Sequence
atgc intronic sequence ATGC exonic sequencegtaaaacaaacaagacctcctcgaaacctgtgaaattgttcttgatggtttgattagcgtttgtccataaagctagagactttttgaattcttaccatatcggacatgtgtaatggttttgtgatgcagGTAGTAGAAGACGGGTATGAGTTTTTCGCAAAACGGAGATTAGTCACGATATTCTCAGCTCCAAACTATGGTGGGGAGTTTGACAACGCTGGTGCGTTAT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G27840.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G27840.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os01g24750.1 (Oryza sativa), 3'ss of exon 2
gtaaaacaaacaagacctcctcgaaacctgtgaaattgttcttgatggtttgattagcgtttgtccataaagctagagactttttgaattcttaccatatcggacatgtgtaatggttttgtgatgcagGTAGTAGAAGACGGGTATGAGTTTTTCGCAAAACGGAGATTAGTCACGATATTCTCAGCTCCAAACTATGGTGGGGAGTTTGACAACGCTGGTGCGTTAT
| ||| | | || | | | ||| | || | | ||| ||| | | ||| | |||| || || || || || ||||| || || || |||||||||| || || || ||||||||||||||| ||||||| ||||| || || ||||| | |
----------------------------------------------------gtaagcactaatt-attttgatctttattttgtctgttgagatc-tatataacaatttcagcatgaatgtctt-tagGTTGTTGAGGATGGCTACGAGTTCTTTGCGCAAAGGAGATTAGTGACAATCTTTTCAGCTCCAAACTATTGTGGGGAATTTGATAATGCGGGTGCTCTGT
upper sequence: AT5G27840.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G137286_T02 (Zea mays), 3'ss of exon 2
gtaaaacaaacaagacctcctcgaaacctgtgaaattgttcttgatggtttgatt-agcgtttgtccataaagctagagactttttgaattcttaccatatcggacatgtgtaatggttttgtgatgcagGTAGTAGAAGACGGGTATGAGTTTTTCGCAAAACGGAGATTAGTCACGATATTCTCAGCTCCAAACTATGGTGGGGAGTTTGACAACGCTGGTGCGTTAT
||||||| | | | | | || | | || || | | | |||| || || || || || | | ||| | | ||||||| ||||| || ||||||||||| ||| |||| |||||||| || || || ||||||||||| || |||| ||||| || ||||| ||||| | |
-------------------------gtttgtgaaagtctatcttctatcctattttatcaattatcttttacattttgatctttac-----ctgacaatgctgg-cacgcttcatgaatg---gccctagGTAGTTGAAGATGGTTATGAGTTTTTTGCACAACGAAGATTAGTGACAATCTTTTCAGCTCCAAATTACTGTGGAGAGTTCGATAACGCCGGTGCTCTGT
upper sequence: AT5G27840.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM5G899390_T01 (Zea mays), 3'ss of exon 2
gtaaaacaaacaagacctcctcgaaacctgtgaaattgttcttgatggtttgatt-agcgtttgtccataaagctagagactttttgaattcttaccatatcggacatgtgtaatggttttgtgatgcagGTAGTAGAAGACGGGTATGAGTTTTTCGCAAAACGGAGATTAGTCACGATATTCTCAGCTCCAAACTATGGTGGGGAGTTTGACAACGCTGGTGCGTTAT
||||||| | | | | || || | | || | | || |||| || || || || || | | ||| | | |||| || ||||| || |||||||| || ||| |||| |||||||| || || || ||||||||||| ||| |||| |||||||| || | ||| || | |
-------------------------gtttgtgaaagtctatcttctatcctgttttatcagttatttttggttctctgatctttac-----ctgacaatgctgg-cacgcttcatgaatgtccc---tagGTGGTTGAAGATGGCTATGAGTTCTTTGCACAACGAAGATTAGTGACAATCTTTTCAGCTCCAAATTATTGTGGAGAGTTTGATAATGTTGGCGCTCTTT
upper sequence: AT5G27840.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA19G42050.1 (Glycine max), 3'ss of exon 2
gtaaaacaaacaagacctcctcgaaacctgtgaaattgttcttgatggtttgattagcgtttgtccataaagctagagactttttgaattcttaccatatcggacatgtgtaatggttttgtgatgcagGTAGTAGAAGACGGGTATGAGTTTTTCGCAAAACGGAGATTAGTCACGATATTCTCAGCTCCAAACTATGGTGGGGAGTTTGACAACGCTGGTGCGTTAT
|||| | | | | || ||| | ||| | ||| | | | | || | | || || || || | || | |||| | || |||| || || || || ||||||||||| || ||| | ||||||||||||||||| || |||||||| ||||||||||| |||||||| ||||||||||| |
----------------ttccttgc--tttcttactttaacctttgtcttttat---gtgttacttcttccaact------tcctctgatcaaggcctcattttactttcctattttttttttaat--agGTTGTGGAGGATGGATATGAGTTTTTTGCTAAAAGAAGATTAGTCACGATATTTTCTGCTCCAAATTATGGTGGGGAATTTGACAATGCTGGTGCGTTGT
upper sequence: AT5G27840.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA03G39440.1 (Glycine max), 3'ss of exon 2
gtaaaacaaacaagacctcctcgaaacctgtgaaattgttcttgatggtttgatt-agcgtttgtccataaagctagagactttttgaattcttaccatatcggacatgtgtaatggttttgtgat----gcagGTAGTAGAAGACGGGTATGAGTTTTTCGCAAAACGGAGATTAGTCACGATATTCTCAGCTCCAAACTATGGTGGGGAGTTTGACAACGCTGGTGCGTTAT
|| | | || | ||| || | | |||||| | | | | || | ||| | | || | | | | | | | | |||| || || || || ||||||||||| || ||| | ||||||||||||||||| || |||||||| || |||||||| |||||||| |||||||| || |
----------------------------------atcttccctgcttttttactttaacctttgtcttttatgtgttacttattccaacttcctctggtcaaggtctcattttactttcctattttcttaatagGTTGTGGAGGATGGATATGAGTTTTTTGCTAAAAGAAGATTAGTCACGATATTTTCTGCTCCAAATTACGGTGGGGAATTTGACAATGCTGGTGCATTGT
upper sequence: AT5G27840.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv14s0060g01750.t01 (Vitis vinifera), 3'ss of exon 2
gtaaaacaaacaagacctcctcgaaacctgtgaaattgttcttgatggtttgattagcgtttgtc--cataaagctagagactttttgaattcttaccatatcggacatgtgtaatggttttgtgatgcagGTAGTAGAAGACGGGTATGAGTTTTTCGCAAAACGGAGATTAGTCACGATATTCTCAGCTCCAAACTATGGTGGGGAGTTTGACAACGCTGGTGCGTTAT
| ||| | | ||| || || | | || || ||| | ||| | || | | | ||| | | || | | || ||||||| || || || || ||||| || || || ||||| |||||||||| || || ||||| |||||||||||||| |||||||| || || ||||| | |
---------------------tcataccagccagcttgagtcatatctagggactggtgtctgataacatcatactaaaaac-----aagtggt--ccagactaaaatcgttctaag---ctgaattgcagGTGGTGGAGGATGGATATGAATTCTTTGCTAAACGACGATTAGTCACAATTTTTTCAGCACCAAACTATGGTGGAGAGTTTGATAATGCCGGTGCTCTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agagactttttgaattcttaccatatcggacatgtgtaatggttttgtgatgcagGTAGTAGAAGACGGGTATGAGTTTTTCGCAAAACGGAGATTAGTCACGATATTCTCAGCTCCAAACTATGGTGGGGAGTTTGACAACGCTGGTGCGTTAT
ttcttac putative branch site (score: 2)
tttttgaattctta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaacaaacaagacctcctcgaaacctgtgaaattgttcttgatggtttgattagcgtttgtccataaagctagagactttttgaattcttaccatatcggacatgtgtaatggttttgtgatgcagGTAGTAGAAGACGGGTATGAGTTTTTCGCAAAACGGAGATTAGTCACGATATTCTCAGCTCCAAACTATGGTGGGGAGTTTGACAACGCTGGTGCGTTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG