Sequence
atgc intronic sequence ATGC exonic sequence...tgggttttggcctgaagtttcttttgttatttgaaaaaataaagaaattctttttgcttgaaacttgtttatgacactgtatttggtaaaatctttgaagGTAGTAGAAATGCAAGGGGATATGAATTTGGAAGGACTTATGTTGTGAGGCCTAAAGGAAAGCATCAAGCCACTCTAGTCTGGCTTCATGGTCTTGGTGA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G52700.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G52700.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA13G43990.2 (Glycine max), 3'ss of exon 2
tgggttttggcctgaagtttcttttgttatttgaaaaaataaagaaattctttttg--cttgaaactt----gtttatgacactgtatttggtaaaatctttgaagGTAGTAGAAATGCAAGGGGATATGAATTTGGAAGGACTTATGTTGTGAGGCCTAAAGGAAAGCATCAAGCCACTCTAGTCTGGCTTCATGGTCTTGGTGA
|| |||| | ||| || | | ||||||| || || | | || |||| | | | ||| | || | | || ||| | |||| | | | ||| | | || ||||| | || |||| |||||||| |||||||| |||||||||||| |||| ||||| |||||||||||
-ggatttt--catgattttgtactcatgttttgaaatctgtcagtaactatcttcaaacttggtatgtcacagattagtaagctttctcacttacaattgcagGTAGTAGAACCACTCGAAGAGCTTTCGAGTTTGGGAAAACACATGTAGTGAGGCCAAAAGGAAAACATCAAGCCACTATAGTTTGGCTGCATGGTCTTGG---
upper sequence: AT1G52700.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA07G03670.2 (Glycine max), 3'ss of exon 1
tgggttttggcctga-agtttcttttgtt-atttgaaaaaataaagaaattctttttgc-----ttgaaacttgttta-tgacactgtatttggtaaaatctttgaagGTAGTAGAAATGCAAGGGGA---TATGAATTTGGAAGGACTTATGTTGTGAGGCCTAAAGGAAAGCATCAAGCCACTCTAGTCTGGCTTCATGGTCTTGGTGA
| ||| |||||| || || ||||| || | | | | | ||| | ||||||| | | | | | | || | || ||||||||||| ||| || || | || ||||| | ||| |||| |||||||| ||||||||||| ||||| ||| |||| ||||| |||||||||||
--------gcaatgatagtttccttggtccatttggaatataatcgttactttttccacatgttttgaaacctatcagctatcttcagacattatatgccatctgcagGTAGTAGAACTGCTAGCAGAAGCTTGGAGTTTGGGAAGACACATGTGGTGAGGCCAAAAGGAAAGCACCAAGCTACTATAGTTTGGCTGCATGGTCTTGG---
upper sequence: AT1G52700.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA15G01350.1 (Glycine max), 3'ss of exon 2
tgggttttggcctgaagtttcttttgttatttgaaaaaataaagaaattctttttg--cttgaaac----ttgtttatgacactgtatttggtaaaatctttgaagGTAGTAGAAATGCAAGGGGATATGAATTTGGAAGGACTTATGTTGTGAGGCCTAAAGGAAAGCATCAAGCCACTCTAGTCTGGCTTCATGGTCTTGGTGA
| ||| | ||| ||| | | ||| ||| || || | | || |||| | | ||| | || | | || ||| | |||| | | | ||| | | ||| ||||| | ||| |||| |||||||| |||||||| || ||||||||| |||| ||||| |||||||||||
---ggattgtcatgattttttactcatgttttcaaatctgtcagtaactatcttcaaacttggtatgccacagattagtaagctttctcacttacaattgcagGTAGTAGAACCACTCGAAGAGCTTTTGAGTTTGGGAAGACACATGTAGTGAGGCCAAAAGGAAAACACCAAGCCACTATAGTTTGGCTGCATGGTCTTGG---
upper sequence: AT1G52700.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G22420.1 (Glycine max), 3'ss of exon 1
tgggttttggcctgaagtttcttttgtt-atttgaaaaaataaagaaattctttttgc-----ttgaaacttgttta-tgacactgtatttggtaaaatctttgaagGTAGTAGAAATGCAAGGGGA---TATGAATTTGGAAGGACTTATGTTGTGAGGCCTAAAGGAAAGCATCAAGCCACTCTAGTCTGGCTTCATGGTCTTGGTGA
| |||||| || || ||||| || | | | | ||| | ||||||| | | | | | || || |||| ||||||||||| ||| ||| || | || ||||| | ||| |||| |||||||| |||||||| || ||||| ||| |||| ||||| |||||||||||
-------tcaatgatagtttccttggtccatttggaaggtaatcgttactttttccacatgttttgaaacctatcagctatcttcaaactttatatgccatttgcagGTAGTAGAACTGCTAGGAGAAGCTTGGAGTTTGGGAAGACACATGTGGTGAGGCCAAAAGGAAAACACCAAGCTACTATAGTTTGGCTGCATGGTCTTGG--- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattctttttgcttgaaacttgtttatgacactgtatttggtaaaatctttgaagGTAGTAGAAATGCAAGGGGATATGAATTTGGAAGGACTTATGTTGTGAGGCCTAAAGGAAAGCATCAAGCCACTCTAGTCTGGCTTCATGGTCTTGGTGA
tcttt CT-rich tract
taaaatcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgggttttggcctgaagtttcttttgttatttgaaaaaataaagaaattctttttgcttgaaacttgtttatgacactgtatttggtaaaatctttgaagGTAGTAGAAATGCAAGGGGATATGAATTTGGAAGGACTTATGTTGTGAGGCCTAAAGGAAAGCATCAAGCCACTCTAGTCTGGCTTCATGGTCTTGGTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- ggttttg
- - - - - - - - - - - - - - - - - - aaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatttgg