Sequence
atgc intronic sequence ATGC exonic sequence...ctcatgtgttgctaatatttgctgtcttgcatatttctcaaggaagcctataaattattttgtaagaggagaatgctaagttgctaactacttttctcagATTGGATTTCAAGCCATTGCTGAAGCTCTTGGACTAGCTGCAATCAAAGCAGCAGTTGCTATCACTGGCATAATTGCTGGTGGCCGTCTC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G00630.2 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G00630.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G058948_T01 (Zea mays), 3'ss of exon 8
ctcatgtgttgctaatatttgctgtcttgcatatttc-tcaaggaagcctataaattattttgtaagaggagaatgctaagttgctaactacttttctcagATTGGATTTCAAGCCATTGCTGAAGCTCTTGGACTAGCTGCAATCAAAGCAGCAGTTGCTATCACTGGCATAATTGCTGGTGGCCGTCTC
|||| | || | ||| | | ||| | || |||| |||| | | |||| || |||| || ||||| || || ||||| | ||| | |||||| ||||||||| || |||||| |||| |||||||||||| || |||||
-ccatgggacgccgcaacgcctcaaaaaccatgcccagtttacacctccttttgatctgtttgatccttgagacctttgtgcaatacgtgtttttttatagGTTGGTTTCCAAGCAATAGCAGAAGCCATGGGAATGGCTGCAGTCAAAGCAGTAGCTGCTATAACTGCCATAATTGCTGGAGGTCGTCTG
upper sequence: AT4G00630.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G093643_T01 (Zea mays), 3'ss of exon 9
--ctcatgtgttgctaatatttgctgtcttgcatatttctcaaggaagccta-taaattattttgtaagaggagaatgctaagttgctaactacttttct-cagATTGGATTTCAAGCCATTGCTGAAGCTCTTGGACTAGCTGCAATCAAAGCAGCAGTTGCTATCACTGGCATAATTGCTGGTGGCCGTCTC
||| | ||| | || ||| | | ||| | || | ||| || | | | | | || || |||| | || |||| || ||||| || || ||||| | ||| | |||||| ||||||||| || |||||| |||| |||||||||||| || |||||
ttgccataggatgccgcaac--gcctcaaaaaccattcccagtttacacctccttaactgtttggtccttgaggccttc--gttcaatatctggttttttatagGTTGGTTTCCAAGCAATAGCAGAAGCCATGGGAATGGCTGCAGTCAAAGCAGTAGCTGCTATAACTGCCATAATTGCTGGAGGTCGTCTG
upper sequence: AT4G00630.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA18G46420.1 (Glycine max), 3'ss of exon 16
ctcatgtg-ttgctaatatttgctgtcttgcatatttctcaaggaa--gcctataaattattttgtaagaggagaatgctaagttgctaactacttttctcagATTGGATTTCAAGCCATTGCTGAAGCTCTTGGACTAGCTGCAATCAAAGCAGCAGTTGCTATCACTGGCATAATTGCTGGTGGCCGTCTC
|| |||| ||| | | || | | | ||| | | | | || | | || | | || | | || | | || | || |||| |||| |||||||| ||||||||||| |||||||| ||||| | || ||||||||||| ||||||| |||||||||||| || || |
cttctgtggttgtcattgttattttttctacatgtatactctgctattgcttctttgttgtcct-caactcctcattagaaa--taccaatctatattttcagGTTGGTTTTCAAGCTATTGCTGAAGCACTTGGACTGGCTGCTGTTAAGGCAGCAGTTGCCATCACTGCCATAATTGCTGGGGGACGATTG
upper sequence: AT4G00630.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA09G39770.1 (Glycine max), 3'ss of exon 12
ctcatgtgttgctaatatttgctgtcttgcatatttctcaaggaagcctataaattattttgtaagag-gagaatgctaa---gttgctaactacttttctcagATTGGATTTCAAGCCATTGCTGAAGCTCTTGGACTAGCTGCAATCAAAGCAGCAGTTGCTATCACTGGCATAATTGCTGGTGGCCGTCTC
| | || | | || ||||| || ||| | || | | || | | || | | | | || | || |||| |||| |||||||| ||||||||||| |||||||| ||||| | || ||||||||||| ||||||| |||||||| || || ||| |
----taaatcaaaaaggtcaagacacgaatatctttctaaataaagttggtccatgtaagcgcatgattggtagtgttgacataataccaatctatattttcagGTTGGTTTTCAAGCTATTGCTGAAGCACTTGGACTGGCTGCTGTTAAGGCAGCAGTTGCCATCACTGCTATAATTGCAGGGGGACGTTTG
upper sequence: AT4G00630.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA03G01600.1 (Glycine max), 3'ss of exon 2
---ctcatgtgttgctaatatttgctgtcttg--catatttctcaaggaagc-ctataaattattttgtaagaggagaatgctaagttgctaactacttttctcagATTGGATTTCAAGCCATTGCTGAAGCTCTTGGACTAGCTGCAATCAAAGCAGCAGTTGCTATCACTGGCATAATTGCTGGTGGCCGTCTC
||| | | | | || ||| | || ||||| | || | ||| |||| | | | | | || || || ||| |||| || ||||||||||||||||||||||| || ||||| |||| |||| |||||||| | | ||||||||| ||||| || |
tgttaaatgcttgattgaaagccaatgacttcaccttacttctctcattgtcatcatcatctatgttgtcttt------ttgtgaaataccaatctctgtttccagGTTGGTTTCCAAGCCATTGCTGAAGCTCTTGGTCTGGCTGCTGTCAAGGCAGTGGTTGCTATTTCAGCCATAATTGCAGGTGGACGATTG
upper sequence: AT4G00630.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA07G08030.1 (Glycine max), 3'ss of exon 8
-----ctcatgtgttgctaatatttgctgtcttgcatatttctcaaggaagcc--tataaattattttgtaagaggagaatgctaagttgctaactacttttctcagATTGGATTTCAAGCCATTGCTGAAGCTCTTGGACTAGCTGCAATCAAAGCAGCAGTTGCTATCACTGGCATAATTGCTGGTGGCCGTCTC
||| | || | || ||| || || || | || | ||| | ||| |||| | | | | || | || |||| |||| || ||||||||||||||||||||||| || ||||| | || |||| ||||| || | | ||||||||||||||| || |
catgttaaatgcttgactggaagccaatgactt-caccttacttttgtcagtcattatcatctatcttgtcttt------ttgtgtaataccaatctcagttttcagGTTGGTTTCCAAGCCATTGCTGAAGCTCTTGGTCTGGCTGCTGTTAAGGCAGTGGTTGCCATTTCAGCCATAATTGCTGGTGGACGATTG
upper sequence: AT4G00630.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv15s0046g03390.t01 (Vitis vinifera), 3'ss of exon 7
---ctcatgtgttgctaatatttgctgtcttgcatatttctcaaggaagcctataaattattttgtaagaggagaatgctaagttgctaactacttttctcagATTGGATTTCAAGCCATTGCTGAAGCTCTTGGACTAGCTGCAATCAAAGCAGCAGTTGCTATCACTGGCATAATTGCTGGTGGCCGTCTC
|||| |||| | || || | | || | || | | | || || | || | | | | | | || | || || ||||||||| ||||||||||||||||||||||| ||||| ||||| | || ||| |||||| || ||| ||||||||||||||| || |
ttctccatgcgttgatcatgcttctttgttgtcagttgtcactactattactgctgcttctattcttat--gttgttatcatggcaacaatt-ctgttttcagATTGGTTTTCAAGCCATTGCTGAAGCTCTCGGACTGGCTGCTGTTAAGGCATTAGTTGCCATTGCTGCCATAATTGCTGGTGGACGCTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcctataaattattttgtaagaggagaatgctaagttgctaactacttttctcagATTGGATTTCAAGCCATTGCTGAAGCTCTTGGACTAGCTGCAATCAAAGCAGCAGTTGCTATCACTGGCATAATTGCTGGTGGCCGTCTC
tgctaac putative branch site (score: 1)
ctacttttctc CT-rich tract
taaattattttgtaag 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctcatgtgttgctaatatttgctgtcttgcatatttctcaaggaagcctataaattattttgtaagaggagaatgctaagttgctaactacttttctcagATTGGATTTCAAGCCATTGCTGAAGCTCTTGGACTAGCTGCAATCAAAGCAGCAGTTGCTATCACTGGCATAATTGCTGGTGGCCGTCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG