Sequence
atgc intronic sequence ATGC exonic sequencegtaagtttctgtatgtagacacggatttgagtgataattatcaagttttcacactttgatccttcttgttgtgttcagGTATGGTAGCGGCGCTCACTAACGAGAGCGCTACAAGCAAGTCGGTGTATTTTGCTCATTGTACATCTGAGATGATATTTATAACTCATTTACTAGCAGA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G41540.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G41540.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os01g71280.1 (Oryza sativa), 3'ss of exon 3
---------------------gtaagtttctgtatgtagacacggatttgagtgataattatcaagttttcacactt-tgatccttcttgttgtgttc-agGTATGGTAGCGGCGCTCACTAACGAGAGCGCTACAAGCAAGTCGGTGTATTTTGCTCATTGTACATCTGAGATGATATTTATAACTCATTTACTAGCAGA
||||| || | | | | || | | || | ||| ||||| | | | | || | || ||||| ||| ||||| || || | ||||| ||||| || ||||||||||||||||||||||||||||| || || ||||||||||| || |||||||| || ||||
agttctgtttgaagactgtttacaagttatagttttttctctctctgttcaa-ggtatatgtcatgttttgagattaataataacccactttctgttccagGAATGGTTGCAGCTTTAACTAATGAGAGTGCAACAAGCAAGTCGGTGTATTTTGCTCATTGCACGTCAGAGATGATATTCATTACTCATTTGCTCACAGA
upper sequence: AT2G41540.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G155348_T01 (Zea mays), 3'ss of exon 3
---------------------gtaagtttctgtatgtagacacggatttgagtgataattatcaagttt-tcacactttgatccttcttgttgtgtt-cagGTATGGTAGCGGCGCTCACTAACGAGAGCGCTACAAGCAAGTCGGTGTATTTTGCTCATTGTACATCTGAGATGATATTTATAACTCATTTACTAGCAGA
| | | || | | | | || || ||| ||| | || | |||| || |||| |||| ||||| || || | || |||||||| || |||||||| || || |||||||||||||| || || ||||||||||| || |||||||| || ||||
gacctgaggagtgctactcagaccacctaaccaactcagctagaggccctttcg-cgagtaccagttttatcatatttctctaattctctttatgtttcagGAATGGTGGCAGCTTTAACAAACGAGAGTGCAACAAGCAAATCTGTATATTTTGCTCATTGCACGTCAGAGATGATATTCATTACTCATTTGCTGACAGA
upper sequence: AT2G41540.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA03G28970.1 (Glycine max), 3'ss of exon 2
---------------------gtaagtttctgtatgtagacacggatttgagtgataattatcaagttttca-cactttgatccttcttgttgtgttcagGTATGGTAGCGGCGCTCACTAACGAGAGCGCTACAAGCAAGTCGGTGTATTTTGCTCATTGTACATCTGAGATGATATTTATAACTCATTTACTAGCAGA
| || | | | | | |||| | | ||| ||| | | | || | | | | || ||| ||||| |||||||| || || || || ||||| ||||||||||| || ||||| ||||| || || || || || ||||||||||| |||||||| | || ||
gtttaacatacctctaattttatgagaggcattcccatgtcttacacttgatttctgatttacaatctataaatcctgtttttcattttaatgttgtcagGAATGGTAGCTGCCCTTACCAATGAGAGTGCTACAAGCAAATCTGTGTACTTTGCACACTGCACGTCGGAAATGATATTTATCACTCATTTGTTGGCTGA
upper sequence: AT2G41540.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G15900.1 (Glycine max), 3'ss of exon 2
-------------------------gtaagtttctgtatgtagacacggatttgagtgataattatcaagttttcacactttgatccttcttgttgtgttcagGTATGGTAGCGGCGCTCACTAACGAGAGCGCTACAAGCAAGTCGGTGTATTTTGCTCATTGTACATCTGAGATGATATTTATAACTCATTTACTAGCAGA
| || ||| | | | | | | || | || | || | | ||| || || ||| || |||| |||| |||||||| || || || || ||||| ||||| ||||| || || || ||||| || || ||||| |||||||||||||| |||||||| | || ||
gtttagtattacaagtggcaaatgggaaaatttgactgcgacaataggaacctgccttattcatttccacaacttacatttacattcttattattgt---cagGAATGGTAGCAGCCCTTACCAATGAGAGTGCTACTAGCAAATCTGTCTACTTTGCACACTGCACATCAGAGATGATATTTATCACTCATTTGTTGGCTGA
upper sequence: AT2G41540.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv08s0007g09000.t01 (Vitis vinifera), 3'ss of exon 2
---------------------------------------------------------------------------------------------------------------gtaagtttctgtatgtagaca--cggatttgagtgata--attatcaagttt--tcacactttgatccttcttgttgtg----ttcagGTATGGTAGCGGCGCTCACTAACGAGAGCGCTACAAGCAAGTCGGTGTATTTTGCTCATTGTACATCTGAGATGATATTTATAACTCATTTACTAGCAGA
| | | || | ||| | | | || | || |||| ||| ||| | | || | | || | |||| |||||||| || || || || ||||| ||||| ||||| || || || ||||| ||||||||||| |||||||| || || |||||||| | || ||
gtaagttgttatttctttatgatggtaatataatagagggatcattgtgcttgaagtttcatatatgagcatccttgtcagataaacttcagcaatgatctggttctcattttgacctactaggagaagaaaaccaaaatttaaaaatgttgttattggatttaatcaagagtctcacattttcactttgattttccagGAATGGTAGCAGCCCTGACCAATGAGAGTGCTACCAGCAAATCTGTATACTTTGCACATTGTACATCAGAGATGATCTTCATTACTCATTTGTTGGCTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatttgagtgataattatcaagttttcacactttgatccttcttgttgtgttcagGTATGGTAGCGGCGCTCACTAACGAGAGCGCTACAAGCAAGTCGGTGTATTTTGCTCATTGTACATCTGAGATGATATTTATAACTCATTTACTAGCAGA
ctttgat putative branch site (score: 5)
tccttcttgtt CT-rich tract
ataattatcaagtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtttctgtatgtagacacggatttgagtgataattatcaagttttcacactttgatccttcttgttgtgttcagGTATGGTAGCGGCGCTCACTAACGAGAGCGCTACAAGCAAGTCGGTGTATTTTGCTCATTGTACATCTGAGATGATATTTATAACTCATTTACTAGCAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG