Sequence
atgc intronic sequence ATGC exonic sequencegtgtgttgtgttcttgagaaaatatgtagtgtttcatttgactgctgttgtttcttggttggtaatgttatgatgcttggttactgtagGAGGAAAGAAGAATGTCTTTGCCAAAATATCAGGTGCATGATGAAAGTAGCCAGGTAAGTCATACTACCTCTTTAATAGATGGAGTTGCTTTCACATCTA
Basic information
species | Glycine max |
transcript | GLYMA08G05390.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G05390.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os09g38790.1 (Oryza sativa), 3'ss of exon 5
----------------------gtgtgttgtgttcttgagaaaatatgtagtgttt-catttgactgct-gttgtttcttggttggtaatgtta--tgatgcttggttactgtagGAGGAAAGAAGAATGTCTTTGCCAAAATATCAGGTGCATGATGAAAGTAGCCAGGTAAGTCATACTACCT---CTTTAATAGATGGAGTTGCTTTCACATCTA
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gtatattttccatcctctctttagttgttattctcattagagatcatttggtatatatgttacattactagatatgagtttgagggttatctcaaatatttgttgacttgtgtagGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAGGTAAGTTCTGATTTTTATAATTTTATATCTGTAATATTAATGATAT---
upper sequence: GLYMA08G05390.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os09g38790.3 (Oryza sativa), 3'ss of exon 5
----------------------gtgtgttgtgttcttgagaaaatatgtagtgt-ttcatttgactgct-gttgtttcttggttggtaatgtta--tgatgcttggttactgtagGAGGAAAGAAGAATGTCTTTGCCAAAATATCAGGTGCATGATGAAAGTAGCCAGGTAAGTCATACTACCTCTTTAATAGATGGAGTTGCTTTCACATCTA
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gtatattttccatcctctctttagttgttattctcattagagatcatttggtatatatgttacattactagatatgagtttgagggttatctcaaatatttgttgacttgtgtagGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAG----------------------------------------------
upper sequence: GLYMA08G05390.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G081812_T01 (Zea mays), 3'ss of exon 5
--gtgtgttgtgttcttgagaaaatatgtagtgtttcatttg---actgctgttgtttcttg----gttggtaatgtta--tgatgcttggttactgtagGAGGAAAGAAGAATGTCTTTGCCAAAATATCAGGTGCATGATGAAAGTAGCCAGGTAAGTCATACTACCTCTTTAATAGATGGAGTTGCTTTCACATCTA
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gtatgcttctaaccatcatctatatgtcttttagtttacttgtgcatagcgatatatgattgaaatgttaataatctcaattttttgctgtcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAGGTAAGTTGTGTTTCTTATGATACTATTATTGTAGTTTCTCAAACAA
upper sequence: GLYMA08G05390.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G081812_T02 (Zea mays), 3'ss of exon 5
--gtgtgttgtgttcttgagaaaatatgtagtgtttcatttg---actgctgttgtttcttg----gttggtaatgttatgatgct--tggttactgtagGAGGAAAGAAGAATGTCTTTGCCAAAATATCAGGTGCATGATGAAAGTAGCCAGGTAAGTCATACTACCTCTTTAATAGATGGAGTTGCTTTCACATCTA
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gtatgcttctaaccatcatctatatgtcttttagtttacttgtgcatagcgatatatgattgaaatgttaataatctcaattttttgctgtcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAG----------------------------------------------
upper sequence: GLYMA08G05390.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv03s0017g02160.t01 (Vitis vinifera), 3'ss of exon 5
---gtgtgttgtgttcttgagaaaatatgtagtgtttcatttgactgctgttgtttcttggttggtaatgttatga----tgcttgg--ttactgtagGAGGAAAGAAGAATGTCTTTGCCAAAATATCAGGTGCATGATGAAAGTAGCCAGGTAAGTCATACTACCTCTTTAATAGATGGAGTTGCTTTCACATCTA
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gttagttgttagttacctttctggatgtatcatgcca-atcttttggatgctgtactttggtttaacacactttaaattgtgtttgaaatatctacagGAGGAAAGAAGGATGTCATTACTGAAGTATCAGGTGCATGATGAAACTAGCCAG----------------------------------------------Mapped 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|208259384|gb|GE053870.1|GE053870EST: CTGCCACCAACGAAGTCTACTTAGTTTGGGATGATGAGGCAATGTCCATG GAGGAAAGAAGAATGTCTTTGCCAAAATATCAGGTGCATGATGAAAGTAGC
genomic: CTGCCACCAACGAAGTCTACTTAGTTTGGGATGATGAGGCAATGTCCATGgtgtgttgtg ... gttactgtagGAGGAAAGAAGAATGTCTTTGCCAAAATATCAGGTGCATGATGAAAGTAGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catttgactgctgttgtttcttggttggtaatgttatgatgcttggttactgtagGAGGAAAGAAGAATGTCTTTGCCAAAATATCAGGTGCATGATGAAAGTAGCCAGGTAAGTCATACTACCTCTTTAATAGATGGAGTTGCTTTCACATCTA
atttgac putative branch site (score: 4)
taatgttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtgttgtgttcttgagaaaatatgtagtgtttcatttgactgctgttgtttcttggttggtaatgttatgatgcttggttactgtagGAGGAAAGAAGAATGTCTTTGCCAAAATATCAGGTGCATGATGAAAGTAGCCAGGTAAGTCATACTACCTCTTTAATAGATGGAGTTGCTTTCACATCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA