Sequence
atgc intronic sequence ATGC exonic sequence...gccattacattgaagacaaatcatagttttgctctgtgatcatcgtgtgatagagctaaatctgttgtgaagatgacgttttggtaattggttcttgcagATTAGGAAGATATCCTCCGGTTGTGAAGACAGCAGTGCCGGTAGATGGAAGATTCGAACACATTGTTCTTTCTTGTAACGCAACTTCAGACCACGCCATC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G49050.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G49050.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G085939_T01 (Zea mays), 3'ss of exon 3
gccattacattgaagacaaatcatagttttgc--tctgtgatcatcgtgt--gatagagctaaatctgttgtgaagatgacgttttggtaattggttcttgcagATTAGGAAGATATCCTCCGGTTGTGAAGACAGCAGTGCCGGTAGATGGAAGATTCGAACACATTGTTCTTTCTTGTAACGCAACTTCAGACCACGCCATC
| | |||||| | ||||| | | || ||| || | | |||| ||| | | || | | ||| | ||| | ||||||||||| ||||| || || ||||| |||||||| ||||| ||||| || ||||| |||||||| || || || || | ||||| |||||
----tgatattgaacttgcacagctgttttacatttcttggtcagagtactggttgttgctagtgaagtttccgaaaacacactgaattccttgaaacgcacagGTGCGGAAGATATCCACCGGTAGTCAAAACAGCTGTGCCGGTGGATGGTAGATTTGAGCACATAGTTCTTTCCTGCAATGCCACAGCGGACCATGCCATT
upper sequence: AT3G49050.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G37820.1 (Glycine max), 3'ss of exon 3
-gccattacattgaagacaaatcatagttttgctctgtgatcat-cgtgtgatagagctaaatctgttgtgaagatgacgttttggtaattggttcttgcagATTAGGAAGATATCCTCCGGTTGTGAAGACAGCAGTGCCGGTAGATGGAAGATTCGAACACATTGTTCTTTCTTGTAACGCAACTTCAGACCACGCCATC
| ||| | | | || ||| | || | || || | | ||| | | | | | | | ||| | | | |||||| | ||||| | ||| || ||||||| |||||||||||| ||||||||||| || |||||||| || |||||||| || || || || || || |||||
tgtttttatggtcttgtttattcc--gttggaacatatgctaatacggttaaaagatgtttttataacttttacttctggctttcacattaactctatgcagAATGGGAAGGTTTCCCCCAGTTGTGAGGACAGCAGTGCCAGTAGATGGAAGGTTTGAACACATAGTGCTTTCTTGCAATGCCACATCTGATCATGCCATT
upper sequence: AT3G49050.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv16s0050g00620.t01 (Vitis vinifera), 3'ss of exon 3
-gccattacattgaagacaaatcatagttttgctctgtgat--catcgtgtgatagagctaaatctgttgtgaagatgacgttttggtaattggttcttgcagATTAGGAAGATATCCTCCGGTTGTGAAGACAGCAGTGCCGGTAGATGGAAGATTCGAACACATTGTTCTTTCTTGTAACGCAACTTCAGACCACGCCATC
| |||| | || | | || | | | | | | | || |||| | || || |||| | || || | | || | |||| | ||||||| ||| |||||||||| ||||||||| || |||||||| || || || | ||||||||||||||||| || ||||| ||||| || |||
aactattaagtcaaaaagatat-gttgatcaattttaaggtggcaggaaactttagactttgata-actgggaaggacatgtattaaca-tattttgtggcagGATGGGAAGATTTCCCCCGGTTGTGAGGACAGCAGTACCTGTAGATGGGAGGTTTGAGCGTATTGTTCTTTCTTGTAATGCCACTTCTGACCATGCTATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtgatagagctaaatctgttgtgaagatgacgttttggtaattggttcttgcagATTAGGAAGATATCCTCCGGTTGTGAAGACAGCAGTGCCGGTAGATGGAAGATTCGAACACATTGTTCTTTCTTGTAACGCAACTTCAGACCACGCCATC
agctaaa putative branch site (score: 3)
ttcttgc putative PPT
taaatct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gccattacattgaagacaaatcatagttttgctctgtgatcatcgtgtgatagagctaaatctgttgtgaagatgacgttttggtaattggttcttgcagATTAGGAAGATATCCTCCGGTTGTGAAGACAGCAGTGCCGGTAGATGGAAGATTCGAACACATTGTTCTTTCTTGTAACGCAACTTCAGACCACGCCATC
- - - - - - -agacaaa
- - - - - - - - - - - - agttttg
- - - - - - - - - - - - - - - -ctctgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -ctaaatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttttgg