Sequence
atgc intronic sequence ATGC exonic sequencegtgcaaattctctctctatctctgtctcatattaagcgagaaacattcacctttttctctataattaaaaagaaactaatgatgggacgatttcatgcagATTTTTAGAATCCTCGTAGAGATTACTAAAGATATACAAGGAGCAAAAGTTGAAAATCACAAGTTTTGTGTTTCTGTGCATTACCGTAATGTAGAAGAGA
Basic information
species | Glycine max |
transcript | GLYMA17G14780.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G14780.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G178546_T01 (Zea mays), 3'ss of exon 6
gtgcaaattctctctctatctctgtctcatattaagcgagaaacattcacctttttctctataattaaaaagaaactaatgatgggacgatttcatgc-agATTTTTAGAATCCTCGTAGAGATTACTAAAGATATACAAGGAGCAAAAGTTGAAAATCACAAGTTTTGTGTTTCTGTGCATTACCGTAATGTAGAAGAGA
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----------gtatgttgtaccggcctc---ttgagtttaagttgc-catcttatgtcatatggttgga------cttctga-gtggtg--tacatgccagGTGTATGAAAAACTTGGTGAGAGTGTTAAGGACATTGATGGTGCAAGGATGGAAGACAACAAGTTCTGTGTATCTGTGCATTACCGTAATGTGGCGGAAG
upper sequence: GLYMA17G14780.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv02s0154g00110.t01 (Vitis vinifera), 3'ss of exon 5
gtgcaaattctctctctatct--ctgtctcatat-taagcgagaaacattcacctttt-tctctataattaaaaagaaactaatgatggga----cgatttcatgcagATTTTTAGAATCCTCGTAGAGATTACTAAAGATATACAAGGAGCAAAAGTTGAAAATCACAAGTTTTGTGTTTCTGTGCATTACCGTAATGTAGAAGAGA
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gtgctaaatagttttgtattcaattacctacaatacaagtgtaaaacatttatcagaagtcacgaaagtcatgaagaactgactgtttataattttttttttatgcagGTTTTTAGAGCCCTTGTCGAAACCACTAGAGGAATTGAAGGTGCAAAAGTTGAGAACCATAAGTTTTGCGCCTCTGTACATTACCGTAATGTAGATGAGA
upper sequence: GLYMA17G14780.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv00s0233g00030.t01 (Vitis vinifera), 3'ss of exon 5
gtgc-aaattctctctctatctctgtctcatatta--agcgagaaacattcacctttt-tctctataattaaaaagaaactaatgatggga--cgatttcatgcagATTTTTAGAATCCTCGTAGAGATTACTAAAGATATACAAGGAGCAAAAGTTGAAAATCACAAGTTTTGTGTTTCTGTGCATTACCGTAATGTAGAAGAGA
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gtgctaaatagttttgatttcaattacctacaatacaagtgtaaaacatttatcagaagtcacgaaagtcatgaagaactgactgtttataattttttttatgcagGTTTTTAGAGCCCTTGTTGAAACCACTAGAGGAATTGAAGGCGCAAAAGTTGAGAACCATAAGTTTTGCGCCTCTGTACATTACCGTAATGTAGATGAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcacctttttctctataattaaaaagaaactaatgatgggacgatttcatgcagATTTTTAGAATCCTCGTAGAGATTACTAAAGATATACAAGGAGCAAAAGTTGAAAATCACAAGTTTTGTGTTTCTGTGCATTACCGTAATGTAGAAGAGA
aactaat putative branch site (score: 2)
tttttctctataatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcaaattctctctctatctctgtctcatattaagcgagaaacattcacctttttctctataattaaaaagaaactaatgatgggacgatttcatgcagATTTTTAGAATCCTCGTAGAGATTACTAAAGATATACAAGGAGCAAAAGTTGAAAATCACAAGTTTTGTGTTTCTGTGCATTACCGTAATGTAGAAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA