Sequence
atgc intronic sequence ATGC exonic sequencegtaagtcaccaaattatggaagtgttaaacagactcatgcagttatgcattgaattcaagacttatacatgagtgttcctaatgttgttgcagGATGTAGATGAGAAGCTCTTGTATGACACTTTCAGTGCATTTGGAGTTATTGTTACTAATCCAAAG
Basic information
species | Glycine max |
transcript | GLYMA09G00310.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G00310.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G102639_T02 (Zea mays), 3'ss of exon 3
gtaagtcaccaaattatggaagtgttaaacagactcatgcagttatgcattgaattcaagactta-tacatgagtgttcctaatgttgttgcagGATGTAGATGAGAAGCTCTTGTATGACACTTTCAGTGCATTTGGAGTTATTGTTACTAATCCAAAG
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gtgaaggcctaaatcctaatttcttca-------ttatatgctcttcaattcatctgaatactgagtatatttttatgcttgctttgttaacagGATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAG
upper sequence: GLYMA09G00310.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G170699_T01 (Zea mays), 3'ss of exon 5
gtaagtcaccaaattatggaagtgttaaacagactc---atgcagtt--atgcattgaattcaagact---tatacatgagtgttcctaatgttgttgcagGATGTAGATGAGAAGCTCTTGTATGACACTTTCAGTGCATTTGGAGTTATTGTTACTAATCCAAAG
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gtgaaggcctaaatcctactctttattatcagctcttcaattcatttgaatcaatccatctgaatactgagtatattttcatgtttgcattgtta--acagGATGTTGATGAAAAGCTCCTTTATGATACCTTCAGTGCATTTGGAGTGATTGTGACTAATCCTAAG
upper sequence: GLYMA09G00310.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G18510.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaagtcaccaaattatggaagtgttaaacagactcatgcagttatgcattgaattcaagacttatacatgagtgttcctaatgttgttgcagGATGTAGATGAGAAGCTCTTGTATGACACTTTCAGTGCATTTGGAGTTATTGTTACTAATCCAAAG
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gtaagtatctt--ttgtggtagactctgatt--ttgatactctacaaaggtcatttaatctcttagctgaccaggttttgttttcttttatagGATGTGGATGAGAAGCTCTTGTATGATACTTTCAGTGCATTTGGTGTGATTGCTTCTAATCCTAAG
upper sequence: GLYMA09G00310.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv04s0023g01470.t01 (Vitis vinifera), 3'ss of exon 5
----------------------------------------------gtaagtcaccaaattatggaagtgttaaacagactcatg--cagttat-gcattg--aattcaagacttatacatgagtgttcctaatgttgtt-gcagGATGTAGATGAGAAGCTCTTGTATGACACTTTCAGTGCATTTGGAGTTATTGTTACTAATCCAAAG
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gtaagtagttcaattccttatttttatttatttttattgggaagttgtattgtatcaaaacctttgtgggtgtgaaggactcatggacagttgttgtatcactagtttcaattttaaagttga---ccctggatgttctttgcagGATGTGGATGAGAAACTTCTGTATGATACTTTCAGTGCATTTGGAGTCATTGTCACAAATCCCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcagttatgcattgaattcaagacttatacatgagtgttcctaatgttgttgcagGATGTAGATGAGAAGCTCTTGTATGACACTTTCAGTGCATTTGGAGTTATTGTTACTAATCCAAAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtcaccaaattatggaagtgttaaacagactcatgcagttatgcattgaattcaagacttatacatgagtgttcctaatgttgttgcagGATGTAGATGAGAAGCTCTTGTATGACACTTTCAGTGCATTTGGAGTTATTGTTACTAATCCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG