Sequence
atgc intronic sequence ATGC exonic sequence...ggatgcattaaatataaatattgtgggatgtggcgaataataagcttgtagtgtttgaggtgctgcttatgctgttaatgatttgtatctctattttcagACACAAAGGCATGGGAAGTGGACACCTTGAGAGGGCACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAGCAGGATATCATTGTGTCAAATTCCGA
Basic information
| species | Glycine max |
| transcript | GLYMA10G34310.1 |
| intron # | 2 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G34310.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os09g04110.1 (Oryza sativa), 3'ss of exon 2
ggatgcattaaatataaatattgtgggatgtggcgaataataagcttgtagtgtttgaggtgctgcttatgctgttaatgatttgta-tctctattttcagACACAAAGGCATGGGAAGTGGACACCTTGAGAGGGCACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAGCAGGATATCATTGTGTCAAATTCCGA
| | | | || || ||| || | || || || | ||||||| | ||| || | | ||| | | | | ||||||| ||||| |||||||| || || ||| | ||||||||||||||||| || || || ||||||||||| ||||| || ||||||||||| || || ||
tattctactgcacattggtagactggccaaacgctatta-tatgcataccactattgaggtatttgaaatgatgcaatctaagtgtgctatttttggacagACACCAAGGCTTGGGAAGTTGATACTTTGCGGGGGCACATGAATAATGTGTCCTGCGTGATGTTCCATGCAAAGCAAGACATCATTGTGTCCAACTCAGA
upper sequence: GLYMA10G34310.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g50340.1 (Oryza sativa), 3'ss of exon 2
------ggatgcattaaatataaatattgtgggatgtggcgaataataagcttgtagtgtttgaggtgctgcttatgctgttaatgatttgtatctctattttcagACACAAAGGCATGGGAAGTGGACACCTTGAGAGGGCACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAGCAGGATATCATTGTGTCAAATTCCGA
|| ||| | ||| | | || || | | | ||| || ||||| | || | | | |||| | ||| | | | ||||||| ||||| |||||||| || || ||| | || |||||||||||||| ||||| || ||||||||||| ||||| || ||||||||||| || || ||
attgctagactggccaaacacaaaactatatgcatatgcagcaaaccgctattgaggtatttgaattaatg----taatctaaatg--tgctatttttttggacagACACGAAGGCTTGGGAAGTTGATACTTTGCGGGGACACATGAATAATGTGTCATGCGTGATGTTCCATGCTAAGCAAGACATCATTGTGTCCAACTCAGA
upper sequence: GLYMA10G34310.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g50350.1 (Oryza sativa), 3'ss of exon 2
ggatgcattaaatataaatattgtgggatgtgg----cgaataataagcttgtagtgtttgaggtgctgctta-tgctgttaatgatttgta-tctctattttcagACACAAAGGCATGGGAAGTGGACACCTTGAGAGGGCACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAGCAGGATATCATTGTGTCAAATTCCGA
|| | | ||||| | | | | || | ||| | | ||| | | | | | || || | | ||| | | | || ||||||| ||||| |||||||| || || ||| | |||||||||||||| || || ||||| ||||||||||| ||||| || ||||| ||||| || || ||
------gcaaactttgtggggtgtggaacattcacttccactatcaccattgcattatttaaagggataataggtgatgcaatctaaatgtgctgttttttgacagACACCAAGGCTTGGGAAGTTGATACTTTGCGGGGGCACATGAATAACGTGTCCTGTGTGATGTTCCATGCAAAGCAAGACATCATAGTGTCCAACTCAGA
upper sequence: GLYMA10G34310.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G010054_T01 (Zea mays), 3'ss of exon 2
ggatgcattaaatataaatattgtgggatgtggcgaataataagcttgtagtgtttgaggtgctgctt---atgctgttaatgatttgtat-ctctattttcagACACAAAGGCATGGGAAGTGGACACCTTGAGAGGGCACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAGCAGGATATCATTGTGTCAAATTCCGA
| | | || || || | | | || || | | | | ||| || || |||| | | || ||| | || ||| |||| || ||||| |||||||| || || || || || |||||||||||||| || ||||| ||||||||||| ||||| || ||||| |||||||| || ||
---tttagcagat-caattagtacttagcatatgtgaaaaagagtatacattctacaaggaaatgtttgaaatgcaataatctatatgtgttctttatggacagATACCAAGGCTTGGGAAGTTGATACTTTAAGGGGCCACATGAATAATGTGTCTTGTGTGATGTTCCATGCGAAGCAAGACATCATCGTGTCAAACTCAGA
upper sequence: GLYMA10G34310.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G149406_T01 (Zea mays), 3'ss of exon 2
-ggatgcattaaatataaatattgtgggatgtggcgaataataagcttgtagtgtttgaggtgctgcttatgctgttaatgatttgtatctctatttt-----cagACACAAAGGCATGGGAAGTGGACACCTTGAGAGGGCACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAGCAGGATATCATTGTGTCAAATTCCGA
| || ||| | || | | || || || |||| | | | | ||| | || || ||| |||| | ||| ||| |||| || ||||| |||||||| || || || || || ||| |||||||||| || ||||| ||||||||||| ||||| || ||||||||||| || || ||
tttagctgttcaatt--agtacc-tagcatatgtgaaagaatata--tacattctacaaggaaatatttggaatgc-aataatttatgtctgctctttatggacagATACCAAGGCTTGGGAAGTTGATACTTTAAGGGGTCACGTGAATAATGTGTCCTGTGTGATGTTCCATGCGAAGCAAGACATCATTGTGTCTAACTCAGA
upper sequence: GLYMA10G34310.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G62020.1 (Arabidopsis thaliana), 3'ss of exon 3
---------------------------------------ggatgc-attaaatataaatattgtgg--gatgtggcgaataataagcttg---tagtgtttga---------ggtgctgcttatgct-gttaatgatttgtatct--ctat----tttcagACACAAAGGCATGGGAAGTGGACACCTTGAGAGGGCACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAGCAGGATATCATTGTGTCAAATTCCGA
|||| || || | ||| ||| ||| || |||| | || || || | || | ||| | | ||| | | ||| | | | || || |||| || || || ||||| ||||| || ||| |||| || |||||||| ||||||| ||||||||||||||| || ||||| || ||||| ||||| || ||
gtaattatttggtggtatacttttgtgcttacaatttttatatgctatcaatcgtcaatgatgttactgatatga-aaatattctgcatgccttaatccttagatgaatctcgaaattgcaaagacgagttggtaacatgtttttaacgatatcattgcagAAACTAAAGCTTGGGAGGTGGATACATTGCGAGGCCATATGAATAACGTTTCATCTGTTATGTTCCATGCAAAACAGGACATAATTGTATCAAACTCTGA
upper sequence: GLYMA10G34310.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G21390.1 (Arabidopsis thaliana), 3'ss of exon 3
ggatgcattaaatataaatattgtgggatgtggcgaataataagcttgtagtgtttgaggtgctgcttatgctgttaatgatttgtatctctattttcagACACAAAGGCATGGGAAGTGGACACCTTGAGAGGGCACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAGCAGGATATCATTGTGTCAAATTCCGA
| ||| ||| |||| || | | | | ||| | | | | ||| | || | | | ||| || | | | || |||| || || || ||||| ||||| || ||| |||| || |||||||| ||||||| |||||||||||||| || ||||| || || |||||||| || ||
----gtatttcttatggatatc-tgtcttcttcttcacagaaagttaat--tttatgaa----tcattgaggtactgatgcgtttcaattttgttg-cagAAACTAAAGCTTGGGAGGTGGATACATTGCGAGGTCATATGAATAACGTTTCATCCGTTATGTTCCATGCAAAACAGGACATTATCGTGTCAAACTCTGA
upper sequence: GLYMA10G34310.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0001g13430.t01 (Vitis vinifera), 3'ss of exon 3
------ggatgcattaaatataaatattgtgggatgtggcgaataataagcttgtagtgtttgaggtgctgcttatgctgttaatgatttgtatctctattttcagACACAAAGGCATGGGAAGTGGACACCTTGAGAGGGCACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAGCAGGATATCATTGTGTCAAATTCCGA
|| |||| || | | | | | || | | || |||||| || | ||| | | || | | | | | |||| |||||||||||||||| |||||||| || || ||||| |||||||||||||||||||||||||| | || ||||| | ||||||| | |||||||||||||| ||
tttcatccatttgttaatcgtattttctttttgttagggttat--agaactttgtagaattgaactagctaatggt-ttgcaacttacct---tttctactttcagACACAAAGGCTTGGGAAGTAGATACTTTGAGGGGGCACATGAATAATGTTTCATGTGTCTTCTTTCATGCAAGGCAGGATGTGATTGTGTCAAATTCAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtagtgtttgaggtgctgcttatgctgttaatgatttgtatctctattttcagACACAAAGGCATGGGAAGTGGACACCTTGAGAGGGCACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAGCAGGATATCATTGTGTCAAATTCCGA
tgttaat putative branch site (score: 3)
tctctattttc putative PPT
ttaatgatttgtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggatgcattaaatataaatattgtgggatgtggcgaataataagcttgtagtgtttgaggtgctgcttatgctgttaatgatttgtatctctattttcagACACAAAGGCATGGGAAGTGGACACCTTGAGAGGGCACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAGCAGGATATCATTGTGTCAAATTCCGA
ggatgca
- - - - -aaatataa
- - - - - - - - - - ttgtggg
- - - - - - - - - - - - - -atgtggc
- - - - - - - - - - - - - - - - - - - - - -gcttgta
- - - - - - - - - - - - - - - - - - - - - - - - - gtgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatttg
