Sequence
atgc intronic sequence ATGC exonic sequencegtatgttttggcaatgcataaatactttttctatattttttagttgacagtttctgtgtaattccttttgtggttgtccttctgtagGGGATATCTCTCCTCCACGTGGAGTGAGAGCAGCTATGGAGATGCAAGCAGAAGCAGAAAGAAAAAAGAGAGCTCAAATTCTTGAGTCTGAAG
Basic information
species | Glycine max |
transcript | GLYMA06G14340.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G14340.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os08g06200.1 (Oryza sativa), 3'ss of exon 4
gtatgttttggcaatgcataaatactttttctatattttttagttgacagtttctgtgtaattccttttgtggttgtccttctgtagGGGATATCTCTCCTCCACGTGGAGTGAGAGCAGCTATGGAGATGCAAGCAGAAGCAGAAAGAAAAAAGAGAGCTCAAATTCTTGAGTCTGAAG
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gtatgcctttttgcttc-tgaattgttgagctataactgtttcctgtaacatttctgatg-----tttaataattgac--tatgcagGGGATATATCTCCGCCACGTGGTGTTAAGGTGGCTATGGAGATGCAAGCAGAAGCAGAAAGGAAAAAGCGTGCCCAAATCCTTGAATCAGAAG
upper sequence: GLYMA06G14340.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G023073_T01 (Zea mays), 3'ss of exon 4
gtatgt--tttggcaatgcataaatactttttctatattttttagttgacagtttctgtgtaattccttttgtggttgtccttctgtagGGGATATCTCTCCTCCACGTGGAGTGAGAGCAGCTATGGAGATGCAAGCAGAAGCAGAAAGAAAAAAGAGAGCTCAAATTCTTGAGTCTGAAG-------
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gtatgccgtcttttcctgtttgagcattagagctataatacacgcattgt--ttcaaatgtcaatg-ttttaaatttgacaat--gcagGGGACATAAATCCTCCAGCAGGGATTAGGCAGGCTATGGAGATGCAGGCTGAGGCAGAAAGGAAAAAACGCGCTCAAATCCTTGAGTCAGAAGGGATGAA
upper sequence: GLYMA06G14340.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G27585.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatgttttggcaatgcataaatactttttctatattttttagttgaca-gtttctgtgtaattccttttgtggtt-gtccttctgtagGGGATATCTCTCCTCCACGTGGAGTGAGAGCAGCTATGGAGATGCAAGCAGAAGCAGAAAGAAAAAAGAGAGCTCAAATTCTTGAGTCTGAAG
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----------gtaagttgttcgtgttttttct-tttccggtgatagttacatatctgttttttcctatttctaattcatgtttttccagGGGATATTATGCCCCCTCATGGAGTGCGAGCTGCTATGGAAATGCAAGCTGAAGCTGAGCGTAAAAAGAGAGCCCAGATTCTTGAGTCTGAAG
upper sequence: GLYMA06G14340.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G54100.1 (Arabidopsis thaliana), 3'ss of exon 5
gtatgttttggcaatgcataaatactttttctatattttttagttgacagtttctgtgtaattccttttgtggttgtccttctgtagGGGATATCTCTCCTCCACGTGGAGTGAGAGCAGCTATGGAGATGCAAGCAGAAGCAGAAAGAAAAAAGAGAGCTCAAATTCTTGAGTCTGAAG
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--gtgagttatttttctgttgactctttgctggtgttagctagat-acccttttggccttgtatctaataca--tgtatatc--cagGGGATATCATGCCTCCTAATGGAGTGAGAGTTGCTATGGAAATGCAAGCTGAAGCTGAACGTAAAAAGAGAGCCCAGATTCTTGAGTCTGAAG
upper sequence: GLYMA06G14340.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv09s0002g01630.t01 (Vitis vinifera), 3'ss of exon 4
----------gtatgttttggcaatgcataaatactttttcta-tattttttagttgacagtttctgtgtaattccttttgtggttgtccttctgtagGGGATATCTCTCCTCCACGTGGAGTGAGAGCAGCTATGGAGATGCAAGCAGAAGCAGAAAGAAAAAAGAGAGCTCAAATTCTTGAGTCTGAAG
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gtaggtgaccttttatctaaatatttcttatggactttctttgctatatcacccatagcagcattcctatatgcctcattgtcctc--ttttctttagGGGATATATCTCCTCCTCGTGGAGTGAGGGCAGCTATGGAGATGCAAGCAGAAGCAGAACGTAAAAAGAGAGCTCAAATTCTTGAATCAGAGGMapped 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|192328054|gb|FK021800.1|FK021800EST: TAATATGGCTGCAAAAAGTTGGGGTCTAGAGTGCCTTCGATATGAAATAA GGGATATCTCTCCTCCACGTGGAGTGAGAGCAGCTATGGAGATGCAAGCAG
genomic: TAATATGGCTGCAAAAAGTTGGGGTCTAGAGTGCCTTCGATATGAAATAAgtatgttttg ... ccttctgtagGGGATATCTCTCCTCCACGTGGAGTGAGAGCAGCTATGGAGATGCAAGCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atattttttagttgacagtttctgtgtaattccttttgtggttgtccttctgtagGGGATATCTCTCCTCCACGTGGAGTGAGAGCAGCTATGGAGATGCAAGCAGAAGCAGAAAGAAAAAAGAGAGCTCAAATTCTTGAGTCTGAAG
agttgac putative branch site (score: 4)
ttgtccttct putative PPT
ttttagtt 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 |
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gtatgttttggcaatgcataaatactttttctatattttttagttgacagtttctgtgtaattccttttgtggttgtccttctgtagGGGATATCTCTCCTCCACGTGGAGTGAGAGCAGCTATGGAGATGCAAGCAGAAGCAGAAAGAAAAAAGAGAGCTCAAATTCTTGAGTCTGAAG
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