Sequence
atgc intronic sequence ATGC exonic sequencegtaagactttttttttggttctttctactatctttttaagtatagagtattggatttaagtatagtgatgtaggtttcacaagagcaattgaatttttggtctattcctaattatgcagtatattggacagttattctcgtattcacacttttatgttgcagTGTTTTCTTTGCTGATCCTGTTGCGGTGAGGCATTCACTGGAAATTCTATCTGAGTTAGCCACAAGAGACCCCTATACAGTAGCAATGACATTAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G07360.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G07360.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA08G03020.1 (Glycine max), 3'ss of exon 8
------------------------------gtaagactttttttttggttctttct-actatctttttaagtatagagtattggatttaagtatagtgatgtaggtttcacaagagcaattg--aatttttggtctattcctaattatgcagtatattggacagttattctcgtattcacacttttatgttgcagTGTTTTCTTTGCTGATCCTGTTGCGGTGAGGCATTCACTGGAAATTCTATCTGAGTTAGCCACAAGAGACCCCTATACAGTAGCAATGACATTAG
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gtaagttactctgtgaaccaaaacttagaggaacaaatagttcatggcctctctttgagcaactttttacttcttgctttttgtttattttggagctggcattaactttgtataatttattattagcttttgcattcttcccttgtctctggtctatagttct-caaatctcaaaactagagttg---actgcagGATTTCATTTGCTGATCCAGTTGCTGTGAGGCATGCACTGGAAATTGTTTCTGAGATAGCTACAAGGGATCCTTATGCTGTTGCAATGGCCTTAG
upper sequence: AT2G07360.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA05G36530.1 (Glycine max), 3'ss of exon 8
--------------------------------gtaagactttttttttggttctttctactatctttttaagtatagagtat-tggatttaagtatagtgatgtaggtttcacaagagcaattgaatttttggtctattcctaattatgcagtatattggacagttattctcgtattcacacttttatgttgcagTGTTTTCTTTGCTGATCCTGTTGCGGTGAGGCATTCACTGGAAATTCTATCTGAGTTAGCCACAAGAGACCCCTATACAGTAGCAATGACATTAG
|| || | | ||||| | | | ||||| | | | |||| | | || || || || || | | ||||| | |||| | | || ||| | | | |||| | | | || ||||| ||| ||||||||||| ||||| ||||||||| ||||||||||| | |||||| |||| |||| || || ||| | || |||||| | ||||
gtaagttactcctagaaccaaaacttagaggaacaaatagttcatggcgtctctttgtgcaacttttttcttcttgcttttcgtttattttggagctggcattaagtttgcataatttattattagcttttgcattcttccattgtttctggtctatagttct-caaatctcaaaactagagttg---actgcagGATTTCATTTGCTGATCCAGTTGCTGTGAGGCATGCACTGGAAATTGTTTCTGAGATAGCTACAATGGATCCTTATGCTGTTGCAATGGCCTTAG
upper sequence: AT2G07360.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv07s0031g02090.t01 (Vitis vinifera), 3'ss of exon 9
gtaagactttttttttggttctttctactatctttttaagtatagagtattggatttaagtatagtgatgtaggtttcacaagagcaattgaatttttggtctattcctaattatgcagtatattggacagttattctcgtattcacacttttatgttgcagTGTTTTCTTTGCTGATCCTGTTGCGGTGAGGCATTCACTGGAAATTCTATCTGAGTTAGCCACAAGAGACCCCTATACAGTAGCAATGACATTAG
||| | | | |||| | || | | ||| | | ||| ||| | ||| | | || | ||| || || || | | || | | ||| |||| ||||||||||||||||| || |||||| | |||||||||| || || ||||| |||| |||||| ||| |||| |||||| | ||||
-----------------------------------------------------attcttctgtcctactgta---tccagctgtgatatttagatattgctcttatgctatattttca----aatggccaatt-ttaacatgaattcattcaca-acctcagGGTTTCTTTTGCTGATCCTGTTGCTGTAAGGCATGCTTTGGAAATTCTCTCCGAATTAGCTACAAAAGACCCTTATGCAGTTGCAATGGCCTTAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctaattatgcagtatattggacagttattctcgtattcacacttttatgttgcagTGTTTTCTTTGCTGATCCTGTTGCGGTGAGGCATTCACTGGAAATTCTATCTGAGTTAGCCACAAGAGACCCCTATACAGTAGCAATGACATTAG
tcctaat putative branch site (score: 2)
cactttt putative PPT
ttttatgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagactttttttttggttctttctactatctttttaagtatagagtattggatttaagtatagtgatgtaggtttcacaagagcaattgaatttttggtctattcctaattatgcagtatattggacagttattctcgtattcacacttttatgttgcagTGTTTTCTTTGCTGATCCTGTTGCGGTGAGGCATTCACTGGAAATTCTATCTGAGTTAGCCACAAGAGACCCCTATACAGTAGCAATGACATTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA