Sequence
atgc intronic sequence ATGC exonic sequence...aacatatctcagttatcatctgttgtattttactgccttagtgccttgtccatatttttgagtaaattgattgaaaacctcgcctttttgttttccttagGACCAACCCTTACTGGAATTCTTCCATATGCTGGTTTAAAGTTCTACATGTATGAGAAATTGAAGACTCATGTTCCTGAAGAACATCAAAAGTCCATTAT
Basic information
species | Glycine max |
transcript | GLYMA06G05550.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G05550.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G420119_T01 (Zea mays), 3'ss of exon 4
-------aacatatctcagttatcatctgttgtattttactgccttagtgccttgtccatatttttgagtaaattgattgaaaacctcgcctttttgttttccttagGACCAACCCTTACTGGAATTCTTCCATATGCTGGTTTAAAGTTCTACATGTATGAGAAATTGAAGACTCATGTTCCTGAAGAACATCAAAAGTCCATTAT
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aatatcctgcaaattttagtttaaatttcattaattgagatgcctgtattacgtatt-atatcatgagaggag--gattaaagatt----cttttaatgaatttcagGCCCAACTCTTATTGGTATTCTTCCATATGCTGGCTTGAAGTTTTACATATATGAAGATCTGAAATCTCAAGTTCCAGACGATTACAAGGATTCTGTTAT
upper sequence: GLYMA06G05550.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G14560.1 (Arabidopsis thaliana), 3'ss of exon 4
aacatatctcagttatcatctgttgtattttactgccttagtgccttgtccatatttttgagt--aaattgattga-aaacctcg---cctttttgttttcct-tagGACCAACCCTTACTGGAATTCTTCCATATGCTGGTTTAAAGTTCTACATGTATGAGAAATTGAAGACTCATGTTCCTGAAGAACATCAAAAGTCCATTAT
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-------gttacaaattatcttaaactcttatctctgtgtgtgcacttttcctaatttggatttgaagatgattaacaaaggttggagctttcctgtgtctctgcagGGCCAACGCTGATCGGGATCCTTCCTTACGCGGGGCTTAAGTTCTACATATATGAGGAATTGAAAAGGCATGTTCCTGAAGAGCATCAAAACTCTGTTCG
upper sequence: GLYMA06G05550.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv04s0008g01060.t01 (Vitis vinifera), 3'ss of exon 4
aacatatctcagttatcatctgttgtattttactgccttagtgccttgtccatatttttgagtaaattgat--tgaaaacctcgcctttttgttttcctt----agGACCAACCCTTACTGGAATTCTTCCATATGCTGGTTTAAAGTTCTACATGTATGAGAAATTGAAGACTCATGTTCCTGAAGAACATCAAAAGTCCATTAT
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-----tgctcttttagtttgaatcatttctt-ccatttcagtttgttacttttaagtctgcggaaatgaatcctctcttctttttttcttcatcctttttgagcagGTCCGACACTCATTGGAATCCTTCCTTATGCTGGATTGAAGTTTTACATATATGAAAAACTTAAGAGGCATGTTCCTGAAGAGCACCAAAAGTCTATTGCMapped 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|16343525|gb|BI969120.1|BI969120EST: TACAAGTGTCTATAAGGAAGGGNNNGTTCGTGGACTTNNNAGGGGTGCAG GACCAACCCTTACTGGAATTCTTCCATATGCTGGNNNAAAGTTCTACATGT
genomic: TACAAGTGTCTATAAGGAAGGGGGAGTTCGTGGACTTTATAGGGGTGCAGgtatgtctgt ... ttttccttagGACCAACCCTTACTGGAATTCTTCCATATGCTGGTTTAAAGTTCTACATGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtccatatttttgagtaaattgattgaaaacctcgcctttttgttttccttagGACCAACCCTTACTGGAATTCTTCCATATGCTGGTTTAAAGTTCTACATGTATGAGAAATTGAAGACTCATGTTCCTGAAGAACATCAAAAGTCCATTAT
aattgat putative branch site (score: 4)
cctcgcctttttgttt putative PPT
atatttttgagtaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aacatatctcagttatcatctgttgtattttactgccttagtgccttgtccatatttttgagtaaattgattgaaaacctcgcctttttgttttccttagGACCAACCCTTACTGGAATTCTTCCATATGCTGGTTTAAAGTTCTACATGTATGAGAAATTGAAGACTCATGTTCCTGAAGAACATCAAAAGTCCATTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - tctgttg
- - - - - - - - - - - - - - - - ctgcctt
- - - - - - - - - - - - - - - - - - - - -tgccttg