Sequence
atgc intronic sequence ATGC exonic sequencegtaaattcaccaagtaaaagtatggtttggattttttttgtcatatcttggtatgccagttaatgtctggaatctgtttggaatttgaatttctgaatgcctgattttcaccagATTGCAGAGATCCTTAAAGATCGTCCATCTTGGTTCCGTGACTGTCGGAGCCTAGAAGTTTTTACTATGTTTCCTGCTGGAAATGGAGGAACCATTGAAC
Basic information
species | Glycine max |
transcript | GLYMA12G08080.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G08080.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g01890.1 (Oryza sativa), 3'ss of exon 6
gtaaattcaccaagtaaaagtatggtttggattttttttgtcatatcttggtatgccagttaatgtctggaatctgtttggaatttgaatttctgaatgcctgattttcaccagATTGCAGAGATCCTTAAAGATCGTCCATCTTGGTTCCGTGACTGTCGGAGCCTAGAAGTTTTTACTATGTTTCCTGCTGGAAATGGAGGAACCATTGAAC
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--actgttatca--tcaaatttaatcgtgaagataagcag--atatcttgctttttttgttactttattcagg------agattttgtgtctcatagaactttgttacg--tagGTGGTAGAGATATTGAAAGATCGTCCATCTTGGTTCCGTGATTGTCGAAACCTGGAAGTCTTTACAATGATTCCAGCAGGAAATGGAGGAACGGTTGAAC
upper sequence: GLYMA12G08080.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os10g33960.2 (Oryza sativa), 3'ss of exon 5
gtaaattcaccaagtaaaagtatggtttggattttttttgtcatatcttggtatgccagttaatgtctggaatctgtttggaatttgaatttctgaatgcctgattttcaccagATTGCAGAGATCCTTAAAGATCGTCCATCTTGGTTCCGTGACTGTCGGAGCCTAGAAGTTTTTACTATGTTTCCTGCTGGAAATGGAGGAACCATTGAAC
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---tcttcat-acgtatttggttgatgtgaatattttctagaaagctgaaagacttta-ttgttttcagaaaattgttggga----gattcttatagtgtgctatg-----cagATCGTGGAGATCTTAAAAGACCGCCCATCTTGGTTCCGTGATTGTCGAAGTCTTGAAGTCTTCACAATGTTTCCAGCTGGAAATGGTGGCACGATCGAAC
upper sequence: GLYMA12G08080.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G042250_T03 (Zea mays), 3'ss of exon 6
gtaaattcaccaagtaaaagtatggtttggattttttttgtcatatcttggt--atgccagttaatgtctggaatctgtttggaatttgaatttctga-atgcctgattttcaccagATTGCAGAGATCCTTAAAGATCGTCCATCTTGGTTCCGTGACTGTCGGAGCCTAGAAGTTTTTACTATGTTTCCTGCTGGAAATGGAGGAACCATTGAAC
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----------------tggatttttttcatattttgcctatcaatcaataattgatacaaattttagcatttactttcaagaaattatttgatcctgatatagctgtgtcatgc-agGTCATAGAAATCTTGAAAGATCGTCCCTCTTGGTTCCGTGATTGTCGAAGTCTGGAAGTGTTTACAATGTTTCCAGCTGGAAATGGGGGAACAATTGAAC
upper sequence: GLYMA12G08080.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G469551_T02 (Zea mays), 3'ss of exon 6
gtaaattcaccaagtaaaagtatggtttggattttttttgtcatatcttggtatgccagttaatgtctggaatctgtttggaatttgaatttctgaatgcctgattttcaccagATTGCAGAGATCCTTAAAGATCGTCCATCTTGGTTCCGTGACTGTCGGAGCCTAGAAGTTTTTACTATGTTTCCTGCTGGAAATGGAGGAACCATTGAAC
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--ttttttgccacatggttcaaaacttagaacattttctgaattttttggacataca-------gtctgtaaattatctggaggttt--cttacgattgcttgctt---gatagATAGTGGAAATCTTGAAAGATCGTCCATCTTGGTTTCGTGATTGTCGGAGTCTTGAAGTCTATACAATGTTACCAGCTGGAAATGGTGGAACCATTGAAC
upper sequence: GLYMA12G08080.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G109987_T01 (Zea mays), 3'ss of exon 6
gtaaattcaccaagtaaaagtatggtttggattttttttgtcatatcttggtatgccagttaatgtctggaatctgttt----ggaatt-tgaatttctga-atgcctgattttcaccagATTGCAGAGATCCTTAAAGATCGTCCATCTTGGTTCCGTGACTGTCGGAGCCTAGAAGTTTTTACTATGTTTCCTGCTGGAAATGGAGGAACCATTGAAC
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-------------------ggatacttttcattttttcctgtatcaatcaatagttgatacaaattttagcatttactttcaagaaattatctgatcctgatatggctgtgatatgc-agGGCATAGAGATCTTGAAAGATCGTCCCTCTTGGTTCCGTGATTGCCGAAGTCTTGAAGTGTTTACAAGGTTTCCAGCTGGAAATGGGGGAACAATTGAAC
upper sequence: GLYMA12G08080.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G60690.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaaattcaccaagtaaaagtatggtttggattttttttgtcatatcttggtatgccagttaatgtctggaatctgtttggaatttgaatttctgaatgcctgattttcaccagATTGCAGAGATCCTTAAAGATCGTCCATCTTGGTTCCGTGACTGTCGGAGCCTAGAAGTTTTTACTATGTTTCCTGCTGGAAATGGAGGAACCATTGAAC
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-------------------gtaagaaagggacactcttt-tcgttgctaaagatacaagtcataatgtttcattttcaaccagtttgggttttt-------tgtgttcttacagATTGCAGAGATCCTCAAAGATCGGCCATCTTGGTTCCGTGACTGTAGGAGCCTTGAAGTTTTCACTATGTTCCCGGCTGGTAATGGTGGCACAATCGAGC
upper sequence: GLYMA12G08080.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv06s0004g02800.t01 (Vitis vinifera), 3'ss of exon 5
--------------gtaaattcaccaagtaaa--agtatggtttggattttttttgtcatatcttg--gtatgccagttaatgtctggaatctgtttggaatttgaat--ttctgaatgcctgattttcac----------cagATTGCAGAGATCCTTAAAGATCGTCCATCTTGGTTCCGTGACTGTCGGAGCCTAGAAGTTTTTACTATGTTTCCTGCTGGAAATGGAGGAACCATTGAAC
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gtaagcttcagccaattatgtggtcaggtcatttatgaaaatttgaacatttttcttgatattttattgtaggacctttattttttcatgttataataatattagcatgctttgaaaagtaatatttttgtttgcgactgacagATTGCAGAGATCCTCAAAGATCGTCCATCTTGGTTCCGGGACTGTCGGAGCCTTGAAGTTTTCACCATGTTTCCAGCTGGAAATGGAGGAACTGTTGAACMapped 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|24136783|gb|BU927293.1|BU927293EST: GTGGAGTGGCAGCTCGAGCCTGTGGTCTTGTTAGTTTAGAACCTACGAAG ATTGCAGAGATCCTTAAAGATCGTCCATCTTGGTTCCGTGACTGTCGGAGC
genomic: GTGGAGTGGCAGCTCGAGCCTGTGGTCTTGTTAGTTTAGAACCTACGAAGgtaaattcac ... ttttcaccagATTGCAGAGATCCTTAAAGATCGTCCATCTTGGTTCCGTGACTGTCGGAGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaatgtctggaatctgtttggaatttgaatttctgaatgcctgattttcaccagATTGCAGAGATCCTTAAAGATCGTCCATCTTGGTTCCGTGACTGTCGGAGCCTAGAAGTTTTTACTATGTTTCCTGCTGGAAATGGAGGAACCATTGAAC
gcctgat putative branch site (score: 4)
ttttcacc CT-rich tract
aatttgaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaattcaccaagtaaaagtatggtttggattttttttgtcatatcttggtatgccagttaatgtctggaatctgtttggaatttgaatttctgaatgcctgattttcaccagATTGCAGAGATCCTTAAAGATCGTCCATCTTGGTTCCGTGACTGTCGGAGCCTAGAAGTTTTTACTATGTTTCCTGCTGGAAATGGAGGAACCATTGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA