Sequence
atgc intronic sequence ATGC exonic sequencegtaaaatttcatacttgttaggtgaattgtgcatcattctggcagtatgtagtatcctgcttggaacaacccccttttgtggtttctttttgtagGCGGAATCCCTTGTGAAAGCACAGCAAGACATGGGTGAAACCATGGGTGAACTGGGATTAGCATTCATTAAGCTGACTAAGTTCGAGAACGAGGAAGCTG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G58440.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G58440.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os05g27920.1 (Oryza sativa), 3'ss of exon 1
---------gtaaaatttcatactt-gttaggtgaattgtgcatcattctggcagtatgtagtatcctgcttggaacaacccccttttgtggtttctttttgtagGCGGAATCCCTTGTGAAAGCACAGCAAGACATGGGTGAAACCATGGGTGAACTGGGATTAGCATTCATTAAGCTGACTAAGTTCGAGAACGAGGAAGCTG
||| ||| || | | | | || | | ||||| | | ||| | | || || |||| |||| |||| ||||| ||| | |||||||| || |||||||| ||||||||||| ||||| | ||| ||||| |||||||| || || || || || |||| ||||||||
atgaagctagtagtattgcaactgtagctctctacgttatttggccttctgtttttgtttagagggtagtt---aattgccttctttct--gttttttttcatagGCTGAAGCACTTGTGAAGGCTCAGCAAGATATGGGTGAAACAATGGGGGCACTTGGATTGGCATTCATCAAACTTACAAAATTTGAGACGGAGGAAGCAA
upper sequence: AT5G58440.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA14G37820.2 (Glycine max), 3'ss of exon 1
-gtaaaatttc--atacttgttaggtgaattgtgcatcattctggcagtatg-tagtatcctgcttggaacaacccccttttgtggtttctttt-tgtagGCGGAATCCCTTGTGAAAGCACAGCAAGACATGGGTGAAACCATGGGTGAACTGGGATTAGCATTCATTAAGCTGACTAAGTTCGAGAACGAGGAAGCTG
| | || | ||| | | ||| || || ||||| | | | || ||| || | |||| | ||| ||||||| ||||| ||||| |||||||||||||| ||||| || || ||||||||||| || | ||||| ||||| |||| || | ||||| || || |||
gctgatgttgtgaacactgaccaatttttaaaaccatgtttatgattgtatgattattggttcctatgaattttccagtcatgtgctaattttgatgtagGCTGAATCACTTGTCAAAGCACAGCAAGATATGGGAGAGACAATGGGTGAACTAGGGCTGGCATTTATTAAATTGACAAAATATGAGAATGAAGAGGCTA
upper sequence: AT5G58440.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G39760.1 (Glycine max), 3'ss of exon 1
gtaaaatttcatacttgttaggtgaattgtgca-tcat---tctggcagtatgtagtatc--ctgcttggaacaacccccttttgtggtttctttt-tgtagGCGGAATCCCTTGTGAAAGCACAGCAAGACATGGGTGAAACCATGGGTGAACTGGGATTAGCATTCATTAAGCTGACTAAGTTCGAGAACGAGGAAGCTG
|| || | | | || | | ||| | || | ||||| ||| | || ||| || | || ||| || |||| ||||| ||||| |||||||||||||| ||||| ||||| ||||| ||||| || | ||||| ||||| |||| || || ||||| || || |||
--ctgatgtcgtggccactgaccaatttttataaccatgtatatgactgtatggtttattgattactacgaattttccaatcacatgccaattttggtgcagGCTGAATCACTTGTTAAAGCACAGCAAGATATGGGAGAAACAATGGGAGAACTAGGTCTGGCATTTATTAAATTGACAAAATTTGAGAATGAAGAGGCTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggcagtatgtagtatcctgcttggaacaacccccttttgtggtttctttttgtagGCGGAATCCCTTGTGAAAGCACAGCAAGACATGGGTGAAACCATGGGTGAACTGGGATTAGCATTCATTAAGCTGACTAAGTTCGAGAACGAGGAAGCTG
cccccttttgtggttt CT-rich tract
tttcttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaatttcatacttgttaggtgaattgtgcatcattctggcagtatgtagtatcctgcttggaacaacccccttttgtggtttctttttgtagGCGGAATCCCTTGTGAAAGCACAGCAAGACATGGGTGAAACCATGGGTGAACTGGGATTAGCATTCATTAAGCTGACTAAGTTCGAGAACGAGGAAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG