Sequence
atgc intronic sequence ATGC exonic sequence...ctgtttgcatcgactcggtagaaagttaaaacaaataggctattatttgatcaaaagtaattattttgtttcttgtttcctccacttgtcaaatggacagGTTGGTTTGCCAGCAGATAGAGAACAGTATATACATAGACTCGGTAGAACAGGGCGAAGAGGGAAAGAAGGGCAGGGCATACTGCTGCTGGCTCCTTGGG
Basic information
species | Glycine max |
transcript | GLYMA07G06240.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G06240.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os01g43130.1 (Oryza sativa), 3'ss of exon 8
ctgtttgcatcgactcggtagaaagttaaaacaaataggctattatttgatcaaaagtaattattttgtttcttgtttcctccacttgtcaaatggacagGTTGGTTTGCCAGCAGATAGAGAACAGTATATACATAGACTCGGTAGAACAGGGCGAAGAGGGAAAGAAGGGCAGGGCATACTGCTGCTGGCTCCTTGGG
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-------------------------gtgggtcgcat-gattacatctcataccaaaataattcatctccatttattgaaatttgtttgcc---ctcgcagGTTGGGCTGCCAGCTGATAGAGAACAGTATATACATAGACTTGGTAGAACTGGACGGAAAGGCAAAGATGGGCTAGGTCTCTTACTGTTGGCTCCCTGGG
upper sequence: GLYMA07G06240.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os01g43120.1 (Oryza sativa), 3'ss of exon 8
--------------------------------------------------------------------------------------------------ctgtttgcatcgactcggtagaaagttaaaacaaataggctattatttgatcaaaagtaattattttgtttcttgtttcctccacttgtcaaatggacagGTTGGTTTGCCAGCAGATAGAGAACAGTATATACATAGACTCGGTAGAACAGGGCGAAGAGGGAAAGAAGGGCAGGGCATACTGCTGCTGGCTCCTTGGG
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gtacctgttattatttcccctcacaaaattcttcttgtaaactgatattgctatattgttgttatttatttttcttttctttatgaatgtttggaaaactatttctgttgaccaa--aatatggcaatgcaaatatgcttgcagtttgttgt--gttctgataaagtttttt--ctccttgaatatttgctcttgcagGTTGGGGTGCCAGCTGATAGACAGCAATATATACATAGACTTGGTAGAACTGGACGGAAGGGAAAGGAAGGGCAAGGCCTATTACTGTTGGCTCCATGGG
upper sequence: GLYMA07G06240.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G156158_T02 (Zea mays), 3'ss of exon 8
-ctgtttgcatcgactcggtagaaagttaaaacaaataggctattatttgatcaaaagtaattattttgtttc-ttgtttcctccacttgtcaaatggacagGTTGGTTTGCCAGCAGATAGAGAACAGTATATACATAGACTCGGTAGAACAGGGCGAAGAGGGAAAGAAGGGCAGGGCATACTGCTGCTGGCTCCTTGGG
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gtgagtcatat-aattgtgtaccttgccaaaagaaaggaa---------aataaaagaaaaatgtgtggattcatcaagaaatttatttg-cacatg--tagGTTGGTCTGCCAGCTGATAGAGAACAGTATATACATAGACTCGGAAGGACTGGACGGAAAGGCAAGGAAGGGCAAGGCATCTTACTACTGGCTCCCTGGG
upper sequence: GLYMA07G06240.1 (Glycine max), 3'ss of exon 8
lower sequence: AT5G08610.1 (Arabidopsis thaliana), 3'ss of exon 8
ctgtttgcatcgactcggtagaaagttaaaacaaataggctattatttgatcaaaagtaattattttgtttcttgtttcctccacttgtcaaatgg-acagGTTGGTTTGCCAGCAGATAGAGAACAGTATATACATAGACTCGGTAGAACAGGGCGAAGAGGGAAAGAAGGGCAGGGCATACTGCTGCTGGCTCCTTGGG
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-----------------gtaaccatagttttctgacatggaattgttctgcgactacaaattttatctcttttgtttaactgaagttgtttgcttttgcagATGGGATTGCCATCAGACAGGGAGCAGTATATACATAGACTTGGCAGAACCGGGCGGAAAGGGAAGGAAGGGGAAGGAGTCTTATTGTTGGCACCATGGG
upper sequence: GLYMA07G06240.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv15s0046g01010.t01 (Vitis vinifera), 3'ss of exon 9
--ctgtttgcatcgactcggtagaaagttaaaacaaataggctattatttgatcaaaa-gtaattattttgtttcttgtttcctccacttgtcaaatggacagGTTGGTTTGCCAGCAGATAGAGAACAGTATATACATAGACTCGGTAGAACAGGGCGAAGAGGGAAAGAAGGGCAGGGCATACTGCTGCTGGCTCCTTGGG
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ttgaacttgc-tttatactgtggatttagtataaagatttgagaatatttcttcagaccgctatgggcttgaacctagaaaa-tatatttctgtaattt-cagGTCGGTTTGCCATCTGATAAAGAACAGTATATACATCGACTTGGTAGAACTGGGCGTAAGGGTAAAGAAGGGCAAGGCATATTGTTACTGGCACCTTGGGMapped 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|298171162|gb|HO016194.1|HO016194EST: ATGTATCTGCACGTGGAGTTGATTATCCAGATGTCACTCTTGTTATACAG GTTGGTTTGCCAGCAGATAGAGAACAGTATATACATAGACTCGGTAGAACA
genomic: ATGTATCTGCACGTGGAGTTGATTATCCAGATGTCACTCTTGTTATACAGgtaatacata ... aaatggacagGTTGGTTTGCCAGCAGATAGAGAACAGTATATACATAGACTCGGTAGAACA
EST:
gi|20813627|gb|BQ298105.1|BQ298105EST: ATGTATCTGCACGTGGAGTTGATTATCCAGATGTCACTCTTGTTATACAG GTTGGTTTGCCAGCAGATAGAGAACAGTATATACATCGACTCGGTAGAACA
genomic: ATGTATCTGCACGTGGAGTTGATTATCCAGATGTCACTCTTGTTATACAGgtaatacata ... aaatggacagGTTGGTTTGCCAGCAGATAGAGAACAGTATATACATAGACTCGGTAGAACA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgatcaaaagtaattattttgtttcttgtttcctccacttgtcaaatggacagGTTGGTTTGCCAGCAGATAGAGAACAGTATATACATAGACTCGGTAGAACAGGGCGAAGAGGGAAAGAAGGGCAGGGCATACTGCTGCTGGCTCCTTGGG
atttgat putative branch site (score: 5)
aaaagtaattattttg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctgtttgcatcgactcggtagaaagttaaaacaaataggctattatttgatcaaaagtaattattttgtttcttgtttcctccacttgtcaaatggacagGTTGGTTTGCCAGCAGATAGAGAACAGTATATACATAGACTCGGTAGAACAGGGCGAAGAGGGAAAGAAGGGCAGGGCATACTGCTGCTGGCTCCTTGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
-tgtttgc
- - - - - - - - - - - - - - aaacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - aaaagtaa