Sequence
atgc intronic sequence ATGC exonic sequencegtaacaataataaatttacaaacagatacgtactactacattattattattattactgatattcaattattaattatatgcaattgtaattaatttagtagtaatgctatgcttttccgattgttattatgcttagATGGAAGGAGTTAAGCATTCGGGTCCGACCAAATTGGTTCTATATTTTACGGGGGCCACAAACATTCTCTACACATTCGGGGGACATGCTGTTACTGT
Basic information
species | Glycine max |
transcript | GLYMA11G11310.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G11310.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g14080.1 (Oryza sativa), 3'ss of exon 4
gtaaca-ataataaatttacaaacagatacgtactactacattattattattattactgatattcaattat-taattatatgcaattgtaattaatttagtagtaatgctatgcttttccgattgttattatgcttagATGGAAGGAGTTAAGCATTCGGGTCCGACCAAATTGGTTCTATATTTTACGGGGGCCACAAACATTCTCTACACATTCGGGGGACATGCTGTTACTGT
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gtagtacaacacaaaagcaccatctgttagcatgcagcatgcttgcatttctcgtctgaatagcgaggcgcatgcctgaacattattacattgcgtt--gtgctgaaaaaacacttgtgttttttgtatgaatatcagGTCGATGGAGTGAAGCACTCGGGCCCTACAAAGATGGTCCTCTACTTCACCGGGGCCACAAACATTCTCTACACCTTCGGTGGGCACGCTGTTACTGT
upper sequence: GLYMA11G11310.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G149481_T03 (Zea mays), 3'ss of exon 5
gtaacaataataaatttacaaacagatacgtactactacattattattattattactgatattcaattattaattatatgcaattgtaattaatttagtagtaatgctatgcttttccgattgttattatgcttagATGGAAGGAGTTAAGCATTCGGGTCCGACCAAATTGGTTCTATATTTTACGGGGGCCACAAACATTCTCTACACATTCGGGGGACATGCTGTTACTGT--
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-------------------gtacgcaagcgtagcgttgaagcataatatgcatt-ctgtgggcctgtggcctgtggcctgtgg--gtgaccggccgagacgatgtg-tgtgcttctgctgctctacttgt-tgcagGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACCGGGGCCACAAACATTCTCTACACTTTCGGAGGGCACGCTGTTACCGTGT
upper sequence: GLYMA11G11310.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G149481_T02 (Zea mays), 3'ss of exon 4
gtaacaataataaatttacaaacagatacgtactactacattattattattattactgatattcaattattaattatatgcaattgtaattaatttagtagtaatgctatgcttttccgattgttattatgcttagATGGAAGGAGTTAAGCATTCGGGTCCGACCAAATTGGTTCTATATTTTACGGGGGCCACAAACATTCTCTACACATTCGGGGGACATGCTGTTACTGT
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-------------------gtacgcaagcgtagcgttgaagcataatatgcatt-ctgtgggcctgtggcctgtggcctgtgg--gtgaccggccgagacgatgtg-tgtgcttctgctgctctacttgt-tgcagGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACCGGGGCCACAAACATTCTCTACACTTTCGGAGGGCACGCTGTTACCGT
upper sequence: GLYMA11G11310.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G21050.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaacaataataaatttacaaacagatacgtactactacattattattattattactgatattcaattattaattatatgcaattgtaattaatttagtagtaatgctatgcttttccgattgt-tattatgcttagATGGAAGGAGTTAAGCATTCGGGTCCGACCAAATTGGTTCTATATTTTACGGGGGCCACAAACATTCTCTACACATTCGGGGGACATGCTGTTACTGT
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--------------------------------ttaatgcataaatgttat--atacttgta--gagttgtagataat-tgaattttcttatagaaggagaataatgtaatgtaccaatgttggaataataaaaatagGTAGAAGGAGTGAAGCATTCAGGACCAAGCAAGCTGGTTTTATACTTCACAGGGGCCACAAACATTCTTTACACATTCGGTGGACATGCTGTTACTGT
upper sequence: GLYMA11G11310.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv03s0038g02140.t01 (Vitis vinifera), 3'ss of exon 4
gtaacaataataaatttacaaacagatacgtactactacattattattattattactgatattcaat-tattaattatatgcaattgtaattaatttagtagtaatgctatgcttttccgattgttattatgcttagATGGAAGGAGTTAAGCATTCGGGTCCGACCAAATTGGTTCTATATTTTACGGGGGCCACAAACATTCTCTACACATTCGGGGGACATGCTGTTACTGT
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-----------------------------gtacta-tacatatatctcattcaaccaaatatccaaaacatatgatattaaaattagtaaatgattttatt-tatttatttatttatttatttgtta--atgggcagATGGAAGGAGTGAAACACTCAGGTCCATCCAAGCTGGTGCTATACTTCACAGGGGCTACAAACATTCTCTACACATTCGGGGGACATGCTGTGACTGTMapped 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|24206334|gb|BU965587.1|BU965587EST: CTTCTTACACTGCTTGGTATCTCACAGTTGCCTCTCTCCTTCACGGTCAG ATGGAAGGAGTTAAGCATTCGGGTCCGACCAAATTGGTTCTATATTTTACG
genomic: CCACTTACACTGCTTGGTATCTCACAGTTGCCTCTCTCCTTCACGGTCAGgtaacaataa ... ttatgcttagATGGAAGGAGTTAAGCATTCGGGTCCGACCAAATTGGTTCTATATTTTACG
EST:
gi|209726328|gb|BW659628.1|BW659628EST: CCACTTACACTGCTTGGTATCTCACAGTTGCCTCTCTCCTTCACGGTCAG ATGGAAGGAGTTAAGCATTCGGGTC
genomic: CCACTTACACTGCTTGGTATCTCACAGTTGCCTCTCTCCTTCACGGTCAGgtaacaataa ... ttatgcttagATGGAAGGAGTTAAGCATTCGGGTC
EST:
gi|298180126|gb|HO025341.1|HO025341EST: CCACTTACACTGCCTGGTATCTCACAGTTGCCTCTCTCCTTCACGGTCAG ATGGAAGGAGTTAAGCATTCGGGTCCGACCAAATTGGTTCTATATTTTACG
genomic: CCACTTACACTGCTTGGTATCTCACAGTTGCCTCTCTCCTTCACGGTCAGgtaacaataa ... ttatgcttagATGGAAGGAGTTAAGCATTCGGGTCCGACCAAATTGGTTCTATATTTTACG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattgtaattaatttagtagtaatgctatgcttttccgattgttattatgcttagATGGAAGGAGTTAAGCATTCGGGTCCGACCAAATTGGTTCTATATTTTACGGGGGCCACAAACATTCTCTACACATTCGGGGGACATGCTGTTACTGT
aattaat putative branch site (score: 3)
taattaatttagtagt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacaataataaatttacaaacagatacgtactactacattattattattattactgatattcaattattaattatatgcaattgtaattaatttagtagtaatgctatgcttttccgattgttattatgcttagATGGAAGGAGTTAAGCATTCGGGTCCGACCAAATTGGTTCTATATTTTACGGGGGCCACAAACATTCTCTACACATTCGGGGGACATGCTGTTACTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT