Sequence
atgc intronic sequence ATGC exonic sequencegtaagtgtgcattaacgtcttgttttattaatctctgtggttattctcattatcaatgtttgtgagtctggctgatgattctgtgcagTGGCTTGTGGAGTATAATGCAGCACTAGCATCTATTTGCTTCATGATTTTGCTTGGATTTGTAGATGATGTCCTTGATGTGCCTTGGAGAGT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G41490.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G41490.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os07g46640.1 (Oryza sativa), 3'ss of exon 2
-----gtaagtgtgcattaacgt--cttgttttattaatctctg--tggttattctcattatcaatgtttgtgagtctggctgatgattctgt-gcagTGGCTTGTGGAGTATAATGCAGCACTAGCATCTATTTGCTTCATGATTTTGCTTGGATTTGTAGATGATGTCCTTGATGTGCCTTGGAGAGT
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gtatgttgactagaagttactataattggcattcataaacgttgctttgtgacctgaaacatgtgttacaattactgtttttgacttccttgttgcagTGGCTTGTTGAATACAACGCGGCACTAGCATCAGTCTGCTTTATGGTGCTTCTTGGATTTATTGATGATGTTCTTGATGTTCCATGGAGAGT
upper sequence: AT2G41490.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM5G827205_T02 (Zea mays), 3'ss of exon 2
---------------------------------------------------------gtaagtgtgcattaacgtcttgttttattaatctctgtggttattctcattatca-----atgttt----gtgagtctggctgatgattctgtgcagTGGCTTGTGGAGTATAATGCAGCACTAGCATCTATTTGCTTCATGATTTTGCTTGGATTTGTAGATGATGTCCTTGATGTGCCTTGGAGAGT
|| ||| | || || || || || ||| || | |||||| || | | | || | ||||||||||||| || |||||||||||| | |||| || ||||| |||||| | ||||||||||| |||||||| |||||||| || ||||||||
gtatgcagtgacgagcagtattttttaacatttacaaactactccctccgttcttttttatttgt-cgccggcgaaaaaattcgagaacggaggtagtatgtcttatgtcctgaaacatgtttcacagttgtttttgttgtcttcttgttgcagTGGCTTGTTGAATATAATGCAGCATTGACATCCATCTGCTTTATGATTCTTCTTGGATTTGTTGATGATGTTCTTGATGTTCCATGGAGAGT
upper sequence: AT2G41490.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G137707_T01 (Zea mays), 3'ss of exon 2
gtaag-tgtg--cattaacgtcttgtttta-ttaatctctgtggttattctcattatcaatgtttgtgagtctggctgatgattctgtgcagTGGCTTGTGGAGTATAATGCAGCACTAGCATCTATTTGCTTCATGATTTTGCTTGGATTTGTAGATGATGTCCTTGATGTGCCTTGGAGAGT
||| | |||| || | | || || | ||| |||| | | || | ||| | | |||| | | ||||||||||||| || ||||||||||| | ||||| | || || |||||| | ||||||||||| |||||||| |||||||| || ||||||||
gtatgctgtgaccaccagtatttttttacacttacaaactgttatgtcctgaagcatatttaacagtggcttttgctgtcttctttttgcagTGGCTTGTTGAATATAATGCAGCGTTGGCATCAGTCTGTTTTATGATTCTTCTTGGATTTGTCGATGATGTTCTTGATGTTCCATGGAGAGT
upper sequence: AT2G41490.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G16320.1 (Glycine max), 3'ss of exon 2
----------------gtaagtgtgcattaacgtcttgttttattaatctctg--tggttattctcattatcaatgtttgtgagtctggctgatgatt--ctgtgcagTGGCTTGTGGAGTATAATGCAGCACTAGCATCTATTTGCTTCATGATTTTGCTTGGATTTGTAGATGATGTCCTTGATGTGCCTTGGAGAGT
|||| | || | || ||| | |||| | | ||| | | || | | | || | || || | ||||||||||||| || || ||||||||| |||| | ||||| ||||||| |||| |||||||| ||||||||||||||||| || ||||||||
gtaagttatgagtatggtaaatctgagtatttgttttgactctaatatcttggaactgatatcaatagaagaaaggagcattgttatgaattatttttggttttgcagTGGCTTGTTGAATACAATGCAGCATTAGCGTGCATTTGTTTCATGACACTGCTAGGATTTGTCGATGATGTCCTTGATGTCCCATGGAGAGT
upper sequence: AT2G41490.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G34640.1 (Glycine max), 3'ss of exon 2
-----------gta-agtgtgcattaacgtcttgttttat--taatctct-gtggttattctcattatcaatgtttgtgagtctggctgatgattctg----tgcagTGGCTTGTGGAGTATAATGCAGCACTAGCATCTATTTGCTTCATGATTTTGCTTGGATTTGTAGATGATGTCCTTGATGTGCCTTGGAGAGT
||| || | | | | ||| | |||| ||| || | | ||| || | | | || | || || ||||||||||||| || || |||||||| ||||| | || || ||||||| ||||| |||||||| || |||||||||||||| || ||||||||
gtaagttatgtgtatggtaaatctgagtatttagttcaactctaatatcttgtaactgatatcaatagaagaaaggagcactttgtgaattatttttggttttgcagTGGCTTGTTGAATACAATGCAGCGCTAGCGTGCATCTGTTTCATGACATTGCTAGGATTTGTTGACGATGTCCTTGATGTCCCATGGAGAGT
upper sequence: AT2G41490.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv08s0007g05920.t01 (Vitis vinifera), 3'ss of exon 2
-------gtaagtgtgcattaacgtcttgttttattaatctctgtggttattctcattatcaatgtttgtgagtctggctgatgatt-------ctgtgcagTGGCTTGTGGAGTATAATGCAGCACTAGCATCTATTTGCTTCATGATTTTGCTTGGATTTGTAGATGATGTCCTTGATGTGCCTTGGAGAGT
|| | || || | | ||| | || || | ||| || | | | ||| || | || ||| | ||||||||||||| ||||| |||||||| ||||||| || |||||||||| |||||||||||||||||||||| |||||| | || ||||||||
atttaagttagctaagcccta--ggttagttaggtctgactttgaagacattttcttcttttaacttttagaattaaaatgttgactacttcattcatgcagTGGCTTGTTGAGTACAATGCAGCCTTAGCATCCATCTGCTTCATGACCCTGCTTGGATTTGTAGATGATGTTCTTGATATTCCATGGAGAGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctgtggttattctcattatcaatgtttgtgagtctggctgatgattctgtgcagTGGCTTGTGGAGTATAATGCAGCACTAGCATCTATTTGCTTCATGATTTTGCTTGGATTTGTAGATGATGTCCTTGATGTGCCTTGGAGAGT
ggctgat putative branch site (score: 4)
attatcaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtgtgcattaacgtcttgttttattaatctctgtggttattctcattatcaatgtttgtgagtctggctgatgattctgtgcagTGGCTTGTGGAGTATAATGCAGCACTAGCATCTATTTGCTTCATGATTTTGCTTGGATTTGTAGATGATGTCCTTGATGTGCCTTGGAGAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA