Sequence
atgc intronic sequence ATGC exonic sequencegtaatgttttttgctttggcttttgaattgtggatgctgattattgctgaaccttataaatgaaaatgatctttattgcagAATACAACCTCAAAAGAAAATGAAACACTTTTAGCCATTGGTACTGCTTATGTGCAAGGAGAGGATGTTGCTGCAAGAGGACGTATCCTCTTGTTCTCTT
Basic information
species | Glycine max |
transcript | GLYMA09G28030.1 |
intron # | 21 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G28030.1 (Glycine max), 3'ss of exon 21
lower sequence: LOC_Os04g18010.1 (Oryza sativa), 3'ss of exon 21
----gtaatgttttttgctttggcttttga--attgtggatgctgattattg----ctgaaccttat--------aaatgaaaatg-atctttattgcagAATACAACCTCAAAAGAAAATGAAACACTTTTAGCCATTGGTACTGCTTATGTGCAAGGAGAGGATGTTGCTGCAAGAGGACGTATCCTCTTGTTCTCTT
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gcttgagatttatcttgtttgaaaatttaatgatcaaaggtacacatgtctgtaggtttaattatattattcactgaacagttatgcatttttacttcagAATACAACCACCAAGGAAAATGAGACCCTGTTGGCCATTGGGACTGCTTATGTTCTTGGGGAGGATGTAGCTGCTAGAGGACGTGTGCTTCTGTTCTCTT
upper sequence: GLYMA09G28030.1 (Glycine max), 3'ss of exon 21
lower sequence: GRMZM2G453879_T02 (Zea mays), 3'ss of exon 6
gta---atgttttttgctttggcttttgaattgtggatgctgattattgctgaaccttata-aatgaaaatgatctttattgcagAATACAACCTCAAAAGAAAATGAAACACTTTTAGCCATTGGTACTGCTTATGTGCAAGGAGAGGATGTTGCTGCAAGAGGACGTATCCTCTTGTTCTCTT
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gtatgtatgtcttctacacttg--tatggatactgcactcaaactaaaattttatttaccagaatattattgattttcgcctcagAACACATCTACGAAGGAAAATGAAACCCTGATGGCCATTGGAACTGCTTATGTTCAAGGGGAGGATGTTGCTGCTAGAGGACGGGTGCTTCTGTTCTCTT
upper sequence: GLYMA09G28030.1 (Glycine max), 3'ss of exon 21
lower sequence: GRMZM2G453879_T01 (Zea mays), 3'ss of exon 6
gta---atgttttttgctttggcttttgaattgtggatgctgattattgctgaaccttata-aatgaaaatgatctttattgcagAATACAACCTCAAAAGAAAATGAAACACTTTTAGCCATTGGTACTGCTTATGTGCAAGGAGAGGATGTTGCTGCAAGAGGACGTATCCTCTTGTTCTCTT
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gtatgtatgtcttctacacttg--tatggatactgcactcaaactaaaattttatttaccagAATATTATTGATTTTCGCCTCAGAACACATCTACGAAGGAAAATGAAACCCTGATGGCCATTGGAACTGCTTATGTTCAAGGGGAGGATGTTGCTGCTAG-----------------------
upper sequence: GLYMA09G28030.1 (Glycine max), 3'ss of exon 21
lower sequence: AT5G51660.1 (Arabidopsis thaliana), 3'ss of exon 21
------------------------gtaatgttttttgctttggcttttgaattgtggatgctgattatt--gctgaaccttataaatgaaaatgatctttattgcagAATACAACCTCAAAAGAAAATGAAACACTTTTAGCCATTGGTACTGCTTATGTGCAAGGAGAGGATGTTGCTGCAAGAGGACGTATCCTCTTGTTCTCTT
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gtaagttagctactaacccgcctaatgtcatatttggatcagatctctctgttttaattgc-aataaccaagccacattctcttactccctggggtgttt----cagAATGCAAGCACAGGGGAGAATGAAACACTTCTTGCTGTTGGGACTGCGTATGTCCAAGGGGAGGATGTTGCTGCAAGGGGCCGTGTGCTTCTTTTCTCTT
upper sequence: GLYMA09G28030.1 (Glycine max), 3'ss of exon 21
lower sequence: Vv16s0022g01860.t01 (Vitis vinifera), 3'ss of exon 21
------------------------------------------------------------------------------------------------------------gtaatgttttt--------tgctttggcttttg---aattgtggatgctgattattgctgaaccttataaatgaaaatgatctttattgcagAATACAACCTCAAAAGAAAATGAAACACTTTTAGCCATTGGTACTGCTTATGTGCAAGGAGAGGATGTTGCTGCAAGAGGACGTATCCTCTTGTTCTCTT
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gtgagttaattctttgccattccaactgtttctttgtgttttggttttggcttctttcttgaattctcgtcatgggagaggcgtgtggtgagtgttggggggggattagatatgttcttggtgaagctgggttggtgtttgtttaattcttatttctgcctgttctagaaaatcataattaccatgtgtcttacctgcagAATACTACCACAAAAGAAAATGAAACACTTTTGGCCATTGGGACTGCTTACGTACAAGGGGAGGATGTTGCTGCAAGGGGACGGGTGCTTTTATTTTCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgtggatgctgattattgctgaaccttataaatgaaaatgatctttattgcagAATACAACCTCAAAAGAAAATGAAACACTTTTAGCCATTGGTACTGCTTATGTGCAAGGAGAGGATGTTGCTGCAAGAGGACGTATCCTCTTGTTCTCTT
tgctgat putative branch site (score: 3)
tctttatt putative PPT
ttataaatgaaaatga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgttttttgctttggcttttgaattgtggatgctgattattgctgaaccttataaatgaaaatgatctttattgcagAATACAACCTCAAAAGAAAATGAAACACTTTTAGCCATTGGTACTGCTTATGTGCAAGGAGAGGATGTTGCTGCAAGAGGACGTATCCTCTTGTTCTCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA