Sequence
atgc intronic sequence ATGC exonic sequence...ctctgtaagtgctgcgatttttttttttttttaatttatgaacttaaagatggtgggataattttcttttcgtgacaactcatgtgcttatagtatacagAGACTGGAGCCTGAGAAGAAAAGGAGAATTTATGGAGGACGGCGCAGGAAGAGGTTTGGAATGCCCGAAGACTATGGATGGGAAGGCGAGTAACGGGAAT
Basic information
species | Glycine max |
transcript | GLYMA06G13210.3 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G13210.3 (Glycine max), 3'ss of exon 1
lower sequence: AT5G53120.1 (Arabidopsis thaliana), 3'ss of exon 1
-----ctctgta-agtgctgcgatttttttt--tttttttaatttatgaacttaaagatggtgggataattttcttttcgtgacaactcatgtgcttatagtatacagAGACTGGAGCCTGAGAAGAAAAGGAGAATTTATGGAGGACGGCGCAGGAAGAGGTTTGGAATGCCCGAAGACTATGGATGGGAAGGCGAGTAACGGGAAT
||| | | | || | |||||| | ||||| |||| || | | | | ||| | ||| || | || | | ||| | |||||||||||| ||||||| | ||||||||||| | |||||||| | || |||| |||||||| ||||| ||| |||||||||||||||||||||||
ctgaaatctattcaacggtgttagttttttaagtctttttgatttttgtgccttcaagttgtgtgtggattctcatggtttg-ctgtttttgtttgtgtagTATACAGAGGCTGGAGCTGGGGAAGAAAAGGATTGTCTATGGAGGGAGACGTCGGAATAGGTTTGGTATGCCAGAATACTATGGATGGGAAGGCGAGTAA-------
upper sequence: GLYMA06G13210.3 (Glycine max), 3'ss of exon 1
lower sequence: AT5G53120.5 (Arabidopsis thaliana), 3'ss of exon 1
ctctgtaagtgctgcgatttttttttttttttaatttatgaacttaaagatggtgggataattttcttttcgtgacaactcatgtgcttatagtatacagAGACTGGAGCCTGAGAAGAAAAGGAGAATTTATGGAGGACGGCGCAGGAAGAGGTTTGGAATGCCCGAAGACTATGGATGGGAAGGCGAGTAACGGGAAT
||| | | ||||| | ||||| |||| || | | | | ||| | ||| || | || | | ||| | |||||||||||| ||||||| | ||||||||||| | |||||||| | || |||| |||||||| ||||| ||| |||||||||||||||||||||||
--------gtgtta-gttttttaagtctttttgatttttgtgccttcaagttgtgtgtggattctcatggtttg-ctgtttttgtttgtgtagTATACAGAGGCTGGAGCTGGGGAAGAAAAGGATTGTCTATGGAGGGAGACGTCGGAATAGGTTTGGTATGCCAGAATACTATGGATGGGAAGGCGAGTAA-------
upper sequence: GLYMA06G13210.3 (Glycine max), 3'ss of exon 1
lower sequence: AT5G53120.2 (Arabidopsis thaliana), 3'ss of exon 1
ctctgtaagtgctgcgatttttttt-tttttttaatttatgaacttaaagatggtgggataattttcttttcgtgacaactcatgtgcttatagtatacagAGACTGGAGCCTGAGAAGAAAAGGAGAATTTATGGAGGACGGCGCAGGAAGAGGTTTGGAATGCCCGAAGACTATGGATGGGAAGGCGAGTAACGGGAAT
|| | || | |||||| | ||||| |||| || | | | | ||| | ||| || | || | | ||| | |||||||||||| ||||||| | ||||||||||| | |||||||| | || |||| |||||||| ||||| ||| ||||||||||||||||||||||| || |||
ctattcaacggtgttagttttttaagtctttttgatttttgtgccttcaagttgtgtgtggattctcatggtttg-ctgtttttgtttgtgtagtatacagAGGCTGGAGCTGGGGAAGAAAAGGATTGTCTATGGAGGGAGACGTCGGAATAGGTTTGGTATGCCAGAATACTATGGATGGGAAGGCGAGTAATGGAAAT
upper sequence: GLYMA06G13210.3 (Glycine max), 3'ss of exon 1
lower sequence: AT5G53120.4 (Arabidopsis thaliana), 3'ss of exon 2
ctctgtaagtgctgcgatttttttttttttttaatttatgaacttaaagatggtgggataattttcttttcgtgacaactcatgtgcttatagtatacagAGACTGGAGCCTGAGAAGAAAAGGAGAATTTATGGAGGACGGCGCAGGAAGAGGTTTGGAATGCCCGAAGACTATGGATGGGAAGGCGAGTAACGGGAAT
| | | ||||| | ||||| |||| || | | | | ||| | ||| || | || | | ||| | |||||||||||| ||||||| | ||||||||||| | |||||||| | || |||| |||||||| ||||| ||| |||||||||||||||||||||||
----------gtta-gttttttaagtctttttgatttttgtgccttcaagttgtgtgtggattctcatggtttg-ctgtttttgtttgtgtagTATACAGAGGCTGGAGCTGGGGAAGAAAAGGATTGTCTATGGAGGGAGACGTCGGAATAGGTTTGGTATGCCAGAATACTATGGATGGGAAGGCGAGTAA-------
upper sequence: GLYMA06G13210.3 (Glycine max), 3'ss of exon 1
lower sequence: Vv16s0050g02670.t01 (Vitis vinifera), 3'ss of exon 1
-----ctctgtaag-tgctgcgatttttttttttttttaat--ttatgaacttaaagatggtgggataattttcttttcgtgacaactcatgtgcttatagtatacagAGACTGGAGCCTGAGAAGAAAAGGAGAATTTATGGAGGACGGCGCAGGAAGAGGTTTGGAATGCCCGAAGACTATGGATGGGAAGGCGAGTAACGGGAAT
| | | | || | || | | || || ||| | || || || | || | | | |||| || || | | ||||||||||||| |||||||||| || ||| |||||||| ||||||||||| |||||||||||||||||||| ||||||||||||||||||||||||||
catattttgatgggattttgaagtgaaacattcaatatgatggctactgccttttctactatgaga-aactccattcttcttataact---atgtttg--atttctAGAGACTGGAGCCGGAGAAGAAAAAGATAATCTATGGAGGGCGGCGCAGGAAAAGGTTTGGAATGCCCGAAGATTATGGATGGGAAGGCGAGTAACGGGA--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|151394500|gb|EV264371.1|EV264371EST: TTGTTTGGGTTCGTTCGCCTTCACTCTCCGACATTCATATCATTCATCAG AGACTGGAGCCTGAGAAGAAAAGGAGAATTTATGGAGGACGGCGCAGGAAG
genomic: TTGTTTGGGTTCGTTCGCCTTCACTCTCCGACATTCATATCATTCATCAGgcaagcaacg ... tagtatacagAGACTGGAGCCTGAGAAGAAAAGGAGAATTTATGGAGGACGGCGCAGGAAG
EST:
gi|192325742|gb|FK015099.1|FK015099EST: TTGTTTGGGTTCGTTCGCCTTCACTCTCCGACATTCATATCATTCATCAG AGACTGGAGCCTGAGAAGAAAAGGAGAATTTATGGAGGACGGCGCAGAAAG
genomic: TTGTTTGGGTTCGTTCGCCTTCACTCTCCGACATTCATATCATTCATCAGgcaagcaacg ... tagtatacagAGACTGGAGCCTGAGAAGAAAAGGAGAATTTATGGAGGACGGCGCAGGAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaagatggtgggataattttcttttcgtgacaactcatgtgcttatagtatacagAGACTGGAGCCTGAGAAGAAAAGGAGAATTTATGGAGGACGGCGCAGGAAGAGGTTTGGAATGCCCGAAGACTATGGATGGGAAGGCGAGTAACGGGAAT
ataattttctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctctgtaagtgctgcgatttttttttttttttaatttatgaacttaaagatggtgggataattttcttttcgtgacaactcatgtgcttatagtatacagAGACTGGAGCCTGAGAAGAAAAGGAGAATTTATGGAGGACGGCGCAGGAAGAGGTTTGGAATGCCCGAAGACTATGGATGGGAAGGCGAGTAACGGGAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
ctctgta
- - - - gtgctgc
- - - - - - - - - - - - - - - - - - tatgaac
- - - - - - - - - - - - - - - - - - - - - - - - - tggtggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgtgc