Sequence
atgc intronic sequence ATGC exonic sequencegtaaatctctttcctgtaatctcaactcttttatctcacatgaatccttgttatctcgtcctgagcttatcatattgctttctagATATCAGACGCTATACGAGACGGAGCTGAAGGATTTTTCAGGACCCAGTATGGGAGTATATCTAAGATGGCCATGTTGCTTGCACTTGTCATTCTTTGCA
Basic information
species | Glycine max |
transcript | GLYMA08G24120.4 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G24120.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g33490.1 (Oryza sativa), 3'ss of exon 3
-----------------gtaaatctctttcctgtaatctcaactcttttatctcacatgaatccttgttatctcgtcctgagcttatcatattgctttctagATATCAGACGCTATACGAGACGGAGCTGAAGGATTTTTCAGGACCCAGTATGGGAGTATATCTAAGATGGCCATGTTGCTTGCACTTGTCATTCTTTGCA
| | | | | | || | || |||| || || || || | | | | | | | | ||| | | ||||||| || || ||| |||| || |||||||||||||| ||||| || ||||||| ||| ||||| ||||| | || ||||||||||||||| |||
cctacatcctactgttcttgagagttgtacttagtatattgacatctttacctgtca--gatttatgctgtattttttattgggtgccttcttgatgttcagATATCTGATGCCATAAGAGATGGTGCTGAAGGATTTTTTAGGACACAATATGGGACTATTTCTAAAATGGCTTGTATCCTGGCACTTGTCATTCTTGGCA
upper sequence: GLYMA08G24120.2 (Glycine max), 3'ss of exon 3
lower sequence: AT1G78920.2 (Arabidopsis thaliana), 3'ss of exon 3
------------------------gtaaatctctttcctgtaatctcaactcttttatctcacatgaatccttgttatctcg--tcctgagcttatcatattgctttctagATATCAGACGCTATACGAGACGGAGCTGAAGGATTTTTCAGGACCCAGTATGGGAGTATATCTAAGATGGCCATGTTGCTTGCACTTGTCATTCTTTGCA
|| | || | || || | || ||| | || |||| || | |||| | || | || ||| ||||||||||| |||||||| || ||||||||||| |||||||| || |||||| | | |||||| ||||||||||| ||||| || |||| ||||||||||
gtaagctcactcagattatgtggtgttagtcatgatgttgacatttttccttctttgttctcatcaaaaatttgtaattctaatttgtgaggtaattctcttactta-tagATATCAGATGCTATACGTGATGGAGCTGAAGGTTTTTTCAGAACGCAGTATAGCACTATATCCAAGATGGCCATTTTGCTAGCTTTTGTGATTCTTTGCA
upper sequence: GLYMA08G24120.2 (Glycine max), 3'ss of exon 3
lower sequence: AT1G16780.1 (Arabidopsis thaliana), 3'ss of exon 4
----------------gtaaatctctttcct--gtaatctcaactcttttat--ctcacatgaatccttgttatctcgtcctgagcttatcatattgctttctagATATCAGACGCTATACGAGACGGAGCTGAAGGATTTTTCAGGACCCAGTATGGGAGTATATCTAAGATGGCCATGTTGCTTGCACTTGTCATTCTTTGCA
| ||| | || | || || || ||| | |||| || || | | | ||||||||| | || || | ||||||||||| |||||||| || ||||||||||||||||| || || |||||||| | |||||| || ||||| | ||||| || |||| || |||||||
gtaatttcacacaagttttaatttgttctattcgtgattgtgtcttctttgttactcagttgcattttcagttctgtgctatgagcttattct-tttctgtttagATATCAGATGCTATACGTGATGGAGCTGAAGGATTTTTAAGAACGCAGTATGGTACTATATCCAAAATGGCGTTCTTGCTAGCTTTTGTGATCCTTTGCA
upper sequence: GLYMA08G24120.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0054g00700.t01 (Vitis vinifera), 3'ss of exon 3
--------------gtaaatctctttcctgtaatctcaactcttttatctcacatgaatcctt-gttatctcgtcctgagcttatcatattgctttctagATATCAGACGCTATACGAGACGGAGCTGAAGGATTTTTCAGGACCCAGTATGGGAGTATATCTAAGATGGCCATGTTGCTTGCACTTGTCATTCTTTGCA
|| || || | | | | |||| || ||| ||| || | || ||||||||||||| || |||||||||||||||| || ||||| || ||||| ||||| || ||||||||||| ||||||| ||| || |||||||| ||||| || || ||||| || ||| |||
attatctgagaatgaccaaacttaagaatgaagtattctcatggttataattcagaaattctttgtgaacttgtcctgagcttattattccactttctagATATCAGATGCGATACGTGATGGAGCAGAAGGTTTCTTCAGGACCCAATATGGGACTATTTCCAAGATGGCAATGTTACTAGCTCTTGTGATCCTTAGCAMapped 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|308098348|gb|HO760089.1|HO760089EST: TTACAAAGTGGGTCCTCGCAAAAGATGAGGGCCCTCCTGAAATGGTTCAG ATATCAGACGCTATACGAGACGGAGCTGAAGGATTTTTCAGGACCCAGTAT
genomic: TTACAAAGTGGGTCCTCGCAAAAGATGAGGGCCCTCCTGAAATGGTTCAGgtaaatctct ... tgctttctagATATCAGACGCTATACGAGACGGAGCTGAAGGATTTTTCAGGACCCAGTAT
EST:
gi|193707476|gb|FK642750.1|FK642750EST: AAAAGATGAGGGCCCTCCTGAAATGGTTCAG ATATCAGACGCTATACGAGACGGAGCTGAAGGATTTTTCAGGACCCAGTAT
genomic: AAAAGATGAGGGCCCTCCTGAAATGGTTCAGgtaaatctct ... tgctttctagATATCAGACGCTATACGAGACGGAGCTGAAGGATTTTTCAGGACCCAGTAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatctcacatgaatccttgttatctcgtcctgagcttatcatattgctttctagATATCAGACGCTATACGAGACGGAGCTGAAGGATTTTTCAGGACCCAGTATGGGAGTATATCTAAGATGGCCATGTTGCTTGCACTTGTCATTCTTTGCA
atctcac putative branch site (score: 3)
ttgctttct putative PPT
ttatcatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatctctttcctgtaatctcaactcttttatctcacatgaatccttgttatctcgtcctgagcttatcatattgctttctagATATCAGACGCTATACGAGACGGAGCTGAAGGATTTTTCAGGACCCAGTATGGGAGTATATCTAAGATGGCCATGTTGCTTGCACTTGTCATTCTTTGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG