Sequence
atgc intronic sequence ATGC exonic sequence...catattttgaatgaatagcattctgcctatgatataattttcaaccataagtgtaagttccttgatgctttgaacaaaatcagtgtttgacatttggcagCAAAATTGGAAGAACTCATCTAGATCTGTAAATCCAATGTTCATGGATCCAACCAATCCAAGCTGGGGTTGGAGCTGGTTGGAACGATGGATGGCAGCCC
Basic information
species | Glycine max |
transcript | GLYMA03G33560.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G33560.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g03190.1 (Oryza sativa), 3'ss of exon 5
catattttgaatgaatagcattctgcctatgatataattttcaaccataagtgtaagttccttgatgctttgaacaaaatcagtgttt---gacatttggcagCAAAATTGGAAGAACTCATCTAGATCTGTAAATCCAATGTTCATGGATCCAACCAATCCAAGCTGGGGTTGGAGCTGGTTGGAACGATGGATGGCAGCCC------
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----------gtagatatctgtgcttctcaatgacagatgccaatctgtactctgactcactcaaccacacatgcttaa--aatgtttcgaaacttctgtcttctgcagTGGAAGAGCACTTCAAGGTCAGTCAACCCAATGTTTGTAGACCCTAACAACCCACAATGGGGATGGAGCTGGTTGGAACGCTGGATGGCAGCAAAGCCTT
upper sequence: GLYMA03G33560.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G03040.3 (Arabidopsis thaliana), 3'ss of exon 5
-----------------catatt-ttgaatgaatagcattctgc--ctatgatataattttcaaccataagtgtaagttccttgatgc-tttgaacaaaatcagtgtttgacat-------ttggcagCAAAATTGGAAGAACTCATCTAGATCTGTAAATCCAATGTTCATGGATCCAACCAATCCAAGCTGGGGTTGGAGCTGGTTGGAACGATGGATGGCAGCCC
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gtactccagtcgttacctataatgctgaatgtgtggaaagatacaattaaaaagtgaaca-catccattgaagttgaatctgtggttcatttgaatgttgtaatgatcctatatgttcatgtttgcagCAAAACTGGAAGAACAACTCTAAATCTGGAAACCCGATGTTCATGGATCCAAGCAACCCGACATGGGGTTGGAGCTGGTTAGAGAGATGGATGGCTGGTA
upper sequence: GLYMA03G33560.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv08s0040g02360.t01 (Vitis vinifera), 3'ss of exon 5
-------------------------------------------------------------------------------------catattttgaatgaatagcattctgcctatgatataatttt-caaccataagtgtaagttccttgatgctttgaacaaaatcag-tgtttgacatttggcagCAAAATTGGAAGAACTCATCTAGATCTGTAAATCCAATGTTCATGGATCCAACCAATCCAAGCTGGGGTTGGAGCTGGTTGGAACGATGGATGGCAGCCC
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gtatcctattcatcaatactgtttcctgcccattatccatttttaggatcaagaactcactggttggatcttccagttatcttggtatgaaatggaaagaaaatcaaataccagtggtgcactcatgtagacacatgttttattattgcaaattcttgattaatccctgatggaattggtcctacagCAAGCGTGGAAGAATTCTTCAAAGTCCACAAACCTATTGTTCATGGATCCAAGCAACCCCCATTGGGGTTGGAGCTGGTTGGAACGATGGATGGCGGCCCMapped 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|19271218|gb|BM887474.1|BM887474EST: AAGCTACTACGAGAAGAGAAAGAGCGCTGGCTTATGCATTCACTCATCAG CAAAATTGGAAGAACTCATCTAGATCTGTAAATCCAATGTTCATGGATCCA
genomic: AAGCTACTACGAGAAGAGAAAGAGCGCTGGCTTATGCATTCACTCATCAGgtttttctat ... catttggcagCAAAATTGGAAGAACTCATCTAGATCTGTAAATCCAATGTTCATGGATCCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cataagtgtaagttccttgatgctttgaacaaaatcagtgtttgacatttggcagCAAAATTGGAAGAACTCATCTAGATCTGTAAATCCAATGTTCATGGATCCAACCAATCCAAGCTGGGGTTGGAGCTGGTTGGAACGATGGATGGCAGCCC
gtttgac putative branch site (score: 4)
aacaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catattttgaatgaatagcattctgcctatgatataattttcaaccataagtgtaagttccttgatgctttgaacaaaatcagtgtttgacatttggcagCAAAATTGGAAGAACTCATCTAGATCTGTAAATCCAATGTTCATGGATCCAACCAATCCAAGCTGGGGTTGGAGCTGGTTGGAACGATGGATGGCAGCCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - -tgaatga
- - - - - - - - -gcattct
- - - - - - - - - - - - -cctatga
- - - - - - - - - - - - - - - - - - - - -caaccat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatgctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgtttg