Sequence
atgc intronic sequence ATGC exonic sequencegtaaggttttagtaactagttgataatttttgttagggtgcttttcttcagtataaaaaagtgcaagcgtcaattggtgaaaacaaagttctatttcccccctctaaaaaggcaaataattcgatttccttcttttttacagGAGCTGGGACAAATTTGAGGATTCATACAGAGTAATGGTGTTTTCTAATGGTGATAAATGCTGGAATGGTCCTGATAGGAGTTTGAAG
Basic information
species | Glycine max |
transcript | GLYMA07G35090.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G35090.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os01g16970.1 (Oryza sativa), 3'ss of exon 12
gtaaggttttagtaactagttgataatttttgttagggtgcttttcttcagtataaaaaagtgcaagcgtcaattggtgaaaacaaagttctatttcccccctctaaaaaggcaaataattcgatttccttcttttttacagGAGCTGGGACAAATTTGAGGATTCATACAGAGTAATGGTGTTTTCTAATGGTGATAAATGCTGGAATGGTCCTGATAGGAGTTTGAAG
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--------------------------------tacaagtacagaaccattatgttaagcaatac-----tttattactctcagaatagtgattttgcagttgttttgtgcg----ataacataatttttttctgctgt-cagGCGCTGGGACAAATTTGAAGAATCCTACAGAGTAATGCAATTTTCAAATGGAGACAGATGCTGGAATGGCCCTGACCGAAGTCTAAAG
upper sequence: GLYMA07G35090.1 (Glycine max), 3'ss of exon 13
lower sequence: AC213600.3_FGT002 (Zea mays), 3'ss of exon 12
gtaaggttttagtaactagttgataatttttgttagggtgcttttcttcagtataaaaaagtgcaagcgtcaattggtgaaaacaaagttctatttcccccctctaaaaaggcaaataattcgatttccttcttttttacagGAGCTGGGACAAATTTGAGGATTCATACAGAGTAATGGTGTTTTCTAATGGTGATAAATGCTGGAATGGTCCTGATAGGAGTTTGAAG
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------------------------------------------tttagaaagtggatttcagtgatagaataacttgcttgaatgttcggtatgttttttccccacacatccttatgccataaaacgaatttcctatcatcagGCGGTGGGACAAATTTGAAGATTCGTACAGAGTGATGCACTTTTCAAGTGGAGACAAATGCTGGAATGGTCCTGACCGAAGCCTAAAG
upper sequence: GLYMA07G35090.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G052875_T02 (Zea mays), 3'ss of exon 12
gtaaggttttagtaactagttgataatttttgttagggtgcttttcttcagtataaaaaagtgcaagcgtcaattggtgaaaacaaagttctatttcccccctctaaaaaggcaaataattcgatttccttcttttttacagGAGCTGGGACAAATTTGAGGATTCATACAGAGTAATGGTGTTTTCTAATGGTGATAAATGCTGGAATGGTCCTGATAGGAGTTTGAAG
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-------------------------------acttagaaactgca-ttcagtgatagaatg-acttgcttgaatgcttgg---catgttttttgttcacatgtcctgacgccttaaaa---cgaattttctatcat---cagGAGATGGGACAAATTTGAAGAATCGTACAGAGTAATGCACTTTTCAGGTGGAGACAAATGCTGGAATGGTCCTGACCGAAGCCTAAAG
upper sequence: GLYMA07G35090.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv06s0004g00140.t01 (Vitis vinifera), 3'ss of exon 12
gtaaggttttagtaactagttgataatttttgttagggtgcttttcttcagtataaaaaagtgcaagcgtcaattggtgaaaacaaagttctatttcccccctctaaaaaggcaaataattcgatttccttcttttttacagGAGCTGGGACAAATTTGAGGATTCATACAGAGTAATGGTGTTTTCTAATGGTGATAAATGCTGGAATGGTCCTGATAGGAGTTTGAAG
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---------------------gacctgtttttcctacatgtctttttcttg-----aaagttgcatgttttctttcgt----------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|192297387|gb|FG990679.1|FG990679EST: CCCTATAAACAGGCTTCTCAGGAGGAGGGCTATTCCAACACCCGTTTGGG GAGCTGGGACAAATTTGAGGATTCATACAGAGTAATGGTGTTTTCTAATGG
genomic: CCCTATAAACAGGCTTCTCAGGAGGAGGGCTATTCCAACACCCGTTTGGGgtaaggtttt ... ttttttacagGAGCTGGGACAAATTTGAGGATTCATACAGAGTAATGGTGTTTTCTAATGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttctatttcccccctctaaaaaggcaaataattcgatttccttcttttttacagGAGCTGGGACAAATTTGAGGATTCATACAGAGTAATGGTGTTTTCTAATGGTGATAAATGCTGGAATGGTCCTGATAGGAGTTTGAAG
ctctaaa putative branch site (score: 3)
ttcgatttccttcttt putative PPT
aaataattcgattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaggttttagtaactagttgataatttttgttagggtgcttttcttcagtataaaaaagtgcaagcgtcaattggtgaaaacaaagttctatttcccccctctaaaaaggcaaataattcgatttccttcttttttacagGAGCTGGGACAAATTTGAGGATTCATACAGAGTAATGGTGTTTTCTAATGGTGATAAATGCTGGAATGGTCCTGATAGGAGTTTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG