Sequence
atgc intronic sequence ATGC exonic sequencegtaagtaaccaaattatgcaagtgttaatcagactcatgcagttatgcattgaattcaagacttaaacatgagtgttcctaatgttgttgcagGATGTAGACGAGAAGCTCTTGTATGATACTTTCAGTGCATTTGGAGTTATTGTTACTAATCCAAAG
Basic information
species | Glycine max |
transcript | GLYMA12G36950.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G36950.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G102639_T02 (Zea mays), 3'ss of exon 3
gtaagtaaccaaattatgcaagtgttaatcagactcatgcagttatgcattgaattcaagacttaa-acatgagtgttcctaatgttgttgcagGATGTAGACGAGAAGCTCTTGTATGATACTTTCAGTGCATTTGGAGTTATTGTTACTAATCCAAAG
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gtgaaggcctaaatccta-atttcttcatta----tatgc--tcttcaattcatctgaatactgagtatatttttatgcttgctttgttaacagGATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAG
upper sequence: GLYMA12G36950.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G170699_T01 (Zea mays), 3'ss of exon 5
gtaagtaaccaaattatgcaagtgttaatcagactc---atgcagtt--atgcattgaattcaagact---taaacatgagtgttcctaatgttgttgcagGATGTAGACGAGAAGCTCTTGTATGATACTTTCAGTGCATTTGGAGTTATTGTTACTAATCCAAAG
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gtgaaggcctaaatcctactctttattatcagctcttcaattcatttgaatcaatccatctgaatactgagtatattttcatgtttgcattgtta--acagGATGTTGATGAAAAGCTCCTTTATGATACCTTCAGTGCATTTGGAGTGATTGTGACTAATCCTAAG
upper sequence: GLYMA12G36950.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G18510.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaagtaaccaaattatgcaagtgttaatcagactca-tgcagttatgcattgaattcaagacttaaacatgagtgttcctaatgttgttgcagGATGTAGACGAGAAGCTCTTGTATGATACTTTCAGTGCATTTGGAGTTATTGTTACTAATCCAAAG
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gtaagtatcttttgtggtagactctgattttgatactctacaaaggt-catttaatctcttagctgacca--ggttttgtt--ttcttttatagGATGTGGATGAGAAGCTCTTGTATGATACTTTCAGTGCATTTGGTGTGATTGCTTCTAATCCTAAG
upper sequence: GLYMA12G36950.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv04s0023g01470.t01 (Vitis vinifera), 3'ss of exon 5
----------------------------------------------gtaagtaaccaaa--ttatgcaagtgttaatcagactcatg--cagttat-gcattg--aattcaagacttaaacatgagtgttcctaatgttgtt-gcagGATGTAGACGAGAAGCTCTTGTATGATACTTTCAGTGCATTTGGAGTTATTGTTACTAATCCAAAG
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gtaagtagttcaattccttatttttatttatttttattgggaagttgtattgtatcaaaacctttgtgggtgtgaa--ggactcatggacagttgttgtatcactagtttcaattttaaagttga---ccctggatgttctttgcagGATGTGGATGAGAAACTTCTGTATGATACTTTCAGTGCATTTGGAGTCATTGTCACAAATCCCAAGMapped 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|298165828|gb|HO008799.1|HO008799EST: AAAAGAGCCTGGATGTTGGTGCAAATCTTTTCATTGGCAATCTTGATCCT GATGTAGACGAGAAGCTCTTGTATGATACTTTCAGTGCATTTGGAGTTATT
genomic: AAAAGAGCCTGGATGTTGGTGCAAATCTTTTCATTGGCAATCTTGATCCTgtaagtaacc ... gttgttgcagGATGTAGACGAGAAGCTCTTGTATGATACTTTCAGTGCATTTGGAGTTATT
EST:
gi|18040641|gb|BM308944.1|BM308944EST: AAAAGAGCCTGGATGTTGGTGCAAATCTTTTCATTGGCAATCTTGATCCT GATGTAGACGAGAAGCTCTTGTATGATACTTTCAGTGCATTTGGAGTTATT
genomic: AAAAGAGCCTGGATGTTGGTGCAAATCTTTTCATTGGCAATCTTGATCCTgtaagtaacc ... gttgttgcagGATGTAGACGAGAAGCTCTTGTATGATACTTTCAGTGCATTTGGAGTTATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcagttatgcattgaattcaagacttaaacatgagtgttcctaatgttgttgcagGATGTAGACGAGAAGCTCTTGTATGATACTTTCAGTGCATTTGGAGTTATTGTTACTAATCCAAAG
tcctaat putative branch site (score: 2)
attgaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtaaccaaattatgcaagtgttaatcagactcatgcagttatgcattgaattcaagacttaaacatgagtgttcctaatgttgttgcagGATGTAGACGAGAAGCTCTTGTATGATACTTTCAGTGCATTTGGAGTTATTGTTACTAATCCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG