Sequence
atgc intronic sequence ATGC exonic sequencegtaagtgttgctgttaagatttatgttaaattgatttcattttgtgttcaaattctaattcaatgctttgcagATTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCTAGTGGTCAGAGAGAGGATACGTCAG
Basic information
species | Glycine max |
transcript | GLYMA07G04640.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G04640.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os07g42380.1 (Oryza sativa), 3'ss of exon 4
------------gtaagtgttgctgttaa--gatttatgttaaattg-atttcattttgtgttcaa--attctaattcaatg----ctttgcagATTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCTAGTGGTCAGAGAGAGGATACGTCAG
|| || ||| || || | | | |||| ||| |||| | ||| | || ||| || | ||| |||||||||| ||||| |||||||||||||||||||||||| ||||| ||||| || |||
gtaagagaaaagctattcatttctgctagtttgttgaagcttaattatgtttttttttctccccaaaaacactcattgaagaaaaatgatacagTTTTGGGCAGCTTATCAGAGTTAATTGGGCATATGCTAGTGGGCAGAGGGAGGACACAACAG
upper sequence: GLYMA07G04640.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os11g40510.1 (Oryza sativa), 3'ss of exon 4
----------------------------gtaagtgttgctgttaagatttatgttaaattgatttcattttgtg--ttcaaattctaattcaatgctttgcagATTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCTAGTGGTCAGAGAGAGGATACGTCAG
|| | | | ||| |||| || | | |||||| | || | || | | | ||| ||||| ||||| || ||||| |||||||||||||| ||| ||| ||||||||||| ||||
gtaagtatttcaatactatagtattataatatatataaattctaatattttgcttttcctcttaacattttccaacattttcttatgatcctacattac-cagGTTTGGCCAGCCAATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGAGGATACATCAG
upper sequence: GLYMA07G04640.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G54080.2 (Arabidopsis thaliana), 3'ss of exon 4
-------gtaagtgttgctgttaagatttatgttaaattgatttcattttgtgttc----aaattctaattcaatgctttgcagATTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCTAGTGGTCAGAGAGAGGATACGTCAG
| ||| | | | || | | | |||| | ||||||| | ||| |||| || ||||||||| |||||||| |||||||||||||| ||||| | |||||| || || ||||| |||
gtaagaatctaacattgatacttcatgctttgattagtcaatttattcatgtgttctcttagattataatattggatttcacagATTTGGACAGCCTATGAAAGTTAATTGGGCGTATGCAACTGGTCAAAGGGAAGATACATCAA
upper sequence: GLYMA07G04640.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G14100.1 (Arabidopsis thaliana), 3'ss of exon 4
------------gtaagtgttgctgttaagatttatgttaaattgatttcat-tttgtgttcaaattctaattcaatgctttgcagATTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCTAGTGGTCAGAGAGAGGATACGTCAG
| | | || | | || | | || || |||| | || |||| ||| ||| ||||| |||||||||||||| |||||||| ||||| | ||||||||| || ||||| |||
gtaaggaacaattttcatagtttccttcctctcctcttcttatcgttcgaatgcttttgtttaggttataatcgtcgagtttacagGTTTGGACAGCCTATCAAAGTCAATTGGGCGTATGCCACTGGTCAGAGGGAAGATACATCAA
upper sequence: GLYMA07G04640.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv09s0002g00880.t01 (Vitis vinifera), 3'ss of exon 4
gtaagtgttgctgttaagatttatgttaaattgatttcattttgtgttcaaatt-ctaattcaatgctttgcagATTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCTAGTGGTCAGAGAGAGGATACGTCAG
||||| | || | ||||| | | || | | |||| || || ||| | ||||||| |||||||||||||||||||||||||||||||||||||||||||| || ||||| || ||||
gtaagaagaacccttgatttttatttatgttacatgttgggatttgtttctgttgctcattttgtaatttgcagGTTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGAGGACACATCAG
upper sequence: GLYMA07G04640.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S84_50V6.2 (Physcomitrella patens), 3'ss of exon 5
----------------------gtaagtgttgctgttaagatttatgttaaattgatttcattttgtgttcaaattctaatt-----caatgctttgcagATTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCTAGTGGTCAGAGAGAGGATACGTCAG
||| | | | || |||| ||| | ||| | || ||| | ||||| || |||||||| ||||||||||||||||||||||||||||| || || |||||||||||||| |||
cgtcttcactttttgtgctttcctaattttccttacgaatgcaaggaccaaatagatagtaatttctttttctgatctgcgtggtgatgatgctgtgtagATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGAGAGAGGATACTACAG
upper sequence: GLYMA07G04640.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S84_51V6.1 (Physcomitrella patens), 3'ss of exon 4
------------------------gtaagtgttgctgttaagatttatgttaaatt---gatttcattttgtgttcaaattctaattcaatgctttgcagATTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCTAGTGGTCAGAGAGAGGATACGTCAG
|| | | | ||| | | | || ||| | | |||||| || || ||||||| |||||||| |||||||||| |||||||||||||| || || || ||||||||||| |||
tggtcgcaaatagttttaaaacgataaaacgacgaaatccgaattcttatggattttgaaattggctggcattctcaaatactctgaggctgatttgcagGTTTGGGCAATCTATCAAAGTAAATTGGGCATATGCGAGCGGACAAAGAGAGGATACAACAGMapped 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|7146716|gb|AW508638.1|AW508638EST: GATCGCAGATCTGCTGCTCTTGCCATATTATCTCTCAATGGAAGGCATCT ATTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCTAGTGGTCAGAGAGA
genomic: GATCGCAGATCTGCTGCTCTTGCCATATTATCTCTCAATGGAAGGCATCTgtaagtgttg ... tgctttgcagATTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCTAGTGGTCAGAGAGA
EST:
gi|208032967|gb|GD830024.1|GD830024EST: GATCGCAGATCTGCTGCTCTTGCCATATTATCTCTCAATGGAAGGCATCT ATTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCTAGTGGTCAGAGAGA
genomic: GATCGCAGATCTGCTGCTCTTGCCATATTATCTCTCAATGGAAGGCATCTgtaagtgttg ... tgctttgcagATTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCTAGTGGTCAGAGAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttatgttaaattgatttcattttgtgttcaaattctaattcaatgctttgcagATTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCTAGTGGTCAGAGAGAGGATACGTCAG
ttctaat putative branch site (score: 2)
ttaaattgatttcatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtgttgctgttaagatttatgttaaattgatttcattttgtgttcaaattctaattcaatgctttgcagATTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCTAGTGGTCAGAGAGAGGATACGTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT