Sequence
atgc intronic sequence ATGC exonic sequencegtggttcttctacaatttgaagacataactattccattttattgttttcaatcccatgcttgtgttttgcattatatatatatatatatatatatatatatatatatatatataattgtgaaagtatttgctagtcataatttaagtcatacttcatttgatacttacatttattttttgtttgttaatgcgtaagGTGCCTTGTGTTGCTGTTGTGGAGAATATGTGTCATTTTGATGCTGATGGAAAACGATATTACCCATTTGGCAGAGGTTCAGGTTCTCAG
Basic information
species | Glycine max |
transcript | GLYMA09G31980.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G31980.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os01g52170.1 (Oryza sativa), 3'ss of exon 9
gtggttcttctacaatttgaagacataactattccattttattgttttcaatcccatgcttgtgttttgcattatatatatatatatatatatatatatatatatatatatataattgtgaaagtatttgctagtcataatttaagtcatacttcatttgatacttacatttattttttgtttgttaatgcgtaagGTGCCTTGTGTTGCTGTTGTGGAGAATATGTGTCATTTTGATGCTGATGGAAAACGATATTACCCATTTGGCAGAGGTTCAGGTTCTCAG
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---------------------------------------------------------------------------------gtgtgta-atcttcatatcactgttcattt-taattgtaa-----tctaccgtgcttactat---tcgtgcatcaatttgtttctgc-ttcatcttcatcttctttgtg---aagGTTCCGTGCGTTGCAGTTGTTGAGAACATGTGCTACTTCGATGCTGATGGAAAACGATTTTACCCATTTGGGCAAGGTTCTGGAGCTCAG
upper sequence: GLYMA09G31980.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G129208_T01 (Zea mays), 3'ss of exon 8
gtggttcttctacaatttgaagacataactattccattttattgttttcaatcccatgcttgtgttttgcattatatatatatatatatatatatatatatatatatatatataattgtgaaagtatttgctagtc-ataatttaagtcatacttcatttgatacttacatttattttttgtttgttaatgcgtaagGTGCCTTGTGTTGCTGTTGTGGAGAATATGTGTCATTTTGATGCTGATGGAAAACGATATTACCCATTTGGCAGAGGTTCAGGTTCTCAG
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-------------------------------------------------------------------------------------------------------gtgtgtccacaat-gtgatgcattatacaagtctagcgtataaatctaaccttacattg-actagtttctgtatcctcttc--tgtcgc-caagGTTCCTTGTGTTGCGGTTGTAGAGAACATGTGCTATTTTGATGCTGATGGAAAACGTTATTACCCATTTGGACAAGGTTCTGGAACTCAG
upper sequence: GLYMA09G31980.1 (Glycine max), 3'ss of exon 9
lower sequence: AT3G24430.1 (Arabidopsis thaliana), 3'ss of exon 8
gtggttcttctacaatttgaagacataactattccattttattgttttcaatcccatgcttgtgttttgcattatatatatatatatatatatatatatatatatatatatataattgtgaaagtatttgctagtcataatttaagtcatactt-catttgatacttacatttattttttgtttgttaatgcgta--agGTGCCTTGTGTTGCTGTTGTGGAGAATATGTGTCATTTTGATGCTGATGGAAAACGATATTACCCATTTGGCAGAGGTTCAGGTTCTCAG
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----------------------------------------------------gttatttccctgttccagactttgatcataaactctcctttttcttt-----tatatgga-gcttgtgaacttgtttttcttctcaactctgcaacaaacagatatgaacttccgagatttatttcctgtttggttttacggagtagGTGCCTTGCGTTGCTGTTGTGGAGAATATGTGCCACTTTGACGCTGATGGGAAACGTTATTACCCTTTTGGGAAAGGTTCAGGTTCTGAG
upper sequence: GLYMA09G31980.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv11s0016g04250.t01 (Vitis vinifera), 3'ss of exon 8
gtggttcttctacaatttgaagacataactattccattttattgttttcaatcccatgcttgtgttttgcattatatatatatatatatatatatatatatatatatatatataattgtgaaagtatttgctagtcataatttaagtcatacttcatttgatacttacatttattttttgtttgttaatgcgtaagGTGCCTTGTGTTGCTGTTGTGGAGAATATGTGTCATTTTGATGCTGATGGAAAACGATATTACCCATTTGGCAGAGGTTCAGGTTCTCAG
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-------------------------------------------------------gtacttgattctt--attataatcagctaagctta-agaccaagttaattatgatcagacatgcaaaaaaactgt---gtcaatatctac----taattctcttgacacattcgtta------tgtctgtgcatcc---agGTCCCCTGTGTTGCTGTTGTTGAGAATATGTGTCACTTTGATGCTGATGGCAAGCGATATTACCCATTTGGCAGGGGTTCAGGCTCTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaagtcatacttcatttgatacttacatttattttttgtttgttaatgcgtaagGTGCCTTGTGTTGCTGTTGTGGAGAATATGTGTCATTTTGATGCTGATGGAAAACGATATTACCCATTTGGCAGAGGTTCAGGTTCTCAG
atttgatacttacatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtggttcttctacaatttgaagacataactattccattttattgttttcaatcccatgcttgtgttttgcattatatatatatatatatatatatatatatatatatatatataattgtgaaagtatttgctagtcataatttaagtcatacttcatttgatacttacatttattttttgtttgttaatgcgtaagGTGCCTTGTGTTGCTGTTGTGGAGAATATGTGTCATTTTGATGCTGATGGAAAACGATATTACCCATTTGGCAGAGGTTCAGGTTCTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA