Sequence
atgc intronic sequence ATGC exonic sequencegtttgactctctctctctctctctgtctctctctctatctctatctcttataattactgcagataatttgatcatcagattcctaaacttttatgcttaagcagAGACAAGCTGCTCAATGTGTGGGTCGTGTAATCCGTTCAAAGGCTGATTATGGAATGATGATTTTTGCAGACAAAAG
Basic information
species | Glycine max |
transcript | GLYMA16G28290.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G28290.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os05g05260.1 (Oryza sativa), 3'ss of exon 8
---gtttgactctctctctctctc-----tctgtct---ctctctctatctctatctcttataattactgcagataatttgatcatcagattcctaaacttttatgcttaagcagAGACAAGCTGCTCAATGTGTGGGTCGTGTAATCCGTTCAAAGGCTGATTATGGAATGATGATTTTTGCAGACAAAAG
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gtaataatactacttctgccaggggaaagtagggctggatgatttgtagctttatttttc-tagagacatccaacaaagttttcttgacattt-tggattctgttaat--gccagAGGCAAGCTGCGCAATGTGTTGGCCGTGTGATCCGTTCTAAAGCAGATTATGGAATGATGATATTTGCTGACAAGAG
upper sequence: GLYMA16G28290.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G097605_T02 (Zea mays), 3'ss of exon 3
-------------------gtttgactctctctctctctctctgtctctctctctatctctatctcttataattact-gcagataatttgatcatcagattcctaaacttttatgcttaagcagAGACAAGCTGCTCAATGTGTGGGTCGTGTAATCCGTTCAAAGGCTGATTATGGAATGATGATTTTTGCAGACAAAAG
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gtaattcattattactttgaggaaaaaataactccttttgattgacacctcttatctccttatgttgtcgagatatttgtaacacaatttctcgaaataaatttgaaatctcattaatgt-cagAGGCAAGCGGCCCAATGTGTCGGTCGTGTTATTCGCTCCAAAGCTGATTATGGGATGATGATATTTGCTGACAAGAG
upper sequence: GLYMA16G28290.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G03190.2 (Arabidopsis thaliana), 3'ss of exon 9
gtttgactctctctctctctctctgtctctctctctatctctatctcttataattactgcagataatttgatcatcagattcctaaacttttatgcttaagcagAGACAAGCTGCTCAATGTGTGGGTCGTGTAATCCGTTCAAAGGCTGATTATGGAATGATGATTTTTGCAGACAAAAG
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gtatgattcttattttatgatcttat-tagattttggtgtgcaactcttttacctgtttgtgactgtt-----gttaactctttttggcttta-----acacagAGGCAAGCAGCTCAATGTGTAGGGCGAGTAATCCGGTCAAAGGCTGATTATGGGATGATGATATTTGCAGACAAAAG
upper sequence: GLYMA16G28290.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv07s0104g00060.t01 (Vitis vinifera), 3'ss of exon 9
-----gtttgactctctctctctctctctgtctctctctctatctctatctctta--taattactgcagat---aatttgat--catcagattcctaaacttttatgc--ttaagcagAGACAAGCTGCTCAATGTGTGGGTCGTGTAATCCGTTCAAAGGCTGATTATGGAATGATGATTTTTGCAGACAAAAG
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gtattgttcactgcactctgtgtcatttagtgcaatatgcattgtttggcctttggttggttagttcatgtcttgcttaaataatatgagcttcattaatgagaatgtaatggagcagAGGCAAGCTGCACAATGTGTGGGCCGAGTAATCCGTTCAAAGGCAGATTATGGGATGATGATTTTCGCTGACAAAAG
upper sequence: GLYMA16G28290.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S145_26V6.2 (Physcomitrella patens), 3'ss of exon 11
----gtttgactctctctctctctctctgtctctctctcta----tctctat---ctcttataattactgcagataatttgatcatcagattcctaaacttttatgcttaag-cagAGACAAGCTGCTCAATGTGTGGGTCGTGTAATCCGTTCAAAGGCTGATTATGGAATGATGATTTTTGCAGACAAAAG
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gtatgtttcgctactggactggtttatggattcggttcatgaaattctcaacgagttcatgacattactttctcct-tttgctaatgaggtgcatttgtatactcgtgtgggtcagCGTCAAGCTGCACAGTGTGTGGGACGCGTTATTCGTTCTAAAGCAGATTATGGAATGATGATTTTTGCTGACAAGAG
upper sequence: GLYMA16G28290.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ08988 (Selaginella moellendorffii), 3'ss of exon 8
gtttgactctctctctctctctctgtctctctctctatctctatctcttataattactgcagataatttgatcatcagattcctaaacttttatgcttaagcagAGACAAGCTGCTCAATGTGTGGGTCGTGTAATCCGTTCAAAGGCTGATTATGGAATGATGATTTTTGCAGACAAAAG
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-------------------------------------------------gcaagttctttacgt--tctgttctccg----cttattcgtttac-ctgtaccagAGACAAGCTGCTCAATGCGTAGGCCGTGTCATTCGCTCAAAAGCAGATTACGGAATGATGATATTTGCAGACAAGAGMapped 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|208096357|gb|GD892106.1|GD892106EST: GGAGATTTTCTGACTTTTTGTATGCATTG AGACAAGCTGCTCAATGTGTGGGTCGTGTAATCCGTTCAAAGGCTGATTA
genomic: GGAGATTTTCTGAC-TTTTG-ATGCATTGgtttgactct ... gcttaagcagAGACAAGCTGCTCAATGTGTGGGTCGTGTAATCCGTTCAAAGGCTGATTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataattactgcagataatttgatcatcagattcctaaacttttatgcttaagcagAGACAAGCTGCTCAATGTGTGGGTCGTGTAATCCGTTCAAAGGCTGATTATGGAATGATGATTTTTGCAGACAAAAG
tcctaaa putative branch site (score: 2)
taaacttttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgactctctctctctctctctgtctctctctctatctctatctcttataattactgcagataatttgatcatcagattcctaaacttttatgcttaagcagAGACAAGCTGCTCAATGTGTGGGTCGTGTAATCCGTTCAAAGGCTGATTATGGAATGATGATTTTTGCAGACAAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT