Sequence
atgc intronic sequence ATGC exonic sequence...aatgaaagctaaatatttagatatatggctaactctaccatgttatattacactgcaaacatgatgcccttaatttggttgtaaactgtcattttgcagaTCAATAGAAGAATGGAGTTTGTATTTGCTAGTCATAGTTTTGATGTTTGGGAGAACTGGACTCTAGAAGGTTCCTTACAGGAATGCAGACTGGTGAACTG
Basic information
species | Glycine max |
transcript | GLYMA18G47240.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G47240.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g03460.1 (Oryza sativa), 3'ss of exon 4
aatgaaagctaaat--atttagatatatggctaactctaccatgttatattacactgcaaacatgatgcccttaatttggttgtaaactgtcattttgcagaTCAATAGAAGAATGGAGTTTGTATTTGCTAGTCATAGTTTTGATGTTTGGGAGAACTGGACTCTAGAAGGTTCCTTACAGGAA---TGCAGACTGGTGAACTG
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-ccagtagtaaaatgggttgagaaacagaagtgttttgatttcttatcgacacccagggttgctaatgttctaacatttaacttttttaaatgtgctgaagATTAATAGGAGGATGGAGTTTGTGTTTGCAAGTCATACATTTGATGTTTGGGAGAGCTGGATGCTGGAGGGGTCCTTGTTGGAGGGTTGCAAACTTATCA----
upper sequence: GLYMA18G47240.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G476107_T02 (Zea mays), 3'ss of exon 5
-----aatgaaagctaaatatttagatatatggctaactctaccatgttatattacactgcaaaca-tgatgcccttaatttggttgtaaactgtcattttgcagaTCAATAGAAGAATGGAGTTTGTATTTGCTAGTCATAGTTTTGATGTTTGGGAGAACTGGACTCTAGAAGGTTCCTTACAGGAATGCAGACTGGTGAACTG
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ttctgaacgaaaaaaaaagtttgagaaatagaggcatcatt----tttctcagtgc-ccatgatcactgatgttcttataaagatttgttgcactacattgacagATTAATAGGAAGATGGAGTTTGTGTTTGCAAGCCATTCTTTTGATGTTTGGGAGAGCTGGATGCTGGACGGTTCCTTGCTGGAGG----------------
upper sequence: GLYMA18G47240.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM5G841360_T01 (Zea mays), 3'ss of exon 5
-----aatgaaagctaaatatttagatatatggctaactctaccatgttatattacactgcaaaca-tgatgcccttaatttggttgtaaactgtcattttgcagaTCAATAGAAGAATGGAGTTTGTATTTGCTAGTCATAGTTTTGATGTTTGGGAGAACTGGACTCTAGAAGGTTCCTTACAGGAATGCAGACTGGTGAACTG
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ttctgaacgaaaaaaaaagtttgagaaatagaggcatcatt----tttctcagtgc-ccatgatcactgatgttcttataaagatttgttgcactacattgacagATTAATAGGAAGATGGAGTTTGTGTTTGCAAGCCATTCTTTTGATGTTTGGGAGAGCTGGATGCTGGACGGTTCCTTGCTGGAGGGTAGCAAGCTTATCA-
upper sequence: GLYMA18G47240.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G01510.1 (Arabidopsis thaliana), 3'ss of exon 5
aatgaaagctaaatatttagatatatggctaactctaccatgtta-tattacactgcaaacatgatgcccttaatttggttgtaaac-tgtcattttgcagaTCAATAGAAGAATGGAGTTTGTATTTGCTAGTCATAGTTTTGATGTTTGGGAGAACTGGACTCTAGAAGGTTCCTTACAGGAATGCAGACTGGTGAACTG
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---gtagctcttacattagagagtgttacttccattggtaactcaatgttgctcttatggaatc-taaaagtggttgtgtcatgggtgtgtgtgtgtgcagATCAATAGAAGAATGGAGTTTGTGTTTGCTAGCCATAGTTTTGACGTGTGGGAGAGTTGGAGTCTAGAAGGTTCTCTGGACGAATGTCGGCTTGTTAACT-
upper sequence: GLYMA18G47240.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv15s0046g02250.t01 (Vitis vinifera), 3'ss of exon 5
aatga-aagctaaatatttagatatatggctaactctaccatgttatattacactgcaaaca---tgatgcccttaatttggttgtaaactgtcattttgcagaTCAATAGAAGAATGGAGTTTGTATTTGCTAGTCATAGTTTTGATGTTTGGGAGAACTGGACTCTAGAAGGTTCCTTACAGGAATGCAGACTGGTGAACTG
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aacaataattttcataagatgctgcatg-taaattatatgtagtcatactgatgtttatattctttagggaatatagtataattat--attttgatgatgcagATAAATAGAAGAATGGAATTTGTATTTGCCAGTCACAGCTTTGATGTTTGGGAGAGTTGGATGTTGGAAGGTTCTTTGGAGGAATGTAGGTTGGTCAACT-Mapped 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|26058460|gb|CA801374.1|CA801374EST: ACACAATTGGATTGCGATCCCTTGCTGCTGGTGGAAAATTGTTGCAGA TCAATAGAAGAATGGAGTTTGTATTTGCTAGTCATAGTTTTGATGTTTGGG
genomic: ACACAATTGGATTGCGATCCCTTGCTGCTGGTGGAAAATTGTTGCAGGtaagtgcatt ... attttgcagaTCAATAGAAGAATGGAGTTTGTATTTGCTAGTCATAGTTTTGATGTTTGGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattacactgcaaacatgatgcccttaatttggttgtaaactgtcattttgcagaTCAATAGAAGAATGGAGTTTGTATTTGCTAGTCATAGTTTTGATGTTTGGGAGAACTGGACTCTAGAAGGTTCCTTACAGGAATGCAGACTGGTGAACTG
ccttaat putative branch site (score: 4)
tcatttt putative PPT
ttaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatgaaagctaaatatttagatatatggctaactctaccatgttatattacactgcaaacatgatgcccttaatttggttgtaaactgtcattttgcagaTCAATAGAAGAATGGAGTTTGTATTTGCTAGTCATAGTTTTGATGTTTGGGAGAACTGGACTCTAGAAGGTTCCTTACAGGAATGCAGACTGGTGAACTG
- - - - - - - - - - - - - - - - ctctacc
- - - - - - - - - - - - - - - - - - - - - - - - - cactgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggttgta