Sequence
atgc intronic sequence ATGC exonic sequence...tggttgctagcagaggtcttggtccttggagttattgttatgccaaattgtacttgatgatatattttatacttcttttttttttttttgtcaaattcagGTAGCAAAAGAAAGTGCCGATGTAATAATTCTAGATGATAACTTTTCAACTATTGTAACTGTAGCCAAATGGGGCCGCTCGGTCTACATAAACATTCAGA
Basic information
species | Glycine max |
transcript | GLYMA04G04810.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G04810.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G27770.1 (Arabidopsis thaliana), 3'ss of exon 4
------------------tggttgctagcagaggtcttggtccttggagttat-tgttatgccaaattgtacttgatgatatattttatactt-cttttttttttttttgtcaaattcagGTAGCAAAAGAAAGTGCCGATGTAATAATTCTAGATGATAACTTTTCAACTATTGTAACTGTAGCCAAATGGGGCCGCTCGGTCTACATAAACATTCAGA
| || ||| | |||| || || | | | ||| | | | |||| | | || | ||||| |||| |||||||||||||| ||||| || || |||||||||||||| || || ||||| || ||||||||||||||||| || || |||||||| |||||||
gtgtgtactcaatcttcattgtccctatttcattatctggtttgtgagaaaatctaacaattgagtttgggttctcatggaaggacaacacttacatattctatttttcaattttcgtagGTGGCAAAAGAAAGTGCGGATGTGATTATCCTAGATGATAACTTCTCTACGATTGTCACAGTAGCCAAATGGGGCCGTTCTGTGTACATAAATATTCAGA
upper sequence: GLYMA04G04810.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0001g09150.t01 (Vitis vinifera), 3'ss of exon 4
tggttgctagcagaggtcttggtccttg--gagttattgttatgccaaattgtacttgatgatatattttat-acttcttttttttttttttgtcaaattcagGTAGCAAAAGAAAGTGCCGATGTAATAATTCTAGATGATAACTTTTCAACTATTGTAACTGTAGCCAAATGGGGCCGCTCGGTCTACATAAACATTCAGA
| | | | | || || |||||| | | |||| || || | || || | | | || || ||| ||||||| |||||||| ||||| ||||| |||||| | ||||||||||| || |||||||| ||||| | ||||||||| ||||| | || || ||||||||||
--tccatcctctgggcttgtagtttgtgtaaagttatcatcactttgaatttta-ttagttttaagcagaatcatatgctgaaaaacttcttcccaatttcagGTGGCAAAAGAGAGTGCTGATGTCATAATTATGGATGATAACTTCTCCACTATTGTGACTGTGGGCAAATGGGGACGCTCAATTTATATTAACATTCAGA
upper sequence: GLYMA04G04810.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ18007 (Selaginella moellendorffii), 3'ss of exon 2
tggttgctagcagaggtcttggtccttggagttattgttatgccaaattgtacttgatgatatattttatacttcttttttttttttttgtcaaattcagGTAGCAAAAGAAAGTGCCGATGTAATAATTCTAGATGATAACTTTTCAACTATTGTAACTGTAGCCAAATGGGGCCGCTCGGTCTACATAAACATTCAGA
| || | || | || | || || | | | | | |||||||||| | || ||||| ||||| || || || ||| || | |||||||| || || || ||||| || ||||| |||||||||||||||||||||| |||||| || |
----------------------------gtactacttttcatcttgatcttctttaatcgt---tctgagcggccggaattttttttttatgcaa--cagGTGGCAAAGGAGAGCGCTGATATAGTTATTCTAGACGACAAGTTCAACACTATAGTGGTGGTAGCAAAATGGGGCCGCTCGGTCTACACAAACATCCAAA
upper sequence: GLYMA04G04810.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ37088 (Selaginella moellendorffii), 3'ss of exon 4
tggttgctagcagaggtcttggtccttggagttattgttatgccaaattgtacttgatgatatattttatacttcttttttttttttttgtcaaattcagGTAGCAAAAGAAAGTGCCGATGTAATAATTCTAGATGATAACTTTTCAACTATTGTAACTGTAGCCAAATGGGGCCGCTCGGTCTACATAAACATTCAGA
|| | | | | || | | |||| || || || ||| | ||| |||| ||||| | || ||||||||||| || || || ||| || | |||||||| || || || ||||| || ||||| |||||||||||||||||||||| |||||| || |
---------------gtactacttttcatcttgatcttctt--taaatcgttct-gagaggccggaatattttattttattttatttttatgcaa--cagGTAGCAAAGGAGAGCGCTGATATAGTTATTCTAGACGACAAGTTCAACACTATAGTGGTGGTAGCAAAATGGGGCCGCTCGGTCTACACAAACATCCAAAMapped 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|6566478|gb|AW234123.1|AW234123EST: CACTTCATGAAGCAGATATTGGACTTGCAATGGGCATTGCTGGAACTGAG GTAGCAAAAGAAAGTGCCGATGTAATAATTCTAGATGATAACTTTTCAACT
genomic: CACTTCATGAAGCAGATATTGGACTTGCAATGGGCATTGCTGGAACTGAGgtatgccaag ... tcaaattcagGTAGCAAAAGAAAGTGCCGATGTAATAATTCTAGATGATAACTTTTCAACT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattgtacttgatgatatattttatacttcttttttttttttttgtcaaattcagGTAGCAAAAGAAAGTGCCGATGTAATAATTCTAGATGATAACTTTTCAACTATTGTAACTGTAGCCAAATGGGGCCGCTCGGTCTACATAAACATTCAGA
acttgat putative branch site (score: 5)
tattttatacttcttt putative PPT
atatattttatacttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tggttgctagcagaggtcttggtccttggagttattgttatgccaaattgtacttgatgatatattttatacttcttttttttttttttgtcaaattcagGTAGCAAAAGAAAGTGCCGATGTAATAATTCTAGATGATAACTTTTCAACTATTGTAACTGTAGCCAAATGGGGCCGCTCGGTCTACATAAACATTCAGA
tggttgc
- - - - - - - - - - - -ccttgga
- - - - - - - - - - - - - - - - - - - tatgcca
- - - - - - - - - - - - - - - - - - - - - - - - - - cttgatg