Sequence
atgc intronic sequence ATGC exonic sequence...ctagttcaacataaacaatcagttatacagtcttatatttttctaagtgttagtattttatctcaagatgccttaattatttatatttgaaaacgaacagGCTGTGCATGATGGGGTGGATATACTCAGCCTTTCAGTTGGACCAAATAGTCCTCCATCAAACACCAAAACTACATTTTTGAATCCTTTTGATGCTACAC
Basic information
species | Glycine max |
transcript | GLYMA15G17830.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G17830.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os06g48650.3 (Oryza sativa), 3'ss of exon 5
--ctagttcaacataaacaatcagttatacagtcttatatttttctaagtgttagtattttatctcaagatgcc--ttaattatttatatttgaaaacgaacagGCTGTGCATGATGGGGTGGATATACTCAGCCTTTCAGTTGGACCAAATAGTCCTCCATCAAACACCAAAACTACATTTTTGAATCCTTTTGATGCTACAC
||| |||| | | ||||||| | | || | ||| || || || | || | | || | | | | ||||||||||| ||||| || || || |||| |||||| ||||| |||||||| || ||| | || ||||||||||||||||||||||||||| |||
aatgagtgaaacaacatctgccagttatgtaat---gcatgtcactat-cacaagccttcaatatgtaggaactaatgcatggatggcaatctgcattttgcagGCTGTGCAGGATGGTGTTGACATTCTCAACCTTTCTGTTGGCCCAAATAGCCCGCCAACTGCTACGCGGACTACATTTTTGAATCCTTTTGATGCTGCAC
upper sequence: GLYMA15G17830.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G19170.1 (Arabidopsis thaliana), 3'ss of exon 6
ctagttcaacataaacaatcagttatacagtcttatatttttctaagtgttagtattttatctcaagatgccttaattatttatatttgaaaacg-------aacagGCTGTGCATGATGGGGTGGATATACTCAGCCTTTCAGTTGGACCAAATAGTCCTCCATCAAACACCAAAACTACATTTTTGAATCCTTTTGATGCTACAC
| ||| || || | | |||| || | || ||| || || ||| | |||| || | || ||||| || | ||||||||| |||||||| || ||||| || ||||| |||||||| |||||||||||||| ||| ||||| || || || |||||||| ||||||||||| |
ccggttatctattttagatt--tcaacgagtcaagtaatcttataactgc---tactttccatggagattatcta--tgttgatattaaaagagattttcatgacagGCTGTTCATGATGGAGTTGATATCCTGAGCCTCTCAGTTGGTCCAAATAGTCCTCCCACAACTACCAAGACAACGTTCTTGAATCCATTTGATGCTACCC
upper sequence: GLYMA15G17830.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv11s0103g00550.t01 (Vitis vinifera), 3'ss of exon 6
ctagttcaacataaac-aatcagttatacagtcttatatttttctaagtgtta---gtattttatctcaagatgccttaattatttatatttgaaaacgaacagGCTGTGCATGATGGGGTGGATATACTCAGCCTTTCAGTTGGACCAAATAGTCCTCCATCAAACACCAAAACTACATTTTTGAATCCTTTTGATGCTACAC
|| ||| || || || | | || | |||| | | || || || |||| | | | |||||| | || ||||||||||| |||||||| ||||| || |||| || || || || ||||||||||||||| ||| |||||| || || ||||| || |||||||||||| |||
--ttttgcccatgaattaagcatctttttagg-tgatatctgttggggtattctttgttttttgttttttcgtttattaattgaagac-ttcttctgtgaacagGCTGTTCATGATGGTGTGGACATTCTCAATCTCTCTGTGGGGCCAAATAGTCCTCCAGCAACCACCAAGACCACGTTTTTAAACCCTTTTGATGCTGCACMapped 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|26048244|gb|CA784780.1|CA784780EST: ATAGACTCTTTGGAGGATTTATTGCAGATGTAGTTGCTGCAATTGATCAG GCTGTGCATGATGGGGTGGATATACTCAGCCTTTCAGTTGGACCAAATAGT
genomic: ATAGACTCTTTGGAGGATTTATTGCAGATGTAGTTGCTGCAATTGATCAGgtatgcaact ... aaacgaacagGCTGTGCATGATGGGGTGGATATACTCAGCCTTTCAGTTGGACCAAATAGT
EST:
gi|208028006|gb|GD824066.1|GD824066EST: ATAGACTCTTTGGAGGATTTATTGCAGATGTAGTTGCTGCAATTGATCAG GCTGTGCATGATGGGGTGGATATACTCAGCCTTTCAGTTGGACCAAATAGT
genomic: ATAGACTCTTTGGAGGATTTATTGCAGATGTAGTTGCTGCAATTGATCAGgtatgcaact ... aaacgaacagGCTGTGCATGATGGGGTGGATATACTCAGCCTTTCAGTTGGACCAAATAGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtgttagtattttatctcaagatgccttaattatttatatttgaaaacgaacagGCTGTGCATGATGGGGTGGATATACTCAGCCTTTCAGTTGGACCAAATAGTCCTCCATCAAACACCAAAACTACATTTTTGAATCCTTTTGATGCTACAC
ccttaat putative branch site (score: 4)
ttaattatttatattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctagttcaacataaacaatcagttatacagtcttatatttttctaagtgttagtattttatctcaagatgccttaattatttatatttgaaaacgaacagGCTGTGCATGATGGGGTGGATATACTCAGCCTTTCAGTTGGACCAAATAGTCCTCCATCAAACACCAAAACTACATTTTTGAATCCTTTTGATGCTACAC
- - - - - - - - - - - - - - - - - - - - - ctaagtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatgcct