Sequence
atgc intronic sequence ATGC exonic sequence...catcctatttattgcatacctgtcacacttaattgaatccccattgttgtgcaagttctgatgtattttgacttactaatatgtaatttcatttctacagATGGGCAATGTTTGGTTTTGCTGTTGGGTTGCTAACAGAGTATGCAACAGGTTCGGACTTTGTTGATCAAGTAAAGATCCTTCTATCGAATTTTGGAATA
Basic information
species | Glycine max |
transcript | GLYMA02G08740.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G08740.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g40710.1 (Oryza sativa), 3'ss of exon 1
catcctatttattgcatacctgtc-acacttaattgaatccccattgttgtgcaagttctgatgtattttgacttactaatatgtaatt----tcat-----ttctacagATGGGCAATGTTTGGTTTTGCTGTTGGGTTGCTAACAGAGTATGCAACAGGTTCGGACTTTGTTGATCAAGTAAAGATCCTTCTATCGAATTTTGGAATA
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------aataaaagcagggtgacctagacttaggttcggtgtt-ttgttgaatagggtaagatttgctt--gtttactaatg-gtgattctgatcatcaaaatctcgcagATGGGCTATGTTTGGGTTTGCAGTAGGGATGCTAACAGAGTACGCAACCGGCTCGGATTTTGTTCAACAAGTGAAGATCCTTCTCTCCAATTTTGGGATT
upper sequence: GLYMA02G08740.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G019807_T01 (Zea mays), 3'ss of exon 1
catcctatttattgcatacctgtcacacttaattgaatcccca--ttgttgtgcaagttctgatg---tattttgacttactaat--atgtaatttcat-ttctacagATGGGCAATGTTTGGTTTTGCTGTTGGGTTGCTAACAGAGTATGCAACAGGTTCGGACTTTGTTGATCAAGTAAAGATCCTTCTATCGAATTTTGGAATA
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-------aaaaatgcaagataggtagacgtaag-gattcaccacgttgttgagtacgttaagacagcttgtctctatgcgctaattcaccttgctacacatcttgcagGTGGGCCATGTTTGGGTTTGCAGTAGGGATGCTAACAGAGTATGCAACAGGCTCGGATTTTGTTCAGCAAATGAAGATCCTTCTCTCCAATTTTGGAATT
upper sequence: GLYMA02G08740.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G143469_T01 (Zea mays), 3'ss of exon 1
catcctatttattgcatacctgtcacacttaattgaatcccca---ttgttgtgcaagttc--tgatgtattttgacttactaatatgtaatttcatttctacagATGGGCAATGTTTGGTTTTGCTGTTGGGTTGCTAACAGAGTATGCAACAGGTTCGGACTTTGTTGATCAAGTAAAGATCCTTCTATCGAATTTTGGAATA
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---aatacacgatgggtagatgcaaagattcaccacgttcttgagtaggttaaggaagctcatctctatgcgctaattcatcagctttctaca--aaccttgcagGTGGGCCATGTTTGGGTTTGCAGTAGGGATGCTAACAGAGTACGCAACAGGCTCTGATTTTGTTCAGCAATTGAAGATCCTTCTTTCCAATTTCGGAATT
upper sequence: GLYMA02G08740.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G34000.1 (Arabidopsis thaliana), 3'ss of exon 1
catcctatttattgcatacctgtcacacttaat-tgaatccccattgttgt--gcaagttctgatgtattttgacttactaatatgtaatttcatttctacagATGGGCAATGTTTGGTTTTGCTGTTGGGTTGCTAACAGAGTATGCAACAGGTTCGGACTTTGTTGATCAAGTAAAGATCCTTCTATCGAATTTTGGAATA
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attgatgtttcttcaaattcagacatatatagcctaaagtttcacacttgtcagttggtactgcctagacaagagataactctgtgtgttttg---tttgtagGTGGGCTATGTTTGGTTTCGCAGTTGGTATGCTCACAGAGTATGCAACAGGATCAGACCTTGTTGATCAAGTTAAGATCCTTCTCTCAAATTTCGGCATT
upper sequence: GLYMA02G08740.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0072g00120.t01 (Vitis vinifera), 3'ss of exon 1
--catcctatttattgcatacctgtcacacttaattgaatccccattgttgtgcaagttctgatgt-attttgacttactaatatgtaatttcatttctacagATGGGCAATGTTTGGTTTTGCTGTTGGGTTGCTAACAGAGTATGCAACAGGTTCGGACTTTGTTGATCAAGTAAAGATCCTTCTATCGAATTTTGGAATA
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tcctttataaacattattatgttggcctatattaatgtatttct-tcatcagccaatctagcttcttacttgggtctgtctctgtctgggatg--ttaatcagATGGGCAATGTTCGGTTTTGCTGTTGGGATGCTAACAGAGTACGCAACAGGCTCTGACTTTGTTGATCAAGTAAAGATCCTTCTCTCCAATTTTGGGATAMapped 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|27425149|gb|CA936669.1|CA936669EST: CAGGGTCCTTTCTTTGGTTTCATTGGGAAAAACGAGATTAGCAATGGAAG ATGGGCAATGTTTGGTTTTGCTGTTGGGTTGCTAACAGAGTATGCAACAGG
genomic: CAGGGTCCTTTCTTTGGTTTCATTGGGAAAAACGAGATTAGCAATGGAAGgtaaaaaagt ... atttctacagATGGGCAATGTTTGGTTTTGCTGTTGGGTTGCTAACAGAGTATGCAACAGG
EST:
gi|31474310|gb|CD416338.1|CD416338EST: CAGGGTCCTTTCTTTGGTTTCATTGGGAAAAACGAGATTAGCAATGGAAG ATGGGCAATGTTTGGTTTTGCTGTTGGGTTGCTAACAGAGTATGCAACAGG
genomic: CAGGGTCCTTTCTTTGGTTTCATTGGGAAAAACGAGATTAGCAATGGAAGgtaaaaaagt ... atttctacagATGGGCAATGTTTGGTTTTGCTGTTGGGTTGCTAACAGAGTATGCAACAGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttgtgcaagttctgatgtattttgacttactaatatgtaatttcatttctacagATGGGCAATGTTTGGTTTTGCTGTTGGGTTGCTAACAGAGTATGCAACAGGTTCGGACTTTGTTGATCAAGTAAAGATCCTTCTATCGAATTTTGGAATA
tactaat putative branch site (score: 1)
tttcatttct putative PPT
ttactaatatgtaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catcctatttattgcatacctgtcacacttaattgaatccccattgttgtgcaagttctgatgtattttgacttactaatatgtaatttcatttctacagATGGGCAATGTTTGGTTTTGCTGTTGGGTTGCTAACAGAGTATGCAACAGGTTCGGACTTTGTTGATCAAGTAAAGATCCTTCTATCGAATTTTGGAATA
- - - - - - -gcatacc
- - - - - - - - - - tgtcaca
- - - - - - - - - - - - - - - - - - - ccccatt
- - - - - - - - - - - - - - - - - - - - - - - - -tgcaagt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tctgatg