Sequence
atgc intronic sequence ATGC exonic sequence...ttgttgtgcaagttctgctagttttttattttttttttattttatcggttgcaagttctgctgtattttgacttactaatcagtaatttcatttctacagATGGGCAATGTTTGGTTTTGCTGTAGGGTTGCTAACAGAGTATGCAACAGGTTCAGACTTTGTTGATCAAGTGAAGATCCTTCTATCGAATTTTGGGATA
Basic information
species | Glycine max |
transcript | GLYMA16G27850.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G27850.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g40710.1 (Oryza sativa), 3'ss of exon 1
ttgttgtgcaagttctgctagttttttatttttt-ttttattttatcggttgcaagttctgctgtattttgacttactaatc-agtaatttcatttctacagATGGGCAATGTTTGGTTTTGCTGTAGGGTTGCTAACAGAGTATGCAACAGGTTCAGACTTTGTTGATCAAGTGAAGATCCTTCTATCGAATTTTGGGATA
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aataaaagcagggtgacctagacttaggttcggtgttttgttgaatagg--gtaagatttgcttgtttactaatggtgattctgatcatcaaaatctcgcagATGGGCTATGTTTGGGTTTGCAGTAGGGATGCTAACAGAGTACGCAACCGGCTCGGATTTTGTTCAACAAGTGAAGATCCTTCTCTCCAATTTTGGGATT
upper sequence: GLYMA16G27850.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G019807_T01 (Zea mays), 3'ss of exon 1
ttgttgtgcaagttctgctagttttttattttttttttattttatcggttgcaagttctgctgtattttgacttactaatcagtaatttcat---ttctacagATGGGCAATGTTTGGTTTTGCTGTAGGGTTGCTAACAGAGTATGCAACAGGTTCAGACTTTGTTGATCAAGTGAAGATCCTTCTATCGAATTTTGGGATA
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-aaaaatgcaagatagg-tagacgtaaggattcaccacgttgttgagtacgttaagacagct-tgtctctatgcgctaattcaccttgctacacatcttgcagGTGGGCCATGTTTGGGTTTGCAGTAGGGATGCTAACAGAGTATGCAACAGGCTCGGATTTTGTTCAGCAAATGAAGATCCTTCTCTCCAATTTTGGAATT
upper sequence: GLYMA16G27850.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G143469_T01 (Zea mays), 3'ss of exon 1
ttgttgtgcaagttctgctagttttttattttttttttatttt---atcggttgcaagttctgctgtattttgacttactaatcagtaatttc--atttctacagATGGGCAATGTTTGGTTTTGCTGTAGGGTTGCTAACAGAGTATGCAACAGGTTCAGACTTTGTTGATCAAGTGAAGATCCTTCTATCGAATTTTGGGATA
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----aatacacgatggg-tagatgcaaagattcaccacgttcttgagtaggttaaggaagctcatctctatgcgctaattcatcagctttctacaaaccttgcagGTGGGCCATGTTTGGGTTTGCAGTAGGGATGCTAACAGAGTACGCAACAGGCTCTGATTTTGTTCAGCAATTGAAGATCCTTCTTTCCAATTTCGGAATT
upper sequence: GLYMA16G27850.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G34000.1 (Arabidopsis thaliana), 3'ss of exon 1
-----ttgttgtgcaagttctgctagttttttattttttttttat-tttatcggttgcaagttctgctgtattttgacttactaatcagtaatttcatttctacagATGGGCAATGTTTGGTTTTGCTGTAGGGTTGCTAACAGAGTATGCAACAGGTTCAGACTTTGTTGATCAAGTGAAGATCCTTCTATCGAATTTTGGGATA
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attgatgtttcttcaaattcagacatatatagcctaaagtttcacacttgtcagttg---gtactgcctagacaagagata--actctgtg-tgttttgtttgtagGTGGGCTATGTTTGGTTTCGCAGTTGGTATGCTCACAGAGTATGCAACAGGATCAGACCTTGTTGATCAAGTTAAGATCCTTCTCTCAAATTTCGGCATT
upper sequence: GLYMA16G27850.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0072g00120.t01 (Vitis vinifera), 3'ss of exon 1
ttgttgtgcaagttctgcta-gttttttattttttttttattttatcggttgcaagttctgctg--tattttgacttacta--atcagtaatttcatttctacagATGGGCAATGTTTGGTTTTGCTGTAGGGTTGCTAACAGAGTATGCAACAGGTTCAGACTTTGTTGATCAAGTGAAGATCCTTCTATCGAATTTTGGGATA
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-tcctttataaacattattatgttggcctatattaatgtatttcttcatcagccaatctagcttcttacttgggtctgtctctgtctgggatgttaat----cagATGGGCAATGTTCGGTTTTGCTGTTGGGATGCTAACAGAGTACGCAACAGGCTCTGACTTTGTTGATCAAGTAAAGATCCTTCTCTCCAATTTTGGGATAMapped 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|10253060|gb|BE820826.1|BE820826EST: CAGGGTCCTTTCTTTGGTTTCATCGGGAAAAATGAGATTAGCAATGGAAG ATGGGCAATGTTTGGTTTTGCTGTAGGGTTGCTAACAGAGTATGCAACAGG
genomic: CAGGGTCCTTTCTTTGGTTTCATCGGGAAAAATGAGATTAGCAATGGAAGgtaaaagttt ... atttctacagATGGGCAATGTTTGGTTTTGCTGTAGGGTTGCTAACAGAGTATGCAACAGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cggttgcaagttctgctgtattttgacttactaatcagtaatttcatttctacagATGGGCAATGTTTGGTTTTGCTGTAGGGTTGCTAACAGAGTATGCAACAGGTTCAGACTTTGTTGATCAAGTGAAGATCCTTCTATCGAATTTTGGGATA
tactaat putative branch site (score: 1)
tttcatttct putative PPT
taatttcatttcta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgttgtgcaagttctgctagttttttattttttttttattttatcggttgcaagttctgctgtattttgacttactaatcagtaatttcatttctacagATGGGCAATGTTTGGTTTTGCTGTAGGGTTGCTAACAGAGTATGCAACAGGTTCAGACTTTGTTGATCAAGTGAAGATCCTTCTATCGAATTTTGGGATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - tgcaagt
- - - - - - -tctgcta
- - - - - - - - - - - - - - - - - - - - - - -cggttgc