Sequence
atgc intronic sequence ATGC exonic sequencegtaaggttttagtaactagttgataatttttgttagggtgcttttcttcagtataaataaaataaaaaaagtgcaagcgtcaattggtggaaacaaagttctatttccccccctctaaaaaggtaaataattcaatttccttctttttaacagGAGCTGGGACAAATTTGAGGATTCGTACAGAGTAATGGTGTTTTCTAATGGTGATAAATGCTGGAATGGTCCAGATAGGAGTTTGAAG
Basic information
species | Glycine max |
transcript | GLYMA20G02950.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G02950.2 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os01g16970.1 (Oryza sativa), 3'ss of exon 12
gtaaggttttagtaactagttgataatttttgttagggtgcttttcttcagtataaataaaataaaaaaagtgcaagcgtcaattggtggaaacaaagttctatttccccccctctaaaaaggtaaataattcaatttccttctttttaacagGAGCTGGGACAAATTTGAGGATTCGTACAGAGTAATGGTGTTTTCTAATGGTGATAAATGCTGGAATGGTCCAGATAGGAGTTTGAAG
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---------------------------------------------tacaagtacagaaccattatgttaag--caatactttattactctcagaatagtgattttgcagttgttttgtgcg-----ataacataatttttttctgct-gtcagGCGCTGGGACAAATTTGAAGAATCCTACAGAGTAATGCAATTTTCAAATGGAGACAGATGCTGGAATGGCCCTGACCGAAGTCTAAAG
upper sequence: GLYMA20G02950.2 (Glycine max), 3'ss of exon 10
lower sequence: AC213600.3_FGT002 (Zea mays), 3'ss of exon 12
gtaaggttttagtaactagttgataatttttgttagggtgcttttcttcagtataaataaaataaaaaaagtgcaagcgtcaattggtggaaacaaagttctatttccccccctctaaaaaggtaaataattcaatttccttctttttaacagGAGCTGGGACAAATTTGAGGATTCGTACAGAGTAATGGTGTTTTCTAATGGTGATAAATGCTGGAATGGTCCAGATAGGAGTTTGAAG
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---------------------------------------------------tttaga-aagtggatttcagtgatagaataacttgcttgaatgttcggtatgttttttccccac-acatccttatgccataaaacgaatttcctatcatcagGCGGTGGGACAAATTTGAAGATTCGTACAGAGTGATGCACTTTTCAAGTGGAGACAAATGCTGGAATGGTCCTGACCGAAGCCTAAAG
upper sequence: GLYMA20G02950.2 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G052875_T02 (Zea mays), 3'ss of exon 12
gtaaggttttagtaactagttgataatttttgttagggtgcttttcttcagtataaataaaataaaaaaagtgcaagcgtcaattggtggaaacaaagttctatttccccccctctaaaaaggtaaataattcaatttccttctttttaacagGAGCTGGGACAAATTTGAGGATTCGTACAGAGTAATGGTGTTTTCTAATGGTGATAAATGCTGGAATGGTCCAGATAGGAGTTTGAAG
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-------------------------------------------acttagaaactgcattcagtgatagaatgacttgcttgaatgcttgg---catgttttttgttcacatgtcctgacgccttaaaacg---aattttcta----tcatcagGAGATGGGACAAATTTGAAGAATCGTACAGAGTAATGCACTTTTCAGGTGGAGACAAATGCTGGAATGGTCCTGACCGAAGCCTAAAG
upper sequence: GLYMA20G02950.2 (Glycine max), 3'ss of exon 10
lower sequence: Vv06s0004g00140.t01 (Vitis vinifera), 3'ss of exon 12
gtaaggttttagtaactagttgataatttttgttagggtgcttttcttcagtataaataaaataaaaaaagtgcaagcgtcaattggtggaaacaaagttctatttccccccctctaaaaaggtaaataattcaatttccttctttttaacagGAGCTGGGACAAATTTGAGGATTCGTACAGAGTAATGGTGTTTTCTAATGGTGATAAATGCTGGAATGGTCCAGATAGGAGTTTGAAG
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------------------------------------gacctgtttttcctacatgtctttttcttgaaagttgcatgttttctttcgt----------cttgatttgcttact-------gagcattttctttctttcattatctgcaaatagGCGCTGGGATAAATTTGAAGATTCATACAGAACTATGCTGTTTTCAAATGGCGAAAAATGCTGGAATGGACCTGATAGGAGTTTGAAGMapped 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|208330421|gb|GE130252.1|GE130252EST: CCCTATAAACAGGCTTCTCAGGAGGAGGGCTATTCCAACACCCGTTTGGG GAGCTGGGACAAATTTGAGGATTC
genomic: CCCTATAAGCAGGCTTCTCAGGAGGAGGGTTATTCCAATACCCGTTTGGGgtaaggtttt ... tttttaacagGAGCTGGGACAAATTTGAGGATTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctatttccccccctctaaaaaggtaaataattcaatttccttctttttaacagGAGCTGGGACAAATTTGAGGATTCGTACAGAGTAATGGTGTTTTCTAATGGTGATAAATGCTGGAATGGTCCAGATAGGAGTTTGAAG
ctctaaa putative branch site (score: 3)
ttcaatttccttcttt putative PPT
taaataattcaatttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaggttttagtaactagttgataatttttgttagggtgcttttcttcagtataaataaaataaaaaaagtgcaagcgtcaattggtggaaacaaagttctatttccccccctctaaaaaggtaaataattcaatttccttctttttaacagGAGCTGGGACAAATTTGAGGATTCGTACAGAGTAATGGTGTTTTCTAATGGTGATAAATGCTGGAATGGTCCAGATAGGAGTTTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG