Sequence
atgc intronic sequence ATGC exonic sequence...tcagaaaaaaaagtttatagatgtgctactttttgtctcaagtgtgccactttgttgatcagctgtgaaccttatgtttcactctggttgtttctcctagGCACATTTGCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGATTCAGCTAGACAGAACCTTGCTGCAACTTTTGTTAATGCATTTGTAAATGCTGGCT
Basic information
species | Glycine max |
transcript | GLYMA06G44340.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G44340.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G314233_T01 (Zea mays), 3'ss of exon 4
tcagaaaaaaaagtttatagatgtgctactttttgtctcaagtgtgccactttgtt--gatcagctgtgaaccttatgtttcactctggttgtttctcctagGCACATTTGCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGATTCAGCTAGACAGAACCTTGCTGCAACTTTTGTTAATGCATTTGTAAATGCTGGCT---
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-------------gtgatgtatattttactgcttatcatatttttaatagcatgattaaatcctctataataattatgatcatgttttacaatatgt---agGTCCATTTGATTGATGGCCG---TGGTGCCAGCTCCAGTCTTGATTCCGCAAGACAGAATTTAGCTGCAACATTTGTAAATGCATTTGTGAATGCTGGGTTTG
upper sequence: GLYMA06G44340.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G155384_T02 (Zea mays), 3'ss of exon 12
tcagaaaaaaaagtttatagatgtgctactttttgtctcaagtgtgccactttgttgatcagctgtgaaccttatgtttcactctggttgtttctcctagGCACATTTGCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGATTCAGCTAGACAGAACCTTGCTGCAACTTTTGTTAATGCATTTGTAAATGCTGGCT---
|| | | || || | |||| ||| | | | ||| | | || || | | || || || | | | | ||| |||||| ||||||| || | |||| | | ||| ||||||| || |||||||| | |||||||| ||||| ||||||||||| |||||||| |
-gtgatgtatattttcattattttgctgcttaccatatttgtaatagcacaat-taaattttctataataattgtggttgtgttttacaatatgc---agGTCCATTTGATTGATGGTCG---TGGTGCCAGCTCCAGTCTTGATTCTGCAAGACAGAATTTAGCTGCAACATTTGTAAATGCATTTGTGAATGCTGGGTTTG
upper sequence: GLYMA06G44340.1 (Glycine max), 3'ss of exon 12
lower sequence: AT2G20580.1 (Arabidopsis thaliana), 3'ss of exon 10
tcagaaaaaaaagtttatagatgtgctactttttgtctcaagtgtgccactttg--ttgatcagctgtgaaccttatgtttcactctggttgtttctcctagGCACATTTGCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGATTCAGCTAGACAGAACCTTGCTGCAACTTTTGTTAATGCATTTGTAAATGCTGGCT
||| ||||| | ||| ||| | |||| | | | || | | | ||| || | || ||| | | ||||| || || || || ||| ||||||| | |||||||| || ||||| ||||||||||| | ||||| || ||||| |||||||| ||||||||||| |
----gtaaatcagttttaatgtgttaggcttgcta-ctcatttatttagttacaaattatgtttccctcagtctt-tgacctgccctttttgaattttatagGCTCACTTACTCGACGGCAGGGCTAGCTCCGGTGCAAGCGTGGATTCTGCTAGACAGAATTTGGCTGCTACCTTTGTCAATGCATTCGTAAATGCTGGTT
upper sequence: GLYMA06G44340.1 (Glycine max), 3'ss of exon 12
lower sequence: AT4G28470.1 (Arabidopsis thaliana), 3'ss of exon 10
-----tcagaaaaaaaagtttatagatgtgctactttttgtctcaagtgtgccactttgttgatcagctgtgaaccttatgtttcactctggttgtttctcctagGCACATTTGCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGATTCAGCTAGACAGAACCTTGCTGCAACTTTTGTTAATGCATTTGTAAATGCTGGCT
|||| || | || | || |||| || | | | | |||| || | ||| |||| | || | ||| || | |||| || ||||||||||| ||||||| ||||| ||||||| || |||||||| || || || |||| |||||||| |||||||||||||||||||| |
gtatatcagtttaattgaatattatgtctgttactggtttatttggttacagga-tatgtttat-ggaagtgcctcttacctgtc-cactgaaatttgc----agGCTCACTTGCTTGATGGTAGGGCTAGCTCTGGTCCAAGTGTGGACTCAGCTAGGCAAAATCTATCTGCGACTTTTGTGAATGCATTTGTAAATGCTGGAT
upper sequence: GLYMA06G44340.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv12s0028g03130.t01 (Vitis vinifera), 3'ss of exon 12
---tcagaaaaaaaagtttatagatgtgctactt-tttgtctcaagtgtgccactttgttgatcagctgtgaaccttatgtttcactctggttgtttctcctagGCACATTTGCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGATTCAGCTAGACAGAACCTTGCTGCAACTTTTGTTAATGCATTTGTAAATGCTGGCT
| | | | || ||||||| || | || || | |||| | | | | || ||| | || || || | | | | || | |||||||||||||||||||||||||||||||||||||||||||||||| || || ||||||||||| || || |||||||| |||||||||||||||||||| |
acatgaaagactcaattttataggtgcttcagttattcagttgaagtttatggtcatctc--ttag-tgttaggctcatactt-atttgcttggattttgctagGCACATTTGCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGACTCTGCCAGACAGAACCTGGCAGCTACTTTTGTCAATGCATTTGTAAATGCTGGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gccactttgttgatcagctgtgaaccttatgtttcactctggttgtttctcctagGCACATTTGCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGATTCAGCTAGACAGAACCTTGCTGCAACTTTTGTTAATGCATTTGTAAATGCTGGCT
tgttgat putative branch site (score: 4)
ttgtttctcct putative PPT
ttatgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcagaaaaaaaagtttatagatgtgctactttttgtctcaagtgtgccactttgttgatcagctgtgaaccttatgtttcactctggttgtttctcctagGCACATTTGCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGATTCAGCTAGACAGAACCTTGCTGCAACTTTTGTTAATGCATTTGTAAATGCTGGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - aaaaaaa
- - - - - - - - - - - -tgctact
- - - - - - - - - - - - - - - - - - - - - - tgccact
- - - - - - - - - - - - - - - - - - - - - - - - - - tgttgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cagctgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccttatg