Sequence
atgc intronic sequence ATGC exonic sequencegtatgtgaaaatttttcaaagcagcataccaagggaatgttttgttctgcatctgtgaatgaaattttgttcaggttgatttagatattaatgtgtgattcatgtagGTTCTGGAGTTAGGAATGAATTTTCTCACAGCTGATGATATGAGTGCAATACTTGCTGTGAAACTAAGAAAAAGATTGGGCTTTGGAATGTGGGCAAAAC
Basic information
species | Glycine max |
transcript | GLYMA13G33580.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G33580.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g14050.2 (Oryza sativa), 3'ss of exon 4
gtatgtgaaaatttttcaaagcagcataccaagggaatgttttgttctgcatctgtgaatgaaattttgttcaggttgatttagatattaatgtgtgattcatgtagGTTCTGGAGTTAGGAATGAATTTTCTCACAGCTGATGATATGAGTGCAATACTTGCTGTGAAACTAAGAAAAAGATTGGGCTTTGGAATGTGGGCAAAAC
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----gtgggtact------aatgtcttctgatttgagtatttcttttt-cgtccatggtaaaaattgtaat------gatttttgtgccatctgatggcc-----agGTTCTGGAGATAGGGATGAATTTTCTATCTGCTGAAGATATGAGTGCTGTACTTTCTATGCAGCTGCATAAGAGTGTCGGACTTGGAATGACTGCAAACA
upper sequence: GLYMA13G33580.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G14590.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatgtgaaaatttttcaaagcagcataccaagggaatgttttgttctgcatctgtgaatgaaattttgttcaggttgatttagatattaatgtgtgattcatgtagGTTCTGGAGTTAGGAATGAATTTTCTCACAGCTGATGATATGAGTGCAATACTTGCTGTGAAACTAAGAAAAAGATTGGGCTTTGGAATGTGGGCAAAAC
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-----------------------gtatagttgcacaat-ttcagttctataa----gctctaagttctatagag---aaagtataacttatattggagtgtgtacagGTACTGGAACTTGGAATGAATTTCCTCACAGCAGATGATATGAGCGCAATACTCGCTGTGAAGTTAAGAAAAAGACTTGGGTTTGGAATGTGGACAAAGT
upper sequence: GLYMA13G33580.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G53590.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatgtgaaaatttttcaaagcagcataccaagggaatgttttgttctgcatctgtgaatgaaattttgttcaggttgatttagatattaatgtgtgattcatgtagGTTCTGGAGTTAGGAATGAATTTTCTCACAGCTGATGATATGAGTGCAATACTTGCTGTGAAACTAAGAAAAAGATTGGGCTTTGGAATGTGGGCAAAAC
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------gtatatttgt-aacgcctcata------gaacatcatactttggcctctt--------ccctccttgatctatagtagaacttatgctggagtttatgcagGTACTGGAACTTGGTATGAATTTTCTCGCAGCAGATGATATGAGTGCAATACTTGCTGTGAAATTAAGGAAAAGGCTTGGTTTTGGGATGTGGACAAAGT
upper sequence: GLYMA13G33580.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv19s0138g00140.t01 (Vitis vinifera), 3'ss of exon 4
gtatgtgaaaatttttcaaagcagcataccaagggaatgttttgttctgcatctgtgaatgaaattttgttcaggttgatttagatattaatgtgtgattcatgtagGTTCTGGAGTTAGGAATGAATTTTCTCACAGCTGATGATATGAGTGCAATACTTGCTGTGAAACTAAGAAAAAGATTGGGCTTTGGAATGTGGGCAAAAC
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------gtatgtttgactagccctggaatggtggaaccttactgtgttatctattgggatactattg-acataagtcttcagagattcagtgattcaattaatgcagGTTTTGGGGTTGGGAATGAATTTTCTCACTGCTGATGATATGAGTGCAATACTAGCTATAAAACTGAGGAGAAGATTGGGATTTGGAATGTGGGCAAAATMapped 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|23725489|gb|BU760700.1|BU760700EST: CTTTGATCACTGAAGTTAGGGTTCTTCGCCAGAGTGATGATGATCACTTG GTTCTGGAGTTAGGAATGAATTTTCTCACAGCTGATGATATGAGTGCAATA
genomic: CTTTGATCACTGAAGTTAGGGTTCTTCGCCAGAGTGATGATGATCACTTGgtatgtgaaa ... attcatgtagGTTCTGGAGTTAGGAATGAATTTTCTCACAGCTGATGATATGAGTGCAATA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgtgaatgaaattttgttcaggttgatttagatattaatgtgtgattcatgtagGTTCTGGAGTTAGGAATGAATTTTCTCACAGCTGATGATATGAGTGCAATACTTGCTGTGAAACTAAGAAAAAGATTGGGCTTTGGAATGTGGGCAAAAC
tattaat putative branch site (score: 2)
ttgatttagatattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtgaaaatttttcaaagcagcataccaagggaatgttttgttctgcatctgtgaatgaaattttgttcaggttgatttagatattaatgtgtgattcatgtagGTTCTGGAGTTAGGAATGAATTTTCTCACAGCTGATGATATGAGTGCAATACTTGCTGTGAAACTAAGAAAAAGATTGGGCTTTGGAATGTGGGCAAAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA