Sequence
atgc intronic sequence ATGC exonic sequencegtgcttcttctacaatttgaagacataactattccattttattgttttcaatcccatgcttgtgttttgcattttttatccttcctctgtttatatatatttaaaaaaaaatgtgaaagtatttgctagtcatacttcttttgattctattttcatttaatacttatatttagttttcgtctgttaatgcataagGTGCCTTGTGTTGCTGTTGTGGAGAACATGTGTCATTTTGATGCTGATGGAAAACGATATTACCCATTTGGCAGAGGTTCAGGTTCTCAG
Basic information
species | Glycine max |
transcript | GLYMA07G09820.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G09820.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os01g52170.1 (Oryza sativa), 3'ss of exon 9
gtgcttcttctacaatttgaagacataactattccattttattgttttcaatcccatgcttgtgttttgcattttttatccttcctctgtttatatatatttaaaaaaaaatgtgaaagtatttgctagtcatacttcttttgattctattttcatttaatacttatatttagttttcgtctgttaatgcataagGTGCCTTGTGTTGCTGTTGTGGAGAACATGTGTCATTTTGATGCTGATGGAAAACGATATTACCCATTTGGCAGAGGTTCAGGTTCTCAG
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----------------------------------------------------------------------------------------gtgtgta-atcttcatatcactgt-tcattttaattgtaatctaccgtgcttactattcgtgcatcaatt--tgtttctgcttcatcttcatcttctt-tgtg-aagGTTCCGTGCGTTGCAGTTGTTGAGAACATGTGCTACTTCGATGCTGATGGAAAACGATTTTACCCATTTGGGCAAGGTTCTGGAGCTCAG
upper sequence: GLYMA07G09820.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G129208_T01 (Zea mays), 3'ss of exon 8
gtgcttcttctacaatttgaagacataactattccattttattgttttcaatcccatgcttgtgttttgcattttttatccttcctctgtttatatatatttaaaaaaaaatgtgaaagtatttgctagtcatacttcttttgattctattttcatttaatacttatatttagttttcgtctgttaatgcataagGTGCCTTGTGTTGCTGTTGTGGAGAACATGTGTCATTTTGATGCTGATGGAAAACGATATTACCCATTTGGCAGAGGTTCAGGTTCTCAG
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----------------------------------------------------------------------------------------------gtgtgtccacaa-----tgtgatgcattatacaagtctagcgtat---aaatctaaccttacattg-actagtttctg--tatcctcttctgtcgc-caagGTTCCTTGTGTTGCGGTTGTAGAGAACATGTGCTATTTTGATGCTGATGGAAAACGTTATTACCCATTTGGACAAGGTTCTGGAACTCAG
upper sequence: GLYMA07G09820.1 (Glycine max), 3'ss of exon 9
lower sequence: AT3G24430.1 (Arabidopsis thaliana), 3'ss of exon 8
gtgcttcttctacaatttgaagacataactattccattttattgttttcaatcccatgcttgtgttttgcattttttatccttcctctgtttatatatatttaaaaaaaaatgtgaaagtatttgctagtcatacttcttttgattctattttcatttaatacttatatttagttttcgtctg--ttaatgcataagGTGCCTTGTGTTGCTGTTGTGGAGAACATGTGTCATTTTGATGCTGATGGAAAACGATATTACCCATTTGGCAGAGGTTCAGGTTCTCAG
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----------------------------------------------gttatttccctgttccagactttgatcataaactctcctttttcttttatat-------ggagcttgtgaacttgttt-ttcttctcaactctgc--aacaaacagatatgaacttccgagatttatttcctgtttggttttacggagtagGTGCCTTGCGTTGCTGTTGTGGAGAATATGTGCCACTTTGACGCTGATGGGAAACGTTATTACCCTTTTGGGAAAGGTTCAGGTTCTGAG
upper sequence: GLYMA07G09820.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv11s0016g04250.t01 (Vitis vinifera), 3'ss of exon 8
gtgcttcttctacaatttgaagacataactattccattttattgttttcaatcccatgcttgtgttttgcattttttatccttcctctgtttatatatatttaaaaaaaaatgtgaaagtatttgctagtcatacttcttttgattctattttcatttaatacttatatttagttttcgtctgttaatgcataagGTGCCTTGTGTTGCTGTTGTGGAGAACATGTGTCATTTTGATGCTGATGGAAAACGATATTACCCATTTGGCAGAGGTTCAGGTTCTCAG
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----------------------------------------------------------------------gtacttgattcttattataatcagctaagcttaagaccaagttaattatgatcagacatgcaaaaaaactgtgtcaatatctactaattctcttgacacattcgttatgtctgtgcatcca---gGTCCCCTGTGTTGCTGTTGTTGAGAATATGTGTCACTTTGATGCTGATGGCAAGCGATATTACCCATTTGGCAGGGGTTCAGGCTCTCAGMapped 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|51345383|gb|CO986116.1|CO986116EST: TGTCGTTCATTGATGTTGCAAAAGGAGTTCGGATGTTTTCAAAACTTAAG GTGCCTTGTGTTGCTGTTGTGGAGAACATGTGTCATTTTGATGCTGATGGA
genomic: TGTCGTTCATTGATGTTGCAAAAGGAGTTCGGATGTTTTCAAAACTTAAGgtgcttcttc ... aatgcataagGTGCCTTGTGTTGCTGTTGTGGAGAACATGTGTCATTTTGATGCTGATGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgattctattttcatttaatacttatatttagttttcgtctgttaatgcataagGTGCCTTGTGTTGCTGTTGTGGAGAACATGTGTCATTTTGATGCTGATGGAAAACGATATTACCCATTTGGCAGAGGTTCAGGTTCTCAG
tgttaat putative branch site (score: 3)
tctattttcatttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcttcttctacaatttgaagacataactattccattttattgttttcaatcccatgcttgtgttttgcattttttatccttcctctgtttatatatatttaaaaaaaaatgtgaaagtatttgctagtcatacttcttttgattctattttcatttaatacttatatttagttttcgtctgttaatgcataagGTGCCTTGTGTTGCTGTTGTGGAGAACATGTGTCATTTTGATGCTGATGGAAAACGATATTACCCATTTGGCAGAGGTTCAGGTTCTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA