Sequence
atgc intronic sequence ATGC exonic sequence...gataaacactgtgtcatcgtcatatccacttttggaactctcagtttgtattcatttggagttttaatcagaaatgtcaccagatctctttctctgtaagGTATTACGACGATGCTGCTTGTGTGCTACGGAAAATGTTTTTGGATGCAAAGGCTCCTCATCTTTCTTCAACAATTCCTCCCATTCTGCCATGGAAAATC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G15070.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G15070.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os03g48300.1 (Oryza sativa), 3'ss of exon 11
gataaacactgtgtcatcgtcatatccacttttggaactctcagtttgtattcatttggagttttaatcagaaatgtcaccagatctctttctctgtaagGTATTACGACGATGCTGCTTGTGTGCTACGGAAAATGTTTTTGGATGCAAAGGCTCCTCATCTTTCTTCAACAATTCCTCCCATTCTGCCATGGAAAATC
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---gtaatttatttaatcctagtgttcttttcttacagactg----tctatggaccttaattagttctgaaagatttgcgtaagtttttctatcattcagGTATTATGACGATGCTGCATGCATCTTACGAAAGATATTTCTAGATGCAAAGGCACCTCATCTTTCTTCAACCATCCCTCCAAGCCTTCCTTGGAAATCT
upper sequence: AT5G15070.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA18G49000.1 (Glycine max), 3'ss of exon 11
-----------------------------------------------------gataaacactgtgtcatcgtcatatccacttttggaactctcagtttgta------ttcatttggagttttaat--cagaaatgtcaccagatctctttctctgt-----aagGTATTACGACGATGCTGCTTGTGTGCTACGGAAAATGTTTTTGGATGCAAAGGCTCCTCATCTTTCTTCAACAATTCCTCCCATTCTGCCATGGAAAATC
||| | | || | | |||| | |||||| ||| | || | | || || || | ||| || |||| || || ||||||||| || |||||||| |||||||| || || ||||| || |||||||| || ||||||||||||||| ||||||| || | | | ||||||||| |
gtaatattttgtgatttattgttttggcactgttatatggttcaaaatgcatcaatagttattcactctgc-ttgtatctataattggaaaagcttatttacaactctttttgcataatatctttatggtgaaattttcatcatttctcgtttgctacttctgaagGTATTATGATGATGCTGCCTGTGTGCTGCGAAAGATGTTCTTAGATGCAAAAGCACCTCATCTTTCTTCAGCAATTCCACCAACTTTACCATGGAAAGTA
upper sequence: AT5G15070.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA19G02260.1 (Glycine max), 3'ss of exon 9
--gataaacactgtgt-catcgtcatatccacttttggaactctcagtttgtattcatttggagttttaatcagaaatgtcaccagatctctttctctgtaagGTATTACGACGATGCTGCTTGTGTGCTACGGAAAATGTTTTTGGATGCAAAGGCTCCTCATCTTTCTTCAACAATTCCTCCCATTCTGCCATGGAAAATC
||| ||| || || | | ||| | | | |||| || || | | || |||| ||| || || ||||||||| || ||| |||| ||||| || ||||| ||||| || |||||||| || ||||||||||||||| ||||||| || | | | || |||||| |
actatattttctgcaaatattttcttttatactaataaatactatacattgttcccaac-atttttgtgctggtgaaaatcac--attctgttgctaatgaagGTATTATGATGATTCTGCCTGTGTTCTGCGGAAGATGTTGTTAGATGCAAAAGCACCTCATCTTTCTTCAGCAATTCCGCCAACTTTACCTTGGAAAGTA
upper sequence: AT5G15070.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA09G37610.1 (Glycine max), 3'ss of exon 9
-----------------------------------------------------gataaacactgtgtcatcgtcatatccacttttggaac-tctcagtttgtattcatttggagt-------tttaatcagaaatgtcaccagatctctttctctgt-----aagGTATTACGACGATGCTGCTTGTGTGCTACGGAAAATGTTTTTGGATGCAAAGGCTCCTCATCTTTCTTCAACAATTCCTCCCATTCTGCCATGGAAAATC
||| | | || | | |||| | |||||| ||| | || | || ||| | | ||| || | | | || ||| || || ||||||||| || ||||| || |||||||| || || ||||| || |||||||| || ||||||||||||||| ||||||| || | | | ||||||||| |
gtaatattttgtgatttattgttttggcattgttgcatggttcaaaatacatcaatagttattcactctgc-ttgtatctataattggaaaatcttatttacaactctttttgcatgatatctttttggtgaaatttttatcatttcttgtttgctacttctgaagGTATTATGATGATGCCGCCTGTGTGCTGCGCAAGATGTTCTTCGATGCAAAAGCACCTCATCTTTCTTCAGCAATTCCACCAACTTTACCATGGAAAGTA
upper sequence: AT5G15070.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA13G05060.1 (Glycine max), 3'ss of exon 12
gataaacactgtgtcatcgtcatatccacttttggaactctcagtttgtattcatttggagttttaatcagaaatgtcaccagatctctttctctgtaagGTATTACGACGATGCTGCTTGTGTGCTACGGAAAATGTTTTTGGATGCAAAGGCTCCTCATCTTTCTTCAACAATTCCTCCCATTCTGCCATGGAAAATC
|| | | || | | ||| | | | | | || | | |||| | | | ||| || || ||||||||| || ||| |||| ||||| || ||||| ||||| || |||||||| || ||||||||||||||| ||||||| || | | | ||||||||| |
actatattttctgcaaatattttattttatactaataaatactatacgttgttcctcaactttttgtgctggtgaaaatcacattctgttgctactgaagGTATTATGATGATTCTGCCTGTGTTCTGCGGAAGATGTTGTTAGATGCAAAAGCACCTCATCTTTCTTCAGCAATTCCGCCAACTTTACCATGGAAAGTA
upper sequence: AT5G15070.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 11
gataaacactgtgtcatcgtcatatccacttttggaactctcagtttgtattcatttggagttttaatc--agaaatgt-caccagatctctttctctgta-agGTATTACGACGATGCTGCTTGTGTGCTACGGAAAATGTTTTTGGATGCAAAGGCTCCTCATCTTTCTTCAACAATTCCTCCCATTCTGCCATGGAAAATC
| | || | | |||| ||| || | || |||||| || || | | |||||| ||| ||||||||| || |||||||| || ||||||||||||||| | |||| |||||| | || || ||||| ||||||||||||||||||||||| || | | | || ||||| ||
---ttttgacatatattctttac-tccattttcatcttactatttcaataatcattttttgtgttggttgtaaaaatgtacacggtatctctttccaactacagGTATTATGATGATGCTGCTTGTGTGTTGAGGAAGATGTTTATAGACGCGAAGGCCCCTCATCTTTCTTCAACAATTCCACCAACTTTACCTTGGAAGGTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtattcatttggagttttaatcagaaatgtcaccagatctctttctctgtaagGTATTACGACGATGCTGCTTGTGTGCTACGGAAAATGTTTTTGGATGCAAAGGCTCCTCATCTTTCTTCAACAATTCCTCCCATTCTGCCATGGAAAATC
ttttaat putative branch site (score: 3)
tctctttctctgt putative PPT
ttttaatcagaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gataaacactgtgtcatcgtcatatccacttttggaactctcagtttgtattcatttggagttttaatcagaaatgtcaccagatctctttctctgtaagGTATTACGACGATGCTGCTTGTGTGCTACGGAAAATGTTTTTGGATGCAAAGGCTCCTCATCTTTCTTCAACAATTCCTCCCATTCTGCCATGGAAAATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- -aaacact
- - - - - - - - - - catatcc
- - - - - - - - - - - - - - - - - - - - - agtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cagaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caccaga