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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcactattcttttggcaacaaggttcacttgcagcatagaatggtacagaatagaatgatttgaattacttaaacttatttattgcccttctttctgcagTTTGTTGTTAAAAAGGGCCGTGTTTTGACCCCTCATGCTGATTACTGTCTTCCTGGCATTACTCGTGCAACT

Basic information

species Glycine max
transcript GLYMA03G40000.2
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G40000.1 (Glycine max), 3'ss of exon 15
lower sequence: LOC_Os03g24460.3 (Oryza sativa), 3'ss of exon 15
--------------------tcactattcttttggcaacaaggttcact-tgcagcatagaatggtacagaatagaatgatttga---attacttaaacttatt-----tattgcccttctttctgcagTTTGTTGTTAAAAAGGGCCGTGTTTTGACCCCTCATGCTGATTACTGTCTTCCTGGCATTACTCGTGCAACT----------------------------
                    ||| ||   | |    ||   |  ||| | |     || ||| |  | ||  ||     |||| |   || ||||    ||  |     |    |  |  |   |||||||| | ||||| ||||||  ||| ||||| ||||||||||| ||||| ||||| |||||||| |||||||||                            
gtaagtgtacatggctgttatcattaacatatctcgaatttgcctcaatattttttattgaaggagagagtttacctcaattttattcataacttttgttttctaaaaatgccactgtgttaattgcagTTTATGGTTAAGAAGGGCATTGTGTTGACACCTCATGCTGAGTACTGCCTTCCAGGCATTACGCGTGCAACTGTAAGTCTAATCAGGTTCCAGTTGGAAA

upper sequence: GLYMA03G40000.1 (Glycine max), 3'ss of exon 15
lower sequence: LOC_Os03g24460.2 (Oryza sativa), 3'ss of exon 15
--------------------tcactattcttttggcaacaaggttcact-tgcagcatagaatggtacagaatagaatgatttga---attacttaaacttatt-----tattgcccttctttctgcagTTTGTTGTTAAAAAGGGCCGTGTTTTGACCCCTCATGCTGATTACTGTCTTCCTGGCATTACTCGTGCAACT
                    ||| ||   | |    ||   |  ||| | |     || ||| |  | ||  ||     |||| |   || ||||    ||  |     |    |  |  |   |||||||| | ||||| ||||||  ||| ||||| ||||||||||| ||||| ||||| |||||||| |||||||||
gtaagtgtacatggctgttatcattaacatatctcgaatttgcctcaatattttttattgaaggagagagtttacctcaattttattcataacttttgttttctaaaaatgccactgtgttaattgcagTTTATGGTTAAGAAGGGCATTGTGTTGACACCTCATGCTGAGTACTGCCTTCCAGGCATTACGCGTGCAACT

upper sequence: GLYMA03G40000.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv14s0128g00100.t01 (Vitis vinifera), 3'ss of exon 25
---tcactattcttttggcaacaaggt--tcacttgcagcatagaatggtacagaatagaatgatttgaattacttaaacttatttattgcccttctttctgcagTTTGTTGTTAAAAAGGGCCGTGTTTTGACCCCTCATGCTGATTACTGTCTTCCTGGCATTACTCGTGCAACT
   || || |  |  | | ||  | |   || |||| || ||  | || |   || |  |  || ||   | ||| |||  ||||   |    ||| |  |||||||  | || || || || | |||| |||| ||||||||||||||||| |||||||| || ||||| || |||
ctttcgctctcatcattgaaaagaagcagtcccttgaag-attcattgattttgactgta--gacttcc-tgactgaaaaatattc-ctctgtttcatattgcagTTCTTAGTGAAGAAAGGTCATGTTCTGACACCTCATGCTGATTACTGCCTTCCTGGGATAACTCGAGCTACT

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|16996517|gb|BM085889.1|BM085889
EST:     TCATGCTCGACCAAGATGGTTATTTATCAGAAACCAATGCAACTAACATT                         TTTGTTGTTAAAAAGGGCCGTGTTTTGACCCCTCATGCTGATTACTGTCTT
genomic: TCATGCTCGACCAAGATGGTTATTTATCAGAAACCAATGCAACTAACATTgtatgtcctc ... ctttctgcagTTTGTTGTTAAAAAGGGCCGTGTTTTGACCCCTCATGCTGATTACTGTCTT
EST: gi|6724770|gb|AW309169.1|AW309169
EST:     TCATGCTCGACCAAGATGGTTATTTATCAGAAACCAATGCAACTAACATT                         TTTGTTGTTAAAAAGGGCCGTGTTTTGACCCCTCATGCTGATTACTGTCTT
genomic: TCATGCTCGACCAAGATGGTTATTTATCAGAAACCAATGCAACTAACATTgtatgtcctc ... ctttctgcagTTTGTTGTTAAAAAGGGCCGTGTTTTGACCCCTCATGCTGATTACTGTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acagaatagaatgatttgaattacttaaacttatttattgcccttctttctgcagTTTGTTGTTAAAAAGGGCCGTGTTTTGACCCCTCATGCTGATTACTGTCTTCCTGGCATTACTCGTGCAACT
                             cttatttattgccctt  CT-rich tract
     atagaatgatttgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcactattcttttggcaacaaggttcacttgcagcatagaatggtacagaatagaatgatttgaattacttaaacttatttattgcccttctttctgcagTTTGTTGTTAAAAAGGGCCGTGTTTTGACCCCTCATGCTGATTACTGTCTTCCTGGCATTACTCGTGCAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT