Sequence
atgc intronic sequence ATGC exonic sequence...caaatcaacttaatacaaaaccttgatgccgaatctaattttatccatgtttaatgaatcactagcacactaagcagagaaatttcttgctaaattgcagGCTTAATGGATTAGTAGACCATTTCAAGATGGCCCTGGATTGCTTCTTTGCAGTTTGGTTTGTAGTAGGAAATGTTTGGATCTTTGGAGGTCACACTTCT
Basic information
species | Glycine max |
transcript | GLYMA15G01570.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G01570.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g54624.1 (Oryza sativa), 3'ss of exon 2
-caaatcaacttaatacaaaaccttgatgccgaatctaattttatccatgtttaatgaatcactagcacactaa-gcagagaaatttcttgctaaattgcagGCTTAATGGATTAGTAGACCATTTCAAGATGGCCCTGGATTGCTTCTTTGCAGTTTGGTTTGTAGTAGGAAATGTTTGGATCTTTGGAGGTCACACTTCT
|| || || || | | | | ||| ||| | | || ||| | | || |||| | || || | || |||| |||||| | | ||||| |||||||||||| ||||||| |||||||| || |||||||| ||||||||||| ||||| ||||| || | |||||
ctgaagcatctgtgtatgagcattgcaag--gaacactattgtttagattgttatttacacatgttcacaatgttgctatttaaagacaaatgccttttcagGATTAATGCTCTTTTTGACCACTTCAAGATGGCCTTGGATTGTTTCTTTGCTGTGTGGTTTGTCGTAGGAAATGTGTGGATATTTGGCGGGCGTTCTTCT
upper sequence: GLYMA15G01570.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G089466_T01 (Zea mays), 3'ss of exon 2
--------------------------------caaatca--acttaatacaaaaccttgatgccgaatctaattttatccatgtttaatg------aatcactagcacactaagcagagaaatttcttgctaaattgcagGCTTAATGGATTAGTAGACCATTTCAAGATGGCCCTGGATTGCTTCTTTGCAGTTTGGTTTGTAGTAGGAAATGTTTGGATCTTTGGAGGTCACACTTCT
||| | ||| | || | | | || |||| | || | | || ||| ||| || ||| | | ||||| |||||| | |||| | | ||||| |||||||||||||||||||| |||||||| || |||||||| || ||||| || ||||| ||||| || | |||||
gtactcatgccttctttttttccttaaaaaaatggatcggtatttacaatgaatatgtttgactgtcacttgttttgtttatttatggtgctgcaaaatggcta-tgcattaaagatgaatgccctgtgctat-ctgcagGATCAATGCGCTGTTTGACCACTTCAAGATGGCCCTGGATTGTTTCTTTGCCGTCTGGTTTGTTGTTGGAAACGTGTGGATATTTGGTGGCCGTTCTTCT
upper sequence: GLYMA15G01570.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G092244_T03 (Zea mays), 3'ss of exon 2
caaatcaacttaatacaaaaccttgatgccgaatctaattttatccatgtttaatgaatcactagcacactaag-cagagaaatttcttgctaaattgcagGCTTAATGGATTAGTAGACCATTTCAAGATGGCCCTGGATTGCTTCTTTGCAGTTTGGTTTGTAGTAGGAAATGTTTGGATCTTTGGAGGTCACACTTCT
| | | || | | | || || | | | | || | ||| | | ||| | | ||| | | || ||| ||| | | || | || || ||||||||||| ||||| |||||||| || || |||||||| || |||||||| ||| | ||||| || || ||||
cctactgttctcatttgatagcagcatacctatacaggtcatcagaatcataaatactttgttggcaagttttctctgagctgcattctcctcg-ttgtagGGCCCAAGCTTTTGCTGATCACTTCAAGATGGCGCTGGACTGCTTCTTCGCTGTATGGTTTGTTGTGGGAAATGTGTGGGTGTTTGGTGGACATTCTTCC
upper sequence: GLYMA15G01570.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G80400.1 (Arabidopsis thaliana), 3'ss of exon 2
caaatcaacttaatacaaaaccttgatgccgaatctaattttatccatgtttaatgaatcactagcacactaagcagagaaatttcttgctaaattgcagGCTTAATGGATTAGTAGACCATTTCAAGATGGCCCTGGATTGCTTCTTTGCAGTTTGGTTTGTAGTAGGAAATGTTTGGATCTTTGGAGGTCACACTTCT
| | | ||| | ||| | | ||| ||| | | | || | || || || | | | ||||||| || || |||| ||||| ||||||||||| | ||||| |||||||| || |||||||| || || ||||| ||||| |||||||||||| | |||
-----------------------gtaagtctaatt--actttgtttggcctcaattaatt--tgggttggttagttaacaa--ttgttaatgactggcagGCTCAACGGGCTAGTGGACCACTTCAAGATGGCGATTGATTGTTTCTTTGCGGTGTGGTTTGTTGTGGGGAATGTATGGATATTTGGAGGTCACTCATCT
upper sequence: GLYMA15G01570.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv09s0002g05120.t01 (Vitis vinifera), 3'ss of exon 2
caaatcaacttaatacaaaaccttgatgccgaatctaattttatccatgtttaatgaatcac-tagcacactaagcagaga---aatttcttgctaaattgcagGCTTAATGGATTAGTAGACCATTTCAAGATGGCCCTGGATTGCTTCTTTGCAGTTTGGTTTGTAGTAGGAAATGTTTGGATCTTTGGAGGTCACACTTCT
|| | || | | | || | |||| | || ||| | | | || | | || | | || || | |||| | | |||| | || |||||||| ||||||||| |||| |||||||||||||| |||||||| || || ||||| ||||| |||||||||||| |||||
----tctgatagttaattattttaaacttttaacccttttttgtatccattcaataatttatatattgtatcggttaatgatgtagctgatttctgatacccagGTTCAGTGGAATGGTGGACCATTTTAAGATGGCCTTGGACTGCTTCTTTGCAGTGTGGTTTGTTGTGGGCAATGTGTGGATATTTGGAGGTCACTCTTCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catgtttaatgaatcactagcacactaagcagagaaatttcttgctaaattgcagGCTTAATGGATTAGTAGACCATTTCAAGATGGCCCTGGATTGCTTCTTTGCAGTTTGGTTTGTAGTAGGAAATGTTTGGATCTTTGGAGGTCACACTTCT
tgctaaa putative branch site (score: 2)
tttcttgct CT-rich tract
ttaatgaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caaatcaacttaatacaaaaccttgatgccgaatctaattttatccatgtttaatgaatcactagcacactaagcagagaaatttcttgctaaattgcagGCTTAATGGATTAGTAGACCATTTCAAGATGGCCCTGGATTGCTTCTTTGCAGTTTGGTTTGTAGTAGGAAATGTTTGGATCTTTGGAGGTCACACTTCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - -caaaacc
- - - - - - - - - - - -tgatgcc
- - - - - - - - - - - - - - - - - - - - - - ccatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacacta