Sequence
atgc intronic sequence ATGC exonic sequence...ttgtttatttgcacctatgccaaaatatcttttctcttttagatttagtaaagtttctggatttgatttcaattcatcaagttttttacttaaatcgcagGCTACCATTTATCAACAAAAAGCTTTGGATATCAACGAGAGGGAGTTAGGTCTGGATCATCCTGATACCATGAAGAGCTATGGGGATCTTGCTGTTTTCT
Basic information
species | Glycine max |
transcript | GLYMA16G02770.1 |
intron # | 18 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G02770.1 (Glycine max), 3'ss of exon 18
lower sequence: LOC_Os07g23990.1 (Oryza sativa), 3'ss of exon 16
ttgtttatttgcacctatgccaaaatatcttttctcttttagatttagtaaagtttctggatttgatttcaattcatcaagttttttacttaaat--cgcagGCTACCATTTATCAACAAAAAGCTTTGGATATCAACGAGAGGGAGTTAGGTCTGGATCATCCTGATACCATGAAGAGCTATGGGGATCTTGCTGTTTTCT
| | | ||| | || | | ||| | | |||||| | | | ||| ||| | | || | | ||| ||||||||| || ||||| ||||| || | || ||||| |||||||| | || || ||||| |||||||| |||||||| ||||| ||||||||||| ||||
caacatgagtattgattaattaaagaagaattgagaatgt-gatgaattgaagttttgaaaaat-accccaagtcaatatgcttatcatagaaaaaatgcagGCTACGATCTATCAGCAAAAGGCCCTAGACATCAATGAGAGGGAACTTGGGCTAGATCACCCTGATACAATGAAGAGTTATGGAGATCTTGCTGTGTTCT
upper sequence: GLYMA16G02770.1 (Glycine max), 3'ss of exon 18
lower sequence: AT1G01320.1 (Arabidopsis thaliana), 3'ss of exon 18
ttgtttatttgcacctatgccaaaatatcttttctcttttagatttagtaaagtttctggatttgatttcaattcatc-aagttttttacttaaatcgcagGCTACCATTTATCAACAAAAAGCTTTGGATATCAACGAGAGGGAGTTAGGTCTGGATCATCCTGATACCATGAAGAGCTATGGGGATCTTGCTGTTTTCT
| | |||| || | | || | | || || || || ||| | | | || ||| ||||| |||||||| || ||||| ||||| ||||| || ||||| |||||||| | || || |||||||| ||||| |||||||| ||||| ||||||||||| ||||
------------------gtctgtatatattatatggttagattgtgatatctttcctttatatgacaattgtgaaactaaaagattttgttaaa--acagGCTACAATATATCAGCAAAAGGCTTTAGACATCAATGAGAGGGAACTTGGACTTGATCATCCAGATACAATGAAGAGTTATGGTGATCTTGCTGTCTTCT
upper sequence: GLYMA16G02770.1 (Glycine max), 3'ss of exon 18
lower sequence: Vv00s0388g00080.t01 (Vitis vinifera), 3'ss of exon 3
-------ttgtttatttgcacctatgccaaaatatcttttctcttttagatttagtaaagtttctggatttgatttcaattcatcaagttttttacttaaatcgcagGCTACCATTTATCAACAAAAAGCTTTGGATATCAACGAGAGGGAGTTAGGTCTGGATCATCCTGATACCATGAAGAGCTATGGGGATCTTGCTGTTTTCT
|| || | | | | | |||| | || |||| ||| | | || || | | | |||||| | || ||| |||| || |||||||||||||| || ||||| ||||| ||||| || |||| || |||||||| || || |||||||| ||||| ||||||||||| ||||
tatggtttttcccatctagggttttccacgtaaatctatgctgtttttttttttttttacttgttg--cctattcttaattcaagag-----ttgtcccaattcaagGCCACAATTTATCAACAAAAGGCATTGGACATCAATGAGAGAGAACTAGGACTTGATCATCCAGACACGATGAAGAGTTATGGAGATCTTGCTGTGTTCT
upper sequence: GLYMA16G02770.1 (Glycine max), 3'ss of exon 18
lower sequence: Vv15s0046g00740.t01 (Vitis vinifera), 3'ss of exon 18
ttgtttatttgcacctatgccaaaatatcttttctcttttagatttagtaaagtttctggatttgatttcaattcatcaagtttt----ttacttaaatcgcagGCTACCATTTATCAACAAAAAGCTTTGGATATCAACGAGAGGGAGTTAGGTCTGGATCATCCTGATACCATGAAGAGCTATGGGGATCTTGCTGTTTTCT
| || | | |||||| | | |||| | |||| | | | | | || || || | || | || || ||| ||||| || |||||||||||||| || ||||| ||||| ||||| || |||| || |||||||| || || |||||||| ||||| ||||||||||| ||||
---tccatgtaaatctatgctgtt-tttttttttttttttccttgttgcctattctcatttttccataactatatggttaattcaagagttgtcccaatttcagGCCACAATTTATCAACAAAAGGCGTTGGACATCAATGAGAGAGAACTAGGACTTGATCATCCAGACACAATGAAGAGTTATGGAGATCTTGCTGTGTTCT
upper sequence: GLYMA16G02770.1 (Glycine max), 3'ss of exon 18
lower sequence: EFJ26734 (Selaginella moellendorffii), 3'ss of exon 17
ttgtttatttgcacctatgccaaaatatcttttctcttttagatttagtaaagtttctggatttgatttcaattcatcaagttttttacttaaatcgcagGCTACCATTTATCAACAAAAAGCTTTGGATATCAACGAGAGGGAGTTAGGTCTGGATCATCCTGATACCATGAAGAGCTATGGGGATCTTGCTGTTTTCT
| | | | || | || || ||| | |||| | || ||| | || ||||||||||| || |||||||| ||||| || ||||| || | ||| | || |||| ||||| |||||||||||||||||||| ||||| ||||| || |
-------------------------------------gtctggtcttgtca--cttgcggtttta--tacaatcta--aacgtttgtcgacgcttctcagGCTACCATCTACCAACAAAAGGCTTTAGACATCAATGAACGCGAGCTTGGCTTGGACCATCCGGATACCATGAAGAGCTATGGAGATCTGGCTGTCTTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagtaaagtttctggatttgatttcaattcatcaagttttttacttaaatcgcagGCTACCATTTATCAACAAAAAGCTTTGGATATCAACGAGAGGGAGTTAGGTCTGGATCATCCTGATACCATGAAGAGCTATGGGGATCTTGCTGTTTTCT
atttgat putative branch site (score: 5)
ttttttactt putative PPT
aagttttttacttaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgtttatttgcacctatgccaaaatatcttttctcttttagatttagtaaagtttctggatttgatttcaattcatcaagttttttacttaaatcgcagGCTACCATTTATCAACAAAAAGCTTTGGATATCAACGAGAGGGAGTTAGGTCTGGATCATCCTGATACCATGAAGAGCTATGGGGATCTTGCTGTTTTCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - -tttgcac
- - - - - - - ctatgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - gtttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caattca