Sequence
atgc intronic sequence ATGC exonic sequence...agaatattttaacttctgaattaatgttttgcaggtaattgaaatataaaatttaaataatgtcattgtaataatattaagctcatcttacacttcatagGAACTGTGAGATTTAATCTCGATCCATTCAATGAACACAATGATGCTGACCTCTGGGAGGCTCTGGAGAGGGCACATTTGAAGGATGTGATACGGAGGAA
Basic information
species | Glycine max |
transcript | GLYMA15G09900.1 |
intron # | 23 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G09900.1 (Glycine max), 3'ss of exon 23
lower sequence: LOC_Os04g52900.2 (Oryza sativa), 3'ss of exon 24
agaatattttaacttctgaattaatgttttgcaggtaattgaaatataaaat--ttaaataatgtcattgtaataatattaagctcatcttacacttcatagGAACTGTGAGATTTAATCTCGATCCATTCAATGAACACAATGATGCTGACCTCTGGGAGGCTCTGGAGAGGGCACATTTGAAGGATGTGATACGGAGGAA
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-------------------gtttgt-ttgtgaaaatacatgatatatcttctcgtttgcttttcttacatcataaatgttttttttggtac-tattgtccagGTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATCTCTGGGAAGCGCTTGAAAGGGCTCATCTAAAAGATGTCATAAGGAGGAA
upper sequence: GLYMA15G09900.1 (Glycine max), 3'ss of exon 23
lower sequence: GRMZM2G084181_T01 (Zea mays), 3'ss of exon 23
agaatattttaacttctgaattaatgttttgcaggtaattgaaatataaaatttaaataatgtcattgtaataatattaagctcatcttacacttcatagGAACTGTGAGATTTAATCTCGATCCATTCAATGAACACAATGATGCTGACCTCTGGGAGGCTCTGGAGAGGGCACATTTGAAGGATGTGATACGGAGGAA
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---gtatgctag-tgaaaaatacatgtt-----agctgctggagcttctttttttggcaacttgggtttagtgaaat---atttattaatgccctttcagGTTCTGTTCGGTTTAATCTGGATCCCTTTAATGAGCACAATGATGCGGACCTCTGGGAGGCTCTGGAAAGGGCTCATCTAAAAGATGTTATAAGGAGGAA
upper sequence: GLYMA15G09900.1 (Glycine max), 3'ss of exon 23
lower sequence: AT1G30400.1 (Arabidopsis thaliana), 3'ss of exon 24
agaatattttaa----cttctga-attaatgttt-tgcaggtaattgaaatataaaatttaaataatgtcattgtaata-atattaagctcatcttacacttcatagGAACTGTGAGATTTAATCTCGATCCATTCAATGAACACAATGATGCTGACCTCTGGGAGGCTCTGGAGAGGGCACATTTGAAGGATGTGATACGGAGGAA
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-gtatgtcttgcatttcttctggtgcttatatttattttcctgcttctggtatttatctttcttaaagtcaaaataatgtatactatgccaataacttatatta-agGTACCGTGAGATTCAATCTTGACCCATTTAGTGAACACAACGACGCCGATCTCTGGGAATCTCTTGAGAGGGCACACTTGAAAGATACTATCCGCAGAAA
upper sequence: GLYMA15G09900.1 (Glycine max), 3'ss of exon 23
lower sequence: Vv10s0003g04390.t01 (Vitis vinifera), 3'ss of exon 23
-------agaatattttaacttctgaatt-aatgttttgcaggtaattgaaatataaaatttaaataatgtcattgtaataatattaagctcatcttacacttcatagGAACTGTGAGATTTAATCTCGATCCATTCAATGAACACAATGATGCTGACCTCTGGGAGGCTCTGGAGAGGGCACATTTGAAGGATGTGATACGGAGGAA
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attactgataagatcctaagttatcaattcaatacattttagttaat--aaattt---tttttaatgaagtttgtgttattctaatgatcacttgtttcac---atagGAACTGTGCGATTCAATCTTGATCCTTTCAACGAGCACAATGATGCTGACCTCTGGGAGGCTTTAGAGAGGGCACATTTGAAGGATGTTATCAGGAGGAAMapped 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|10844476|gb|BF070998.1|BF070998EST: TTTGCGTAAAGTTCTTGGCATTATACCACAATCTCCTGTTCTCTTTTCAG GAACTGTGAGATTTAATCTCGATCCATTCAATGAACACAATGATGCTGACC
genomic: TTTGCGTAAAGTTCTTGGCATTATACCACAATCTCCTGTTCTCTTTTCAGgtatttattt ... cacttcatagGAACTGTGAGATTTAATCTCGATCCATTCAATGAACACAATGATGCTGACC
EST:
gi|19270923|gb|BM887179.1|BM887179EST: CACAATCTCCTGTTCTCTTTTCAG GAACTGTGAGATTTAATCTCGATCCATTCAATGAACACAATGATGCTGACC
genomic: CACAATCTCCTGTTCTCTTTTCAGgtatttattt ... cacttcatagGAACTGTGAGATTTAATCTCGATCCATTCAATGAACACAATGATGCTGACC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataaaatttaaataatgtcattgtaataatattaagctcatcttacacttcatagGAACTGTGAGATTTAATCTCGATCCATTCAATGAACACAATGATGCTGACCTCTGGGAGGCTCTGGAGAGGGCACATTTGAAGGATGTGATACGGAGGAA
atcttac putative branch site (score: 3)
atttaaataatgtcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agaatattttaacttctgaattaatgttttgcaggtaattgaaatataaaatttaaataatgtcattgtaataatattaagctcatcttacacttcatagGAACTGTGAGATTTAATCTCGATCCATTCAATGAACACAATGATGCTGACCTCTGGGAGGCTCTGGAGAGGGCACATTTGAAGGATGTGATACGGAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - -acttctg
- - - - - - - - - - - - - - -tgcaggt
- - - - - - - - - - - - - - - - - - - - -aaatataa