Sequence
atgc intronic sequence ATGC exonic sequencegtatgctttccttactttgctattaaacgagtatgagttaaattttgtgttattcagtaactgagtaagttatttgtgtattttttcggagttgtcagttgtatatggaaagagttaataatatcaattttccttgcagGAGCATGCCAAAGGAGGAAAATGCATTGTTTTTACACAAACAAAACGAGATGCTGATCGCCTTTCATATGCATTGGCTAGAAGCTTCAAATGTGAAGCTT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G22330.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G22330.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os12g41715.1 (Oryza sativa), 3'ss of exon 4
gtatgctttccttactttgctattaaacgagtatgagttaaattttgtgttattcagtaactgagtaagttatttgtgtattttttcggagttgtcagttgtatatggaaagagttaataatatcaattttccttgcagGAGCATGCCAAAGGAGGAAAATGCATTGTTTTTACACAAACAAAACGAGATGCTGATCGCCTTTCATATGCATTGGCTAGAAGCTTCAAATGTGAAGCTT
||| | | ||| ||| ||| || | | || | || | | || | | | | ||| | ||||| | ||| ||| || ||||||||||| ||||| || ||||||||||| ||||||||||||||| ||||||||||||| | || || | ||| | | || ||| | || | ||
--------------------------------gtgaatgtagtttactgtcattttttatgt---ttgaccatatcgaccttaaatactaatttttactataaaatgctttaaattaattgt-tca---ttcatttcagGAGCATGCAAAAGGTGGTAAATGCATTGTATTTACACAAACAAAAAGAGATGCTGATCGATTGTCCTACACCATGGGTCGGAGTTTCCAGTGCCAGGCCC
upper sequence: AT3G22330.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os07g05050.1 (Oryza sativa), 3'ss of exon 4
gtatgctttccttactttgctattaaacgagtatgagttaaattttgtgttattcagtaactgagtaagttatttgtgtattttttcggagttgtcagttgtatatggaaagagttaataatatcaattttccttgcagGAGCATGCCAAAGGAGGAAAATGCATTGTTTTTACACAAACAAAACGAGATGCTGATCGCCTTTCATATGCATTGGCTAGAAGCTTCAAATGTGAAGCTT
|||| | | | || | | | | | || | ||| | || || | | | | | || | ||||||||||| || || |||||||| ||||| ||||| ||||| |||||||| || ||| | | ||||||| ||| || |||| |||| | ||
------------------------------------------------------------gtgagcactct-tctgaatgtatgatgtgttttatagtttgcaccgttaacgactcttttctctacacttcc---acagGAGCATGCTAATGGTGGAAAATGTATTGTGTTTACTCAAACTAAACGAGAGGCAGATAGATTAGCATATGCTATGGGCAGGAGCTATGCATGTCAGGCGC
upper sequence: AT3G22330.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os07g05050.2 (Oryza sativa), 3'ss of exon 4
gtatgctttccttactttgctattaaacgagtatgagttaaattttgtgttattcagtaactgagtaagttatttgtgtattttttcggagttgtcagttgtatatggaaagagttaataatatcaattttccttgcagGAGCATGCCAAAGGAGGAAAATGCATTGTTTTTACACAAACAAAACGAGATGCTGATCGCCTTTCATATGCATTGGCTAGAAGCTTCAAATGTGAAGCTT---------------------------------------------------
|||| | | | || | | | | | || | ||| | || || | | | | | || | ||||||||||| || || |||||||| ||||| ||||| ||||| |||||||| || ||| | | ||||||| ||| || |||| |||| | ||
------------------------------------------------------------gtgagcactct-tctgaatgtatgatgtgttttatagtttgcaccgttaacgactcttttctctacacttcc---acaggagcatgctaatggtggaaaatgtattgtgtttactcaaactaaacgagagGCAGATAGATTAGCATATGCTATGGGCAGGAGCTATGCATGTCAGGCGCTTCATGGGGATATTTCACAGAATCAGAGAGAAAGGACACTATCAGGATTTC
upper sequence: AT3G22330.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G107984_T01 (Zea mays), 3'ss of exon 4
gtatgctttccttactttgctattaaacgagtatgagttaaattttgt-gttattcagtaactgagtaagttatttgtgtattttttcggagttgtcagttgtatatggaaagagttaataatatcaattttccttgcagGAGCATGCCAAAGGAGGAAAATGCATTGTTTTTACACAAACAAAACGAGATGCTGATCGCCTTTCATATGCATTGGCTAGAAGCTTCAAATGTGAAGCTT
|| | ||| || ||||| | || | | ||| | | || | |||| | ||| || |||| ||| ||| | |||| |||| |||| ||| | | || | | ||||||| ||||||||||| || || |||||||||||||||||||||||| | ||||| ||| | | ||| | || | |||| ||| | ||||| |||
gtcaatatagattaggtt-ttattatatttgtcccattaaaacctaattattttccagtga------aagcta---gtgtttttcttctaatttgt----------tggagcatgttagcaat-ttatttgttcatgcagGAACATGCCAAAGGTGGTAAGTGCATTGTTTTTACACAAACAAAAAGGGATGCAGATAGATTGTCACACAATATGAGTCGAAGTTTCCAGTGTGAGGCTC
upper sequence: AT3G22330.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G565140_T01 (Zea mays), 3'ss of exon 4
gtatgctttccttactttgctattaaacgagtatgagttaaattttgtgttattcagtaactgagtaagttatttgtgtattttttcggagttgtcagttgtatatggaaagagttaataatatcaattttccttgcagGAGCATGCCAAAGGAGGAAAATGCATTGTTTTTACACAAACAAAACGAGATGCTGATCGCCTTTCATATGCATTGGCTAGAAGCTTCAAATGTGAAGCTT
|| ||| | |||| | | | ||| |||| |||| || | || | | ||| |||| |||| ||| | | || | || |||| ||||| ||||| || || |||||||||||||||||||||||| | ||||| ||| | | ||| | || | |||| ||| ||||||| ||
------------------------------------gtcggggtttattatatt---tgtcccattaaa--attta---atttctttg---ttctaatttgc---tggagcacgttagcaatttgtttgtttcgtgtagGAACATGCAAAAGGTGGCAAGTGCATTGTTTTTACACAAACAAAAAGGGATGCAGATAGATTGTCACACAATATGAGTCGAAGTTTCCAATGTGAGGCGC
upper sequence: AT3G22330.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA14G03760.1 (Glycine max), 3'ss of exon 4
gtatgctttccttactttgctattaaacgagtatgagttaaattttgtgttattcagtaactgagtaagttatttgtgtattttttcggagttgtcagttgtatatggaaagagttaataatatcaattttccttgcagGAGCATGCCAAAGGAGGAAAATGCATTGTTTTTACACAAACAAAACGAGATGCTGATCGCCTTTCATATGCATTGGCTAGAAGCTTCAAATGTGAAGCTT
| |||| || | | ||||| |||| || || | ||||| | || ||| || | |||| | ||| |||| ||| | |||| ||||| ||||||||||| ||||||||||| || ||||||||||| ||||||||||| | |||||| | |||| ||||| | |||||||| ||||
-------------------ggactaaaagatagtaaaccctatttt----tatttagaaa---aactagttaaggaaacttcttgctggattttttt-ttgtctcc---------taaagatatatcctttgtt---agGAACATGCAAAAGGAGGAAAGTGCATTGTTTTCACTCAAACAAAACGTGATGCTGATCGATTATCATATACCATGGCAAGAAGTGTTAAATGTGAGGCTT
upper sequence: AT3G22330.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G45030.1 (Glycine max), 3'ss of exon 4
gtatgctttccttactttgctattaaacgagtatgagttaaattttgtgttattcagtaactgagtaagttatttgtgtattttttcggagttgtcagttgtatatggaaagagttaataatatcaattttccttgcagGAGCATGCCAAAGGAGGAAAATGCATTGTTTTTACACAAACAAAACGAGATGCTGATCGCCTTTCATATGCATTGGCTAGAAGCTTCAAATGTGAAGCTT
|||| || || | | | ||| | || || | ||||| | |||| | || | |||| | | || | || || || | |||| ||||| ||||||||||| || |||||||| || ||||||||||| ||||||||||| | || ||||| |||| ||||| | |||||||| ||||
----------------------ctaaaaagata---gtagaccctatttttaattagaaa---aactagttaaggaagctttttgttaaagg-attttttgtctctcctaaagat-----atgtcgtttgtt-----agGAACATGCAAAAGGAGGAAAGTGTATTGTTTTCACTCAAACAAAACGTGATGCTGATCGATTATCGTATGCCATGGCAAGAAGTGTTAAATGTGAGGCTT
upper sequence: AT3G22330.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv12s0142g00670.t01 (Vitis vinifera), 3'ss of exon 4
-----------------------gtatgctttcctta--ctttgctattaaacgagtatgagttaaattttgtgtta----ttcagtaa---ctgagtaagttatttgtgtattttttcggagttgtcagttgtatatggaaagagtt---------aataatatcaattttccttgcagGAGCATGCCAAAGGAGGAAAATGCATTGTTTTTACACAAACAAAACGAGATGCTGATCGCCTTTCATATGCATTGGCTAGAAGCTTCAAATGTGAAGCTT
|| | || | || ||| || || ||| | || | | | ||||| || | || |||| || || | | | |||| || | || || | | |||| | | || || | | |||| ||||| ||||| |||||||| |||||||| || ||||||||||| ||||||||||| | ||||||| |||| |||| ||||| |||||| |||
gtatgaacccaggacttcattttgtttctttctcctaatttttactgtttccagagctttaggttttctgtatgttaaagtttttgcaaatgctgaatagcttcccttttttattttagctcattcttgcttttacctccatcaagttttttcccttagcaccatacatgtgtttgttagGAACATGCAAAAGGTGGAAAATGTATTGTTTTCACTCAAACAAAACGCGATGCTGATCGATTGGCATATGCTATGGCAAGAAACTTCAGATGTGAGGCTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcggagttgtcagttgtatatggaaagagttaataatatcaattttccttgcagGAGCATGCCAAAGGAGGAAAATGCATTGTTTTTACACAAACAAAACGAGATGCTGATCGCCTTTCATATGCATTGGCTAGAAGCTTCAAATGTGAAGCTT
agttaat putative branch site (score: 4)
ttttccttgc putative PPT
aaagagttaataatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgctttccttactttgctattaaacgagtatgagttaaattttgtgttattcagtaactgagtaagttatttgtgtattttttcggagttgtcagttgtatatggaaagagttaataatatcaattttccttgcagGAGCATGCCAAAGGAGGAAAATGCATTGTTTTTACACAAACAAAACGAGATGCTGATCGCCTTTCATATGCATTGGCTAGAAGCTTCAAATGTGAAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC