Sequence
atgc intronic sequence ATGC exonic sequencegtagaaatgatttgtttcagcttttttttttttttttcaattcctttataaattaagttttttaatctcatagctaatgctcagcttcgtgtgtgcagATTGTCCAACATATCTTACTTGACATGCCTAGTCTTGCTTTCTTTACAACTTATGCGCTGTTGGTACTGTTCTGGGCTGAGATTTATTACCAG
Basic information
species | Glycine max |
transcript | GLYMA08G09640.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G09640.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g02850.1 (Oryza sativa), 3'ss of exon 3
----gtagaaatgatttgtttcagctttttt--ttttttttttcaattcctttataaattaagttttttaatctcatagctaatgctcagcttcgtgtg--tgcagATTGTCCAACATATCTTACTTGACATGCCTAGTCTTGCTTTCTTTACAACTTATGCGCTGTTGGTACTGTTCTGGGCTGAGATTTATTACCAG
|| | || |||| | || | | || ||| | ||||| ||| || | || | | | |||| | | || || || | | |||||| | | |||| | || | ||||| ||||| ||||| ||||| ||||| || || ||||||||||||||||| || |||
gtttgtggggg-gaacagtttatgtttctctgacttgtttctgcaatttttttcgaaggtg-------caaagtaggaa-tgatgcgtaaccatatggcattgtagGTATTTCAACATGTGCTCATTGATTTTCCGGGGCTTGCATTCTTCACAACCTATGCTCTGTTAGTGCTCTTCTGGGCTGAGATTTACTATCAG
upper sequence: GLYMA08G09640.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G02180.1 (Arabidopsis thaliana), 3'ss of exon 3
gtagaaatgatttgtttcagctttttttttttt--ttttcaattcctttataaattaagttttttaatctcatagctaatgctcagcttcgtgtgtgcagATTGTCCAACATATCTTACTTGACATGCCTAGTCTTGCTTTCTTTACAACTTATGCGCTGTTGGTACTGTTCTGGGCTGAGATTTATTACCAG
| || | ||| | || | |||| | | || | || | | | | || || || ||| ||| | | | || ||||| | ||||||||||| ||||| || || |||||||||||||| || || ||||| || |||| || ||||||||||| |||||||| |||
--------gtttaggatcattcaccatcattgtaattttaatcttattgacttgtttattgtgtcaaccttcta---aatttgcagtgttatctttgtagATTCTGCAACATATCTTGCTTGATATTCCAAGTCTTGCTTTCTTCACCACCTATGCTCTTCTGGTTCTTTTCTGGGCTGAAATTTATTATCAG
upper sequence: GLYMA08G09640.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G14530.1 (Arabidopsis thaliana), 3'ss of exon 3
gtagaaatgatttgtttcagcttttttttttttttttcaattcctttata----aattaagttttttaatctcatagctaatgctcagcttcgtgtgtgcagATTGTCCAACATATCTTACTTGACATGCCTAGTCTTGCTTTCTTTACAACTTATGCGCTGTTGGTACTGTTCTGGGCTGAGATTTATTACCAG
| || || | || | || | ||| || || || | || | ||| ||| || | || | || | || | || ||||| | ||||||||||||||||| || || |||||||||||||| || || |||||||| |||| || || ||||| |||||||| ||||||
--------gtttggtgtttctattgatattgtgatttagcctcattgatggtctatttgaaatttctaaacttgcaagtatcgttcggttt--ttcttgtagATTCTGCAACATATCTTACTTGATATTCCAAGTCTTGCTTTCTTCACTACATATGCGCTTCTGGTTCTCTTTTGGGCAGAGATTTACTACCAGMapped 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|213611111|gb|DB972699.1|DB972699EST: GGTGTTTTGTTTTTGTCTTCCGTCGGGATGTGCAGAAGTTGCAGCCAGAG ATTGTCCAACATATCTTACTTGACATGCCTAGTCTTGCTTTCTTTACAACT
genomic: GGTGTTTTGTTTTTGTCTTCCGTCGGGATGTGCAGAAGTTGCAGCCAGAGgtagaaatga ... gtgtgtgcagATTGTCCAACATATCTTACTTGACATGCCTAGTCTTGCTTTCTTTACAACT
EST:
gi|192314057|gb|FK008797.1|FK008797EST: GGTGTTTTGTTTTTGTCTTCCGTCGGGATGTGCAGAAGTTGCAGCCAGAG ATTGTCCAACATATCTTACTTGACATGCCTAGTCTTGCTTTCTTTACAACT
genomic: GGTGTTTTGTTTTTGTCTTCCGTCGGGATGTGCAGAAGTTGCAGCCAGAGgtagaaatga ... gtgtgtgcagATTGTCCAACATATCTTACTTGACATGCCTAGTCTTGCTTTCTTTACAACT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttataaattaagttttttaatctcatagctaatgctcagcttcgtgtgtgcagATTGTCCAACATATCTTACTTGACATGCCTAGTCTTGCTTTCTTTACAACTTATGCGCTGTTGGTACTGTTCTGGGCTGAGATTTATTACCAG
agctaat putative branch site (score: 3)
taaattaagtttttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagaaatgatttgtttcagcttttttttttttttttcaattcctttataaattaagttttttaatctcatagctaatgctcagcttcgtgtgtgcagATTGTCCAACATATCTTACTTGACATGCCTAGTCTTGCTTTCTTTACAACTTATGCGCTGTTGGTACTGTTCTGGGCTGAGATTTATTACCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT