Sequence
atgc intronic sequence ATGC exonic sequencegtgagtaatttattttatgtaacacgtcaaccccctgcctagatttgaaaaaagttgtatcacctaattggatttctcctgaattgcttacagTTTTCAAAAGCTTTGAATCGCTTCCAAAAAGAAGATCCTACTTTTCGTGTTGGCTTGGACCCGGAGAGTGGGCAG
Basic information
species | Glycine max |
transcript | GLYMA11G16460.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G16460.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os03g36780.1 (Oryza sativa), 3'ss of exon 11
gtgagtaatttattttatgtaacacgtcaaccccctgcctagatttgaaaaaagttgtatcacctaattggatttctcctgaattgc-ttacagTTTTCAAAAGCTTTGAATCGCTTCCAAAAAGAAGATCCTACTTTTCGTGTTGGCTTGGACCCGGAGAGTGGGCAG
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----gtatctacttttctatttt-caagaatgctatat-taactttaataccatacatgtgaca-aat---aattaattaaaataacatttcagTTTTCAAAGGCTCTGAATCGTTTCCAGAAAGAGGATCCTACTTTCCGTGTAGGTCTGGATCCAGAAAGTGGAGAG
upper sequence: GLYMA11G16460.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G056393_T02 (Zea mays), 3'ss of exon 11
gtgagtaatttattttatgtaacacgtcaaccccctgcctagatttgaaaaaagttgtatcacctaattggatttctcctgaattgcttacagTTTTCAAAAGCTTTGAATCGCTTCCAAAAAGAAGATCCTACTTTTCGTGTTGGCTTGGACCCGGAGAGTGGGCAG
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gtatatcatatttttcatcaaaagggtacgactgctatacatagtttgttaccctag-atgtcctaagtgaaaatacaccta-tccctttcagTTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAG
upper sequence: GLYMA11G16460.1 (Glycine max), 3'ss of exon 11
lower sequence: AT1G45332.1 (Arabidopsis thaliana), 3'ss of exon 11
gtgagtaatttattttatgtaac-acgtcaaccccctgcctagatttgaaaaaagttgtatcacct----aattggatttctcctgaattgcttacagTTTTCAAAAGCTTTGAATCGCTTCCAAAAAGAAGATCCTACTTTTCGTGTTGGCTTGGACCCGGAGAGTGGGCAG
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gtaacttatgtgaactttgaagctgaaacaacaacatatttttcctttaatctggttttacgaaatttgcaactgaaatctatttt--ccggtgttagTTCTCGAAAGCACTGAATCGATTCCAGAAAGAGGATCCTACTTTCCGTGTGGGTTTGGATCCCGAGAGTGGCCAG
upper sequence: GLYMA11G16460.1 (Glycine max), 3'ss of exon 11
lower sequence: AT2G45030.1 (Arabidopsis thaliana), 3'ss of exon 11
gtgagtaatttattttatgtaac-acgtcaaccccctgcctagatttgaaaaaagttgt--atcacct--aattggatttctcctgaattgcttacagTTTTCAAAAGCTTTGAATCGCTTCCAAAAAGAAGATCCTACTTTTCGTGTTGGCTTGGACCCGGAGAGTGGGCAG
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gtaacttctgtgaactttgaagctaaaacagcaacatatttttccttcaattctggttttaaacatttgcaactgaaatctatttt--ttggtgttagTTCTCGAAAGCATTGAATCGATTCCAGAAAGAGGATCCTACTTTCCGTGTGGGTTTGGATCCCGAGAGTGGCCAG
upper sequence: GLYMA11G16460.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv15s0021g02450.t01 (Vitis vinifera), 3'ss of exon 11
gtgagtaatttattttatgtaacacgtcaaccccctgcctagatttgaaaaaagttgtatcacctaattggatttctcctgaattgcttacagTTTTCAAAAGCTTTGAATCGCTTCCAAAAAGAAGATCCTACTTTTCGTGTTGGCTTGGACCCGGAGAGTGGGCAG
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----gtgagtacggccaattgagatatcaatttact--------ttgtaactgatggtaccaaatgatggtaattttttatccttg--tacagTTTTCAAAGGCTTTGAATCGCTTTCAGAGAGAGGATCCTACTTTCCGTGTTGGGTTGGACGCTGAGAGTGGGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctagatttgaaaaaagttgtatcacctaattggatttctcctgaattgcttacagTTTTCAAAAGCTTTGAATCGCTTCCAAAAAGAAGATCCTACTTTTCGTGTTGGCTTGGACCCGGAGAGTGGGCAG
acctaat putative branch site (score: 3)
tttgaaaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtaatttattttatgtaacacgtcaaccccctgcctagatttgaaaaaagttgtatcacctaattggatttctcctgaattgcttacagTTTTCAAAAGCTTTGAATCGCTTCCAAAAAGAAGATCCTACTTTTCGTGTTGGCTTGGACCCGGAGAGTGGGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG