Sequence
atgc intronic sequence ATGC exonic sequence...cttcactctttaagtatttttgcagcattgtggcctctctgtgttgatagccagaatcattgtgcaatatgttaattctgtgcattccaaaccatttcagGTGTTCTGGGCGTTTTCTATCTACTTAGAGGCAGTTGCTATCCTTCCCCAGTTGGTTCTGCTACAAAGAAGTGGGAATGTCGACAATTTGACTGGGCAAT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G29330.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G29330.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA05G29410.1 (Glycine max), 3'ss of exon 2
cttcactctttaagtattt--ttgcagcattgtggcctctctgtgttgatagccagaatcattgtg-caatatgt-taattctgtgcattccaaaccatttcagGTGTTCTGGGCGTTTTCTATCTACTTAGAGGCAGTTGCTATCCTTCCCCAGTTGGTTCTGCTACAAAGAAGTGGGAATGTCGACAATTTGACTGGGCAAT
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---caatctgaaaattgttgtttgcattac-atgttacctttatgataattctgttacacattgtaacatcatgaatagttgatggtaagtcaatctgttacagATTTTCTGGGCATTTTCAATATACTTGGAGGCAGTTGCAATATTACCCCAGTTGGTTTTGTTGCAAAGGAGTGGAAATGTGGACAATTTGACTGGGCAAT
upper sequence: AT1G29330.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G12570.1 (Glycine max), 3'ss of exon 2
cttcactctttaagtatttttgcagcattgtggcctctctgtgttgatagccagaatcattgtg-caatat-gttaattctgtgcattccaaaccatttcagGTGTTCTGGGCGTTTTCTATCTACTTAGAGGCAGTTGCTATCCTTCCCCAGTTGGTTCTGCTACAAAGAAGTGGGAATGTCGACAATTTGACTGGGCAAT
|| | | | | | |||||| | || || | || | || | |||||| || || || || | || || | || ||| | |||||||| ||||| || ||||| ||||||||||| || | || ||||||||| || | ||||||||||| ||||| ||||||||||||| |||||
-ttgattgccaatctttgtttgcattac-atgttagctttatgataattctgttacacattgtaacatcatcaatagttgactttatgtaaatctgttacagATTTTCTGGGCATTTTCAATATACTTGGAGGCAGTTGCAATATTACCTCAGTTGGTTTTGTTGCAAAGAAGTGGAAATGTGGACAATTTGACTGTGCAAT
upper sequence: AT1G29330.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv10s0003g01700.t01 (Vitis vinifera), 3'ss of exon 2
cttcactctttaagtatttttgcagcattgtggcctctctgtgttgatagccagaatcattgtgcaatatgttaattctgtgcattccaaaccatttcagGTGTTCTGGGCGTTTTCTATCTACTTAGAGGCAGTTGCTATCCTTCCCCAGTTGGTTCTGCTACAAAGAAGTGGGAATGTCGACAATTTGACTGGGCAAT
| || || || | || || | | || | | | | | | | | | | | ||| || | | ||| ||| | |||||||| ||||| || || || ||||| ||||| || ||||||||||| ||| |||| ||| | ||||| ||||| ||||||||||| |||||||
aatatcttgtttgctagtattatagttgtttttttgcttaattcttaatcttatagttgctatttggcctactgctattgttaatgtatatctattgcagATCTTCTGGGCATTTTCAATATATTTGGAGGCTGTTGCCATTCTTCCCCAGTTAGTTTTGCTCCAACGCAGTGGAAATGTGGACAATTTGACGGGGCAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatagccagaatcattgtgcaatatgttaattctgtgcattccaaaccatttcagGTGTTCTGGGCGTTTTCTATCTACTTAGAGGCAGTTGCTATCCTTCCCCAGTTGGTTCTGCTACAAAGAAGTGGGAATGTCGACAATTTGACTGGGCAAT
tgttaat putative branch site (score: 3)
ccatttc putative PPT
aatatgttaattct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttcactctttaagtatttttgcagcattgtggcctctctgtgttgatagccagaatcattgtgcaatatgttaattctgtgcattccaaaccatttcagGTGTTCTGGGCGTTTTCTATCTACTTAGAGGCAGTTGCTATCCTTCCCCAGTTGGTTCTGCTACAAAGAAGTGGGAATGTCGACAATTTGACTGGGCAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - -cctctct
- - - - - - - - - - - - - - - - - - - - - - - - - - agaatca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -attccaa