Sequence
atgc intronic sequence ATGC exonic sequencegtttgtgcttctctacatgccttaatcttttgatatcttcttaaatatctcctagattggtgttgataattgattgtactttgaaattgtgcttgttttgcaatattgaagtcaccaacctagttatttaatttgttttgatatttggatcagGTTGCCAATTTATGTGCTCCGGTAGAAGAATGGACTGTTGGTGGAACTGCACTCACCTCACTGATGGATGTGGAGAGGAGGCATG
Basic information
species | Glycine max |
transcript | GLYMA15G11890.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G11890.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 12
gtttgtgcttctctacatgccttaatcttttgatatcttcttaaat--atctcctagattggtgttgataattgattgtactttgaaattgtgcttgttt-tgcaatattgaagtca--ccaac--ctagttatttaatt-tgttttgatatttggat-------cagGTTGCCAATTTATGTGCTCCGGTAGAAGAATGGACTGTTGGTGGAACTGCACTCACCTCACTGATGGATGTGGAGAGGAGGCATG
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--gtatgca-cactatagttccctgtcacttgttggatacccagattggaacctaagaacgggctttgtgg--aagtgatgtttgcagc-atgtttgtttacgaaccagcgcaggcagatgaacttctaatgatatgatcatgctcttatgtttgtatttttactcagGTTGGCAACCTCGCTGCTCCTGTGGAAGAATGGACCGTTGGTGGAACTGCATTGACATCGTTGATGGATGTTGAGAGGAGGCACG
upper sequence: GLYMA15G11890.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G143862_T01 (Zea mays), 3'ss of exon 5
gtttgtgcttctctacatgccttaatcttttgatatcttcttaaatatctcctagattggtgttgataattgattgtactttgaaattgtgcttgttttgcaatattgaagtcaccaacctagttatttaatttgttttgatatttggatcagGTTGCCAATTTATGTGCTCCGGTAGAAGAATGGACTGTTGGTGGAACTGCACTCACCTCACTGATGGATGTGGAGAGGAGGCATG
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-------------------------------------------------acctacagtattaggagcatctgggagatgtcttatattgtgattgt---ggctgatcgtatgtacttgcatgatttggtcgct-gtcttttttctttgcttagGTTGGCAACCTTGCGGCTCCAGTAGAAGAATGGACTGTTGGTGGAACAGCATTGACATCACTGATGGATGTTGAGAGGAGGCACG
upper sequence: GLYMA15G11890.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 12
gtttgtgcttctctacatgccttaatcttttgatatcttcttaaatatctcctagattggtgttgataattgattgtactttgaaattgtgcttgtt-ttgcaatattgaagtcac-caacctagttatttaatttgttttgatatttggatcagGTTGCCAATTTATGTGCTCCGGTAGAAGAATGGACTGTTGGTGGAACTGCACTCACCTCACTGATGGATGTGGAGAGGAGGCATG
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-----------------------------------------------------acagtgttaggaatacctgggagatatcttataatgtgtttgtgactgatcttatgtacttgcatgatttaatcgctgtctttttttt--ttcttggctcagGTTGGCAACCTTGCGGCTCCAGTTGAAGAATGGACTGTTGGTGGAACAGCATTAACATCACTGATGGATGTTGAGAGGAGGCACG
upper sequence: GLYMA15G11890.1 (Glycine max), 3'ss of exon 12
lower sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 12
gtttgtgcttctctacatgccttaatcttttgatatcttcttaaatatctcctagattggtgttgataattgattgtactttgaaattgtgcttgttttgcaatattgaagtcaccaacctagttatttaatttgttttgatatttggatcagGTTGCCAATTTATGTGCTCCGGTAGAAGAATGGACTGTTGGTGGAACTGCACTCACCTCACTGATGGATGTGGAGAGGAGGCATG
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------------------gtttgtactccaccatttccactaaaatctgttttccatctgtgatcataatagcctttgg--taaactagtatgtgcttag----------------aatgagatgagttaacttatt---------ggcgcagGTTGGGAACTTGGCTGCTCCTGTGGAAGAATGGACTGTAGGTGGGACTGCTCTCACAGCCTTGATGGATGTCGAGAGGAGACACG
upper sequence: GLYMA15G11890.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 12
----------------gtttgtgcttctctacatgccttaatcttttgatatcttcttaaatatctcctagat-tggtgttgataattgattgtactttgaaattgtgcttgttttgcaatattgaagtcaccaacctag------ttatttaatttgttttgatatttggatcagGTTGCCAATTTATGTGCTCCGGTAGAAGAATGGACTGTTGGTGGAACTGCACTCACCTCACTGATGGATGTGGAGAGGAGGCATG
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gttggttcttcattccgcttaatcatttttgtactttttgatcagtcttccttttttttcatttttccaatatctcattctgcttatagagttcaaactcttgttattct-atcgaaggttatagtagttaataactgaacaaactttttgtaattgtttctcatcatgtcttcagGTTGGGAATCTGTCTGCTCCAGTTGAAGAATGGACTGTTGGTGGAACTGCCTTGACTTCATTAATGGATGTGGAGAGGAGACATGMapped 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|21602004|gb|BQ612335.1|BQ612335EST: ATGGTGCTGGAGCCCTCCTTCATAGTGGGAAGACTGGATTAATATCATCA GTTGCCAATTTATGTGCTCCGGTAGAAGAATGGACTGTTGGTGGAACTGCA
genomic: ATGGTGCTGGAGCCCTCCTTCATAGTGGGAAGACTGGATTAATATCATCAgtttgtgctt ... tttggatcagGTTGCCAATTTATGTGCTCCGGTAGAAGAATGGACTGTTGGTGGAACTGCA
EST:
gi|17021166|gb|BM092200.1|BM092200EST: ATGGTGCTGGAGCCCTCCTTCATAGTGGGAAGACTGGATTAATATCATCA GTTGCCAATTTATGTGCTC
genomic: ATGGTGCTGGAGCCCTCCTTCATAGTGGGAAGACTGGATTAATATCATCAgtttgtgctt ... tttggatcagGTTGCCAATTTATGTGCTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcaatattgaagtcaccaacctagttatttaatttgttttgatatttggatcagGTTGCCAATTTATGTGCTCCGGTAGAAGAATGGACTGTTGGTGGAACTGCACTCACCTCACTGATGGATGTGGAGAGGAGGCATG
ttttgat putative branch site (score: 4)
tagttatttaatttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtgcttctctacatgccttaatcttttgatatcttcttaaatatctcctagattggtgttgataattgattgtactttgaaattgtgcttgttttgcaatattgaagtcaccaacctagttatttaatttgttttgatatttggatcagGTTGCCAATTTATGTGCTCCGGTAGAAGAATGGACTGTTGGTGGAACTGCACTCACCTCACTGATGGATGTGGAGAGGAGGCATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG