Sequence
atgc intronic sequence ATGC exonic sequencegtctgtatatattatatggttagattgtgatatctttcctttatatgacaattgtgaaactaaaagattttgttaaaacagGCTACAATATATCAGCAAAAGGCTTTAGACATCAATGAGAGGGAACTTGGACTTGATCATCCAGATACAATGAAGAGTTATGGTGATCTTGCTGTCTTCT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G01320.2 |
intron # | 18 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G01320.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: LOC_Os07g23990.1 (Oryza sativa), 3'ss of exon 16
--------gtctgtatatattatatgg----ttagattgtgatatctttcctttatatgacaattgtgaaactaaaagattt----tgttaaaa---cagGCTACAATATATCAGCAAAAGGCTTTAGACATCAATGAGAGGGAACTTGGACTTGATCATCCAGATACAATGAAGAGTTATGGTGATCTTGCTGTCTTCT
|| | || |||| | | ||| |||||| || || | | | || || | || | |||| |||||||| || |||||||||||||| ||||||||||||||||||||||||| || ||||| || |||||||||||||||||||| ||||||||||| ||||
caacatgagtattgattaattaaagaagaattgagaatgtgatgaattgaagttttgaaaaataccccaagtcaatatgcttatcatagaaaaaatgcagGCTACGATCTATCAGCAAAAGGCCCTAGACATCAATGAGAGGGAACTTGGGCTAGATCACCCTGATACAATGAAGAGTTATGGAGATCTTGCTGTGTTCT
upper sequence: AT1G01320.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA07G06160.1 (Glycine max), 3'ss of exon 18
------------gtctgtat-atattatatggttagattgtgatatctttcctttatatgac--aattgtgaaactaaaagattttg--ttaaa--acagGCTACAATATATCAGCAAAAGGCTTTAGACATCAATGAGAGGGAACTTGGACTTGATCATCCAGATACAATGAAGAGTTATGGTGATCTTGCTGTCTTCT
|| | | | | ||| | | || |||| | | || | || ||| | | ||| |||| ||||| ||||||||||| ||||| ||||| ||||| || ||||| ||||| || | || || |||||||| ||||| |||||||| ||||| ||||||||||| ||||
atttcagccattgtttatgccaaaatatctattctctttttgatttagtagagtttcaggatttgatttcaattcatcaagttttttacttaaatcgcagGCTACAATTTATCAACAAAAAGCTTTGGATATCAACGAGAGAGAGTTAGGTCTGGATCATCCTGATACCATGAAGAGCTATGGGGATCTTGCTGTTTTCT
upper sequence: AT1G01320.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA16G02770.1 (Glycine max), 3'ss of exon 18
------------------gtctgtatatattatatggttagattgtgatatctttcctttatatgacaattgtgaaactaaaagattttgttaaa--acagGCTACAATATATCAGCAAAAGGCTTTAGACATCAATGAGAGGGAACTTGGACTTGATCATCCAGATACAATGAAGAGTTATGGTGATCTTGCTGTCTTCT
| | |||| || | | || | | || || || || ||| | | | || ||| ||||| |||||||| || ||||| ||||| ||||| || ||||| |||||||| | || || |||||||| ||||| |||||||| ||||| ||||||||||| ||||
ttgtttatttgcacctatgccaaaatatcttttctcttttagatttagtaaagtttctggatttgatttcaattcatc-aagttttttacttaaatcgcagGCTACCATTTATCAACAAAAAGCTTTGGATATCAACGAGAGGGAGTTAGGTCTGGATCATCCTGATACCATGAAGAGCTATGGGGATCTTGCTGTTTTCT
upper sequence: AT1G01320.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: Vv00s0388g00080.t01 (Vitis vinifera), 3'ss of exon 3
-------------gtct-gtatatattatatggttagattgtgatatctttcctttata-----tgacaattgtgaaactaaaagattttgttaaaacagGCTACAATATATCAGCAAAAGGCTTTAGACATCAATGAGAGGGAACTTGGACTTGATCATCCAGATACAATGAAGAGTTATGGTGATCTTGCTGTCTTCT
||| | | | | | | || || | | ||| ||| || || | ||| | || || || | | | |||| ||||| ||||| |||||||| || |||||||||||||| ||||| ||||||||||||||||| || |||||||||||||| ||||||||||| ||||
tatggtttttcccatctagggttttccacgtaaatctatgctgtttttttttttttttacttgttgcctattcttaattcaagagttgtcccaattcaagGCCACAATTTATCAACAAAAGGCATTGGACATCAATGAGAGAGAACTAGGACTTGATCATCCAGACACGATGAAGAGTTATGGAGATCTTGCTGTGTTCT
upper sequence: AT1G01320.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: Vv15s0046g00740.t01 (Vitis vinifera), 3'ss of exon 18
--------------gtctgtatatattatatggttagattgtgatatctttcctttatatgacaattgtgaaactaa---aagattttgttaaaa--cagGCTACAATATATCAGCAAAAGGCTTTAGACATCAATGAGAGGGAACTTGGACTTGATCATCCAGATACAATGAAGAGTTATGGTGATCTTGCTGTCTTCT
|||| | | || | | || |||| | || | || | | || | | ||| |||| || || ||||| ||||| ||||| |||||||| || |||||||||||||| ||||| ||||||||||||||||| ||||||||||||||||| ||||||||||| ||||
tccatgtaaatctatgctgtttttttttttttttttccttgttgcctattctcatttttccataactatatggttaattcaagagttgtcccaatttcagGCCACAATTTATCAACAAAAGGCGTTGGACATCAATGAGAGAGAACTAGGACTTGATCATCCAGACACAATGAAGAGTTATGGAGATCTTGCTGTGTTCT
upper sequence: AT1G01320.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: EFJ24726 (Selaginella moellendorffii), 3'ss of exon 17
gtctgtatatattatatggttagattgtgatatctttcctttatatgacaattgtgaaactaaaagattttgttaaaacagGCTACAATATATCAGCAAAAGGCTTTAGACATCAATGAGAGGGAACTTGGACTTGATCATCCAGATACAATGAAGAGTTATGGTGATCTTGCTGTCTTCT
| | | | | || || || || | | || | | | || ||| | | ||||| | ||||| |||||||| ||||| ||||| ||||||||||| ||||||||||| ||||| ||||||||||| || |||||||| | |||||||| |
---------------gtacacaaaa-gctacatattgtattaatgtaattgatgacttaattgatgactttttgtgatcagGCCATGATATACCAGCAAAAAGCTTTGGACATAAATGAGAGGGAGCTTGGACTTGACCATCCGGATACAATGAAAAGCTATGGTGACTTGGCTGTCTTTT
upper sequence: AT1G01320.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: EFJ26734 (Selaginella moellendorffii), 3'ss of exon 17
gtctgtatatattatatggttagattgtgatatctttcctttatatgacaattgtgaaactaaaagattttgttaaaacagGCTACAATATATCAGCAAAAGGCTTTAGACATCAATGAGAGGGAACTTGGACTTGATCATCCAGATACAATGAAGAGTTATGGTGATCTTGCTGTCTTCT
|| | | || | ||| | || ||| ||||| | | || | | |||||||| || || || ||||||||||||||||||||||| | || ||||| | || ||||| ||||| |||||||| ||||| ||||| |||||||| |
------------------gtctggtcttgtca-cttgcggttttat-acaatctaaacgtttgtcgacgcttct----cagGCTACCATCTACCAACAAAAGGCTTTAGACATCAATGAACGCGAGCTTGGCTTGGACCATCCGGATACCATGAAGAGCTATGGAGATCTGGCTGTCTTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgatatctttcctttatatgacaattgtgaaactaaaagattttgttaaaacagGCTACAATATATCAGCAAAAGGCTTTAGACATCAATGAGAGGGAACTTGGACTTGATCATCCAGATACAATGAAGAGTTATGGTGATCTTGCTGTCTTCT
aactaaa putative branch site (score: 2)
ttttgtt putative PPT
aaactaaaagattttg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctgtatatattatatggttagattgtgatatctttcctttatatgacaattgtgaaactaaaagattttgttaaaacagGCTACAATATATCAGCAAAAGGCTTTAGACATCAATGAGAGGGAACTTGGACTTGATCATCCAGATACAATGAAGAGTTATGGTGATCTTGCTGTCTTCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA