Sequence
atgc intronic sequence ATGC exonic sequence...ctgctgtattttttaaataaattgtatcttggtttactttgctaatgcaatgtgctcaaggatgtttgctgggtgaactaattaatgcttgggtttacagGACAACAAAGATGCTCGTCATGTCAAAACATATGAAGTTTCTCTAAAGGATAAGAACTTTGTCGAAGGTCCATGGTCACAGAACAATCTCGACAATGGTG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G21100.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G21100.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os05g51480.1 (Oryza sativa), 3'ss of exon 8
ctgctgtattttttaaataaattgtatcttggtttactttgctaatgcaatgtgctcaaggatgtttgctgggtgaactaattaa---tgcttgggtttacagGACAACAAAGATGCTCGTCATGTCAAAACATATGAAGTTTCTCTAAAGGATAAGAACTTTGTCGAAGGTCCATGGTCACAGAACAATCTCGACAATGGTG
| || |||| | || || | | | | | | || || || | | | || || ||| | ||| || || ||||| ||||||||||| | ||||| || |||||||||||| | | ||||| || ||||||| || ||||| ||||| ||||||||| | ||||||||||
---atttacttttgatttattcaaaatatctgctggttctcagatctttatttgaccattgtgagatagtaaaagatctgatttaatttgcatgctttaccagGATAACAAAGATGCAAGACATGTTAAGACATATGAAGTTGCATTGAAGGACAAAGACTTTGTTGAGGGTCCTTGGTCGCAGAACAATTTAGACAATGGTG
upper sequence: AT4G21100.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA08G13680.1 (Glycine max), 3'ss of exon 8
ctgctgtattttttaaataaattgtatcttggtttactttgctaatgcaatgt-gctcaaggatgtttg--ctgggtgaactaatta--atgcttgggt---ttacagGACAACAAAGATGCTCGTCATGTCAAAACATATGAAGTTTCTCTAAAGGATAAGAACTTTGTCGAAGGTCCATGGTCACAGAACAATCTCGACAATGGTG
|| |||| | || | | ||| |||||| |||| | | || || || |||| | | || | | ||| ||| || | | |||||| || ||||||||||||||||| ||||||||||| ||| | || |||||||| | ||||| |||||||||||||| |||||||||||||| ||||| |
---ttgcatttcctttatgcaatatat-ttggttgg----aaaaatggtgtttagcataaacatttttgattttgatggatttgttactatgttttcatcaatgacagGATAATAAAGATGCTCGTCATGTTAAAACATATGAGGTTGCACTGAAGGATAAAGATTTTGTTGAAGGTCCATGGTCCCAGAACAATCTCGATAATGGGG
upper sequence: AT4G21100.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA05G30530.1 (Glycine max), 3'ss of exon 8
ctgctgtattttttaaataaattgtatcttggtttactttgctaatgcaatgtgctcaaggatg--tttgctgggtgaactaattaatgcttgg-gtttacagGACAACAAAGATGCTCGTCATGTCAAAACATATGAAGTTTCTCTAAAGGATAAGAACTTTGTCGAAGGTCCATGGTCACAGAACAATCTCGACAATGGTG
|| |||| | || | | ||| ||| | | | | | ||| || |||| ||| | || | | | | | |||||| || ||||||||||||||||| ||||||||||| ||| | || |||||||| | ||| | |||||||||||||| ||||||||||| || ||||| |
---ttgcatttcctttatgcaatatattttgttggaaaaatggtgtttagcataaacaattttgattttgatggatttgttattatgttttcatcgatgacagGATAATAAAGATGCTCGTCATGTTAAAACATATGAGGTTGCACTGAAGGATAAAGATTTTCTTGAAGGTCCATGGTCCCAGAACAATCTTGATAATGGGG
upper sequence: AT4G21100.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv10s0003g04360.t01 (Vitis vinifera), 3'ss of exon 8
ctgctgtattttttaaataaattgtatcttggtttactttgctaatgcaatgtgctcaaggatgtttgctgggtgaactaa---ttaatgcttgggtttacagGACAACAAAGATGCTCGTCATGTCAAAACATATGAAGTTTCTCTAAAGGATAAGAACTTTGTCGAAGGTCCATGGTCACAGAACAATCTCGACAATGGTG
| || | | || || || | | | | |||| | | || | | | ||| || | | || || || ||||| ||||||||||| |||||||| ||||||||||| || || | ||||||||| | ||||| || ||||| ||| | ||||||||||| |||||||| |
aacttagatggccccactgtgttccattatg--tagcatcagaagtgcattaggaagaataac-tcagatggcctcaccatgttctcttgattcaaattgcagGATAACAAAGATGCACGTCATGTTAAAACATATGAGGTGGCTTTGAAGGATAAGGATTTTGTTGAGGGTCCTTGGGCTCAGAACAATCTAGACAATGGGG
upper sequence: AT4G21100.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ23079 (Selaginella moellendorffii), 3'ss of exon 8
ctgctgtattttttaaataaattgtatcttggtttactttgctaatgcaatgtgctcaaggatgtttgctgggtgaactaattaatgcttgggtttacagGACAACAAAGATGCTCGTCATGTCAAAACATATGAAGTTTCTCTAAAGGATAAGAACTTTGTCGAAGGTCCATGGTCACAGAACAATCTCGACAATGGTG
||| ||| || |||| | || | || || ||| || ||||| || |||||||||||||||||||||||| ||||||||||| || | || || || ||| | |||| || || ||||||| ||||| || ||||||||||| |
-------------------------------gttcggtttcct---tcaatatccttttaggaaaaaacttggcgaat--gtt--tgcttcatttgacagGACAACAAAGATGCTCGTCACGTCAAAACATACGAGATACAACTGAAAGAGAAGGATTTTGGTGAGGGGCCATGGTTGCAGAATAACCTCGACAATGGAG
upper sequence: AT4G21100.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ30457 (Selaginella moellendorffii), 3'ss of exon 8
ctgctgtattttttaaataaattgtatcttggtttactttgctaatgcaatgtgctcaaggatgtttgctgggtgaactaattaatgcttgggtttacagGACAACAAAGATGCTCGTCATGTCAAAACATATGAAGTTTCTCTAAAGGATAAGAACTTTGTCGAAGGTCCATGGTCACAGAACAATCTCGACAATGGTG
||| ||| || |||| | || | || || ||| || ||||| || |||||||||||||||||||||||| ||||||||||| || | || || || ||| |||||| || || |||||||| ||||| || ||||||||||| |
-------------------------------gttcggtttcct---tcaatatccttttaggaaaaaacttggcgaat--gtt--tgcttcatttgacagGACAACAAAGATGCTCGTCACGTCAAAACATACGAGATACAACTGAAAGAGAAGGACTTTGGTGAGGGGCCATGGTCGCAGAATAACCTCGACAATGGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcaatgtgctcaaggatgtttgctgggtgaactaattaatgcttgggtttacagGACAACAAAGATGCTCGTCATGTCAAAACATATGAAGTTTCTCTAAAGGATAAGAACTTTGTCGAAGGTCCATGGTCACAGAACAATCTCGACAATGGTG
aactaattaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctgctgtattttttaaataaattgtatcttggtttactttgctaatgcaatgtgctcaaggatgtttgctgggtgaactaattaatgcttgggtttacagGACAACAAAGATGCTCGTCATGTCAAAACATATGAAGTTTCTCTAAAGGATAAGAACTTTGTCGAAGGTCCATGGTCACAGAACAATCTCGACAATGGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
ctgctgt
- - - - - - - aaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aactaat