Sequence
atgc intronic sequence ATGC exonic sequence...atctgtaatgacaggacatggtatatagtatactatttctagcattgtggcaatttctgcattgaggctaattatttctgttggtgatcattctcttcagGATAAGGAATTGTTTGACACAATTATATGCTAAGGACATAACACCAGATGATAAGCAGGAACTTGATGAGGCTTTACAAAGAGAG
Basic information
species | Glycine max |
transcript | GLYMA12G33820.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G33820.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os08g27840.1 (Oryza sativa), 3'ss of exon 2
atctgtaatgacaggacatggtatatagtatactat-ttctagcattgtggcaatttctgcattgaggctaattatttctgttggtgatcattctcttcagGATAAGGAATTGTTTGACACAATTATATGCTAAGGACATAACACCAGATGATAAGCAGGAACTTGATGAGGCTTTACAAAGAGAG
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-----------------gtgagttacagaa-acaatactatgatatca-aacatcctatggtttcttatcatctaattgtgaaatttcaaatataatttagGATAAGGAATTGTTTGGTTCAACTATACTCAAAGGATATCACACCAGATGATAAACAGGAGCTTGATGAGGCTCTCCAGAGGGAG
upper sequence: GLYMA12G33820.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g55350.1 (Oryza sativa), 3'ss of exon 4
atctgtaatgacaggacatggtatatagtatactatttctagcattgtggcaatttctgcattgag-gctaattatttctgttggtgatcattctctt-----cagGATAAGGAATTGTTTGACACAATTATATGCTAAGGACATAACACCAGATGATAAGCAGGAACTTGATGAGGCTTTACAAAGAGAG
| | | | | | || || || | ||| | | ||| ||| | | | || | | | | ||| ||| | || | ||||||||| | |||||| ||| || | ||||| || |||||||| |||||||| ||||||||||| ||||| || | | ||||||
---ttcactaagaatgcttgctagatg---caaggtttgtcggattcgacaaatctatctttcaagtgttgaacaaaatataaggttttcactttcctatatgcagGATAAGAAGTTGTTTAACAAAACTTTATGCAAAAGACATAACTCCAGATGAGAAGCAGGAACTCGATGAAGCACTTAAGAGAGAG
upper sequence: GLYMA12G33820.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G473001_T01 (Zea mays), 3'ss of exon 2
atctgtaatgacaggacatggtatatagtatactatttctagcattgtggcaatttctgcattgaggctaattatttctgttggtgatcattctcttcagGATAAGGAATTGTTTGACACAATTATATGCTAAGGACATAACACCAGATGATAAGCAGGAACTTGATGAGGCTTTACAAAGAGAG
| || || | ||| | | | | ||| ||| ||| || || || ||| | || | || ||||| |||||||| | || |||||| ||| | || | || || || || || ||||||||||||||||||||||||||| | |||||||||
---------gttag--tttgccaaccagtgcattgtagttgacatgc--acaacttc---gttcagcct--ttaatcttgatcccaat-attcttatcagGATACGCAACTGTTTGGTTCAACTCTACTCAAAAGATATCACTCCGGATGATAAGCAGGAACTTGATGAGGCTCTGCAAAGAGAG
upper sequence: GLYMA12G33820.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G473001_T02 (Zea mays), 3'ss of exon 2
atctgtaatgacaggacatggtatatagtatactatttctagcattgtggcaatttctgcattgaggctaattatttctgttggtgatcattctcttcagGATAAGGAATTGTTTGACACAATTATATGCTAAGGACATAACACCAGATGATAAGCAGGAACTTGATGAGGCTTTACAAAGAGAG---------------
| || || | ||| | | | | ||| ||| ||| || || || ||| | || | || ||||| |||||||| | || |||||| ||| | || | || || || || || ||||||||||||||||||||||||||| | |||||||||
---------gttag--tttgccaaccagtgcattgtagttgacatgc--acaacttc---gttcagcct--ttaatcttgatcccaat-attcttatcagGATACGCAACTGTTTGGTTCAACTCTACTCAAAAGATATCACTCCGGATGATAAGCAGGAACTTGATGAGGCTCTGCAAAGAGAGGTACTTCTTTCAATC
upper sequence: GLYMA12G33820.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G110714_T01 (Zea mays), 3'ss of exon 2
--------atctgtaatgacaggacatggtatatagtatactatttctagcattgtggcaatttctgcattgaggctaattatttctgttggtgatcattctcttcagGATAAGGAATTGTTTGACACAATTATATGCTAAGGACATAACACCAGATGATAAGCAGGAACTTGATGAGGCTTTACAAAGAGAG
| ||||| | | | | || | || || | | || ||| || || ||| || || | | | | || ||| | | |||||||| || ||||| || ||| | ||||| |||||||| || |||||||| || |||||||||||||| || | |||||||||
atgaaaagaaaagtaat-atatttctcgagtcatgttgaaccatatgttatat-gtgccatttgttgcctt-agattcttcacatttgcatttgaatgtgc-----agGATAAGAAACTGTTTAACTCAACTTTATGCAAAGGACATCACTCCAGATGAGAAACAGGAACTTGATGAAGCACTTCAAAGAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtggcaatttctgcattgaggctaattatttctgttggtgatcattctcttcagGATAAGGAATTGTTTGACACAATTATATGCTAAGGACATAACACCAGATGATAAGCAGGAACTTGATGAGGCTTTACAAAGAGAG
ggctaat putative branch site (score: 3)
tcattctcttc putative PPT
taattatttctgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atctgtaatgacaggacatggtatatagtatactatttctagcattgtggcaatttctgcattgaggctaattatttctgttggtgatcattctcttcagGATAAGGAATTGTTTGACACAATTATATGCTAAGGACATAACACCAGATGATAAGCAGGAACTTGATGAGGCTTTACAAAGAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - gacatgg
- - - - - - - - - - - - - - - - - - - - - - ttgtggc
- - - - - - - - - - - - - - - - - - - - - - - - - - - ttctgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgaggc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttggtg