ATCTCTATTATCAGCACCGTGTTGACACAACTGTACCCATTGAAGACACC                         ATGGGAGAGCTTAAAAGGCTGGTCCAAGAGGGAAAAATAAGGTACATAGGA
genomic: ATCTCTATTATCAGCACCGTGTTGACACAACTGTACCCATTGAAGACACCgtgagtgctg ... tgaatgacagATGGGAGAGCTTAAAAGGCTGGTCCAAGAGGGAAAAATAAGGTACATAGGA
EST: gi|14125225|gb|BG789655.1|BG789655
EST:     ATCTCTATTATCAGCACCGTGTTGACACAACTGTACCCATTGAAGACACC                         ATGGGAGAGCTTAAAAGGCTGGTCCAAGAGGGAAAAATAAGGTACATAGGA
genomic: ATCTCTATTATCAGCACCGTGTTGACACAACTGTACCCATTGAAGACACCgtgagtgctg ... tgaatgacagATGGGAGAGCTTAAAAGGCTGGTCCAAGAGGGAAAAATAAGGTACATAGGA
EST: gi|151411705|gb|EV281516.1|EV281516
EST:     ATCTCTATTATCAGCACCGTGTTGACACAACTGTACCCATTGAAGACACC                         ATGGGAGAGCTTAAAAGGCTGGTCCAAGAGGGAAAAATAAGGTACATAGGA
genomic: ATCTCTATTATCAGCACCGTGTTGACACAACTGTACCCATTGAAGACACCgtgagtgctg ... tgaatgacagATGGGAGAGCTTAAAAGGCTGGTCCAAGAGGGAAAAATAAGGTACATAGGA
EST: gi|13481916|gb|BG511259.1|BG511259
EST:     ATCTCTATTATCAGCACCGTGTTGACACAACTGTACCCATTGAAGACACC                         ATGGGAGAGCTTAAAAGGCTGGTCCAAGAGGGAAAAATAAGGTACATAGGA
genomic: ATCTCTATTATCAGCACCGTGTTGACACAACTGTACCCATTGAAGACACCgtgagtgctg ... tgaatgacagATGGGAGAGCTTAAAAGGCTGGTCCAAGAGGGAAAAATAAGGTACATAGGA
EST: gi|209699281|gb|BW670243.1|BW670243
EST:     ATCTCTATTATCAGCACCGTGTTGACACAACTGTACCCATTGAAGACACC                         ATGGGAGAGCTTAAAAGGCTGGTCCAAGAGGGAAAAATAAGGTACATAGGA
genomic: ATCTCTATTATCAGCACCGTGTTGACACAACTGTACCCATTGAAGACACCgtgagtgctg ... tgaatgacagATGGGAGAGCTTAAAAGGCTGGTCCAAGAGGGAAAAATAAGGTACATAGGA
EST: gi|12773659|gb|BG238586.1|BG238586
EST:     ATCTCTATTATCAGCACCGTGTTGACACAACTGTACCCATTGAAGACACC                         ATGGGAGAGCTTAAAAGGCTGGTCCAAGAGGGAAAAATAAGGTACATAGGA
genomic: ATCTCTATTATCAGCACCGTGTTGACACAACTGTACCCATTGAAGACACCgtgagtgctg ... tgaatgacagATGGGAGAGCTTAAAAGGCTGGTCCAAGAGGGAAAAATAAGGTACATAGGA
EST: gi|151398884|gb|EV268755.1|EV268755
EST:     ATCTCTATTATCAGCACCGTGTTGACACAACTGTACCCATTGAAGACACC                         ATGGGAGAGCTTAAAAGGCTGGTCCAAGAGGGAAAAATAAGGTACATGGGA
genomic: ATCTCTATTATCAGCACCGTGTTGACACAACTGTACCCATTGAAGACACCgtgagtgctg ... tgaatgacagATGGGAGAGCTTAAAAGGCTGGTCCAAGAGGGAAAAATAAGGTACATAGGA
EST: gi|192298309|gb|FG992099.1|FG992099
EST:     ATCTCTATTATCAGCACCGTGTTGACACAACTGTACCCATTGAAGACACC                         ATGGGAGAGCTTAAAAGGCTGGTCCAAGAGGGAAAA
genomic: ATCTCTATTATCAGCACCGTGTTGACACAACTGTACCCATTGAAGACACCgtgagtgctg ... tgaatgacagATGGGAGAGCTTAAAAGGCTGGTCCAAGAGGGAAAA
EST: gi|42722439|gb|CK768339.1|CK768339
EST:     ATCTCTATTATCAGCACCGTGTTGACACAACTGTACCCATTGAAGACACC                         ATGGGAGAGCTTAAAAGGCTGGTCCAAGAGGGAAAAATAAGGTACATAGGA
genomic: ATCTCTATTATCAGCACCGTGTTGACACAACTGTACCCATTGAAGACACCgtgagtgctg ... tgaatgacagATGGGAGAGCTTAAAAGGCTGGTCCAAGAGGGAAAAATAAGGTACATAGGA
EST: gi|192329671|gb|FK022937.1|FK022937
EST:     ATCTCTATTATCAGCACCGTGTTGACACAACTGTACCCATTGAAGACACC                         ATGGGAGAGCTTAAAAGGCTGGTCCAAGAGGGAAAAA
genomic: ATCTCTATTATCAGCACCGTGTTGACACAACTGTACCCATTGAAGACACCgtgagtgctg ... tgaatgacagATGGGAGAGCTTAAAAGGCTGGTCCAAGAGGGAAAAA
EST: gi|209701736|gb|BW667401.1|BW667401
EST:     ATCTCTATTATCAGCACCGTGTTGACACAACTGTACCCATTGAAGACACC                         ATGGGAGAGCTTAAAAGGCTGGTCCAAGAGGGAAAAATAAGGTACATAGGA
genomic: ATCTCTATTATCAGCACCGTGTTGACACAACTGTACCCATTGAAGACACCgtgagtgctg ... tgaatgacagATGGGAGAGCTTAAAAGGCTGGTCCAAGAGGGAAAAATAAGGTACATAGGA
EST: gi|7146862|gb|AW508784.1|AW508784
EST:     ATCTCTATTATCAGCACCGTGTTGACACAACTGTACCCATTGAAGACACC                         ATGGGAGAGCTTAAAAGGCTGGTCCTAGAGGGAAAAATAATGTACATAGGA
genomic: ATCTCTATTATCAGCACCGTGTTGACACAACTGTACCCATTGAAGACACCgtgagtgctg ... tgaatgacagATGGGAGAGCTTAAAAGGCTGGTCCAAGAGGGAAAAATAAGGTACATAGGA
EST: gi|213603469|gb|DB966620.1|DB966620
EST:     ATCTCTATTATCAGCACCGTGTTGACACAACTGTACCCATTGAAGACACC                         ATGGGAGAGCTTAAAAGGCTGATCCAAGAGGGAAAAATAAGGTACATAGGA
genomic: ATCTCTATTATCAGCACCGTGTTGACACAACTGTACCCATTGAAGACACCgtgagtgctg ... tgaatgacagATGGGAGAGCTTAAAAGGCTGGTCCAAGAGGGAAAAATAAGGTACATAGGA
EST: gi|192314626|gb|FK006384.1|FK006384
EST:     ATCTCTATTATCAGCACCGTGTTGACACAACTGTACCCATTGAAGACACC                         ATGGGAGAGCTTAAAAGGCTGGTCCAAGAGGGAAAAATAAGGTACATAGGA
genomic: ATCTCTATTATCAGCACCGTGTTGACACAACTGTACCCATTGAAGACACCgtgagtgctg ... tgaatgacagATGGGAGAGCTTAAAAGGCTGGTCCAAGAGGGAAAAATAAGGTACATAGGA
EST: gi|254315362|gb|GR825171.1|GR825171
EST:     ATCTCTATTATCAGCACCGTGTTGACACAACTGTACCCATTGAAGACACC                         ATGGGAGAGCTTAAAAGGCTGGTCCAAGAGGGAAAAATAAGGTACATAGGA
genomic: ATCTCTATTATCAGCACCGTGTTGACACAACTGTACCCATTGAAGACACCgtgagtgctg ... tgaatgacagATGGGAGAGCTTAAAAGGCTGGTCCAAGAGGGAAAAATAAGGTACATAGGA
EST: gi|298181942|gb|HO026117.1|HO026117
EST:     ATCTCTATTATCAGCACCGTGTTGACACAACTGTACCCATTGAAGACACC                         ATGGGAGAGCTTAAAAGGCTGGTCCAAGAGGGAAAAATAAGGTACATAGGA
genomic: ATCTCTATTATCAGCACCGTGTTGACACAACTGTACCCATTGAAGACACCgtgagtgctg ... tgaatgacagATGGGAGAGCTTAAAAGGCTGGTCCAAGAGGGAAAAATAAGGTACATAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttatttggtggctctgtgtttgatatgtttgttcggttttctttgaatgacagATGGGAGAGCTTAAAAGGCTGGTCCAAGAGGGAAAAATAAGGTACATAGGATTGTCGGAAGCTAGCCCTGACACAATTAGGAGGGCACATGCTGTTCATC
                   gtttgat  putative branch site (score: 5)
                                      ttttcttt  putative PPT
                    tttgatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgctgccatcaattacttctctttttcatgtgaggattatttatttggtggctctgtgtttgatatgtttgttcggttttctttgaatgacagATGGGAGAGCTTAAAAGGCTGGTCCAAGAGGGAAAAATAAGGTACATAGGATTGTCGGAAGCTAGCCCTGACACAATTAGGAGGGCACATGCTGTTCATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT