Sequence
atgc intronic sequence ATGC exonic sequence...acttgcatgaggtgttttatttttcagttatcaaggaatcttttactggtatgatagattttatcatatgaacttcattctgaaaacaaggtatattcagGTGCTACAGGAAAAAGGCATTCATATTTGGGATGGCAATGCATCCAGAGAATACCTTGATGG
Basic information
species | Glycine max |
transcript | GLYMA06G01280.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G01280.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os11g29390.1 (Oryza sativa), 3'ss of exon 5
acttgcatgaggtgttttatttttcagttatcaaggaatcttttactggtatgatagattttatcatatgaacttcattctgaaaacaagg-----tatattcagGTGCTACAGGAAAAAGGCATTCATATTTGGGATGGCAATGCATCCAGAGAATACCTTGATGG
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-----cagcagatgaggcataagtgaatattgttagattttagtttcttcacatgagctcccatgcttaccactttggtacaatgatacatttttctaccttcagGTTTTACAAGAGAAAGGCATTCATATTTGGGATGGCAATGCTTCGAGAGAGTATCTTGACAG
upper sequence: GLYMA06G01280.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv18s0001g12940.t01 (Vitis vinifera), 3'ss of exon 4
---acttgcatgaggtgttttatttttcagttatcaaggaatcttttactggtatgatagattttatcatatgaacttcattctgaaaacaaggtatatt--cagGTGCTACAGGAAAAAGGCATTCATATTTGGGATGGCAATGCATCCAGAGAATACCTTGATGG------------------------
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attattgtctcagagaaatttatttacaagtccttaa-----tattaaaaaaaaaaactaattatacttgaggaaatggattatagattgatgttattgcaatagGTGCTGCAGAAGAAAGACATTCATATATGGGATGGCAATGCATCCAGAGAGTACCTTGACAGGCAACTACTTGGCTATTGGAATCT
upper sequence: GLYMA06G01280.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv03s0038g04500.t01 (Vitis vinifera), 3'ss of exon 6
acttgcatgaggtgttttatttttcagttatcaaggaatcttttactggtatgatagattttatcatatgaacttcattctgaaaacaaggtatatt---cagGTGCTACAGGAAAAAGGCATTCATATTTGGGATGGCAATGCATCCAGAGAATACCTTGATGG
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-tccaaataccttggtcaagattct--cttctcttccatccagtatagatgtgaaattcagatctaagtgtacatcattctaaaatgtttgtattgttaacagGTCCTACAGGAAAAGGGAATTCATATATGGGATGGCAATGCATCCAGGGACTACCTTGATAGMapped 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|192311470|gb|FK005201.1|FK005201EST: GGGTTGTTGAAGAGCTTCTTTGGTTTATCAGTGGCTCAACAAATGCCAAG GTGCTACAGGAAAAAGGCATTCATATTTGGGATGGCAATGCATCCAGAGAA
genomic: GGGTTGTTGAAGAGCTTCTTTGGTTTATCAGTGGCTCAACAAATGCCAAGgtaatgatat ... gtatattcagGTGCTACAGGAAAAAGGCATTCATATTTGGGATGGCAATGCATCCAGAGAA
EST:
gi|192311469|gb|FK005200.1|FK005200EST: GGGTTGTTGAAGAGCTTCTTTGGTTTATCAGTGGCTCAACAAATGCCAAG GTGCTACAGGAAAAAGGCATTCATATTTGGGATGGCAATGCATCCAGAGAA
genomic: GGGTTGTTGAAGAGCTTCTTTGGTTTATCAGTGGCTCAACAAATGCCAAGgtaatgatat ... gtatattcagGTGCTACAGGAAAAAGGCATTCATATTTGGGATGGCAATGCATCCAGAGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctggtatgatagattttatcatatgaacttcattctgaaaacaaggtatattcagGTGCTACAGGAAAAAGGCATTCATATTTGGGATGGCAATGCATCCAGAGAATACCTTGATGG
atagattttatcatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acttgcatgaggtgttttatttttcagttatcaaggaatcttttactggtatgatagattttatcatatgaacttcattctgaaaacaaggtatattcagGTGCTACAGGAAAAAGGCATTCATATTTGGGATGGCAATGCATCCAGAGAATACCTTGATGG
- -tgcatga
- - - - - ggtgttt
- - - - - - - - - - - - - - - - - - - - - - - -ggtatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaacaa