Sequence
atgc intronic sequence ATGC exonic sequence...tttactctctgtggttcattgggttcttgtgtcttgtagatgatttggatcctctaatgtatgctgtagttgcttatatatttgattttgattcttgcagCTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA
Basic information
species | Glycine max |
transcript | GLYMA03G16660.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G16660.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g26970.1 (Oryza sativa), 3'ss of exon 2
-tttactctctgtggttcattgggttc-ttgtgtcttgtagatgatttggatcctctaatgtatgctgtagttgcttatatatttgattttgattcttgcagCTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA
|||| | | | | |||| | ||| | || |||| ||||| |||| | ||| || | || | | || || | ||||||| |||||||| || ||||| ||||||||||| ||||| ||||| || || |||||||||||
atttattagat-tcctccattacacaggctaggtccataaaattgcttggttcctccaatgcaagct-taataattttgcaaaatatttggtgttgtaacagCTGCTAATGGAGTAGTTATTGCCACCGAGAAGAAGTTGCCTTCTATTTTAGTGGATGAAACATCT
upper sequence: GLYMA03G16660.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g42320.4 (Oryza sativa), 3'ss of exon 2
tttactctctgtggtt--cattgggttcttgtgtcttgtagatga--tttggatcctctaatgtatgctgtagttgcttatatatttgattttgattcttgcagCTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA
| | ||| ||| | | | ||| ||| || | ||| | | | | || | | | | | || | || |||||||||| ||||| || || || || || |||||||||||||| ||||| || || |||||||||||
----ttttgtgtagttactgctcagagactacagtctgttgattctcttcagttcccttttagcctagtttattgattctgaggtatatttgttatgtttgcagCTGCTAATGGTGTAGTTATCGCCACTGAGAAGAAATTGCCTTCTATTTTAGTCGATGAAACATCT
upper sequence: GLYMA03G16660.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g42320.1 (Oryza sativa), 3'ss of exon 2
tttactctctgtggtt--cattgggttcttgtgtcttgtagatga--tttggatcctctaatgtatgctgtagttgcttatatatttgattttgattcttgcagCTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA-----------------------------------
| | ||| ||| | | | ||| ||| || | ||| | | | | || | | | | | || | || |||||||||| ||||| || || || || || |||||||||||||| ||||| || || |||||||||||
----ttttgtgtagttactgctcagagactacagtctgttgattctcttcagttcccttttagcctagtttattgattctgaggtatatttgttatgtttgcagCTGCTAATGGTGTAGTTATCGCCACTGAGAAGAAATTGCCTTCTATTTTAGTCGATGAAACATCTGTAAGTCTAACATCACTCTTAATGCTGAATTCCTC
upper sequence: GLYMA03G16660.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G824831_T04 (Zea mays), 3'ss of exon 3
--tttactctctgtggttcattgggttcttgtgtcttgtagatgatttggatcctctaatgtatgctgtagttgcttatatatttgattttgattcttgcagCTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA
| ||| ||| | | ||| |||| || | || | | | | | | ||| | ||| | || | | || |||||||||| ||||| || |||||||| || |||||||| |||| ||||| || || |||||||||||
ataatgttctatgtaatatacatggtccttg-gttaggcagtacaaccattttgttttacttctgcc-tctttgttaattccgaaatatatcatgtttgcagCTGCCAATGGTGTAGTCATTGCCACTGAGAAGAAGCTGCCTTCTATTTTAGTGGATGAAACATCT
upper sequence: GLYMA03G16660.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G850355_T05 (Zea mays), 3'ss of exon 2
---tttactc-tctgtggttcattgggttcttgtgtcttgtagatgatttggatcctctaatgtatgctgtagttgcttatatatttgattttgattcttgcagCTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA
||| ||| | || || || ||| | | || | | | | | | | ||| | ||| | || | | | | || |||||||||| || || || || ||||| |||||||||||| |||| ||||| || || |||||||||||
tgccataccagtctttttttaatcaaattgctgtattaggcagttcaaccattttattttacttgtgc-atctttgttaat---tctacatgtcatgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCT
upper sequence: GLYMA03G16660.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G850355_T08 (Zea mays), 3'ss of exon 2
--tttactctctgtggttcattgggttcttgtgtcttgtagatgatttggatcctctaatgtatgctgtagttgcttatatatttgattttgattcttgcagCTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA
| | ||| ||| | | ||| ||| || | || | | | | | | ||| | ||| | || | | || |||||||||| || || || || ||||| || ||||||||| |||| ||||| ||||| |||||||||||
gctgtgttctatgtaatatacatggtcattg-gttaggcagtacaaccattttattttacttgtgc-atctttgttaattctgaaatatgtcatgtttgcagCTGCCAACGGTGTAGTGATTGCCACTGAGAAGAAACTGCCTTCTATTTTGGTGGATGAAACATCT
upper sequence: GLYMA03G16660.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G79210.3 (Arabidopsis thaliana), 3'ss of exon 3
tttactctctgtggttcattgggttcttgtgtcttgtagatgatttggatcctctaatgtatgctgtagttgcttat-atatttgat-tttgattcttgcagCTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA
||| || | | || | || | | ||| | | ||| ||| | || || || | ||| || ||||||| ||||||||||||||||||| || || |||||| | || |||||||||||||||||| | ||
-------------gttttttcaatgatctaatc--aaattcgagaggagatttttaaggaacattgtctttggtaatcatgactgttgttttctttatgcagCTTCAAATGGAGTTGTCATTGCAACTGAAAAGAAACTTCCTTCTATATTGGTTGATGAAGCGTCT
upper sequence: GLYMA03G16660.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G16470.2 (Arabidopsis thaliana), 3'ss of exon 2
tttactctctgtggttcattgggttcttgtgtcttgtagatgatt-tggatcctctaatgtatgctgtagttgcttatata-tttgattttgattcttgcagCTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA
||| | || || || | || || | |||| || | | | || | ||| ||| ||| || ||||||| | ||||||||||||||||| || || ||||| ||||| ||||| ||||||||||| ||||
-------------gtttgtcaatgtcatga----tgaaattgtttatagatcaatgaaaaatttgtagatttcttctgataacttggtttc--ttactgcagCTTCTAATGGAGTTGTCATTGCAACTGAAAAGAAGTTGCCTTCTATTCTGGTTGATGAAGCATCTMapped 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|151411475|gb|EV281286.1|EV281286EST: GCGTGCTTTGACAGCCGTTGGCTCTGGACAAACGTCTTTGGGAATAAAAG CTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGG
genomic: GCATGCTTTGACAGCCGTTGGCTCTGGACAAACGTCTTTGGGAATAAAAGgtgattgatt ... attcttgcagCTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGG
EST:
gi|9899371|gb|BE608339.1|BE608339EST: GCATGCTTTGACAGCCGTTGGCTCTGGACAAACGTCTTTGGGAATAAAAG CTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGG
genomic: GCATGCTTTGACAGCCGTTGGCTCTGGACAAACGTCTTTGGGAATAAAAGgtgattgatt ... attcttgcagCTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggatcctctaatgtatgctgtagttgcttatatatttgattttgattcttgcagCTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA
ttcttgc CT-rich tract
ttatatatttgatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttactctctgtggttcattgggttcttgtgtcttgtagatgatttggatcctctaatgtatgctgtagttgcttatatatttgattttgattcttgcagCTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - -tctgtgg
- - - - - - - - - - - - tcttgtg
- - - - - - - - - - - - - - - - - - - - tgatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttgctt