Sequence
atgc intronic sequence ATGC exonic sequence...gtaacttaatcatgaccttttcctagtagcagcttgaagaaaattaacatgtttccaaaatgtatttgtgtctcactttttgttttgggtttttgattagCCGAGACATGTTCAACAAGTTACAAGCTCAACGATGGTGGGCAGATAACTATGACAAAGTAATGGAACTTTACAATGTTCAAAAACTAAGCCGCCAAGCT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G20540.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G20540.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os09g27230.1 (Oryza sativa), 3'ss of exon 2
gtaacttaatcatgaccttttcctagtagcagcttgaagaaaattaacatgtttccaaaatgtatttgt--gtctcactttttgttttgggtt-tttgatt--agCCGAGACATGTTCAACAAGTTACAAGCTCAACGATGGTGGGCAGATAACTATGACAAAGTAATGGAACTTTACAATGTTCAAAAACTAAGCCGCCAAGCT
||| | || | | | | | | | | | ||| | | | || || ||| | || || | || ||| ||| ||||| || ||||||||||||| ||||| ||| |||||||||| || || ||||||||||| ||||| ||||||||||| || | | | | || ||||||
----ctttcttatcatatctgaaaaaaaa-atcatatataaattgtttgtagctgtaacattaccttgctgattctgtttggtgaataaaattgttttattatagCCGTGAGATGTTCAACAAGTGGCAAGCACAAAGATGGTGGGCTGAAAATTATGACAAAGTTATGGAGCTTTACAATGTACAGAGATTTAACCATCAAGCT
upper sequence: AT5G20540.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os08g36020.1 (Oryza sativa), 3'ss of exon 2
gtaacttaatcatgaccttttcctagtagcagct-tgaagaaaattaacatgtttccaaaatgtatttg----tgt-ctcactttttgttttgggtttttgattagCCGAGACATGTTCAACAAGTTACAAGCTCAACGATGGTGGGCAGATAACTATGACAAAGTAATGGAACTTTACAATGTTCAAAAACTAAGCCGCCAAGCT
| || | | | | | || | | || | | |||| | |||| ||| || ||| | || | | |||| ||||| || || |||||||| | ||||| ||| |||||||||| || || ||||| ||||| ||||| |||||||||||||| | | | || ||| ||
-----cttgctgtgtctacctacccatgttaactctcgattaagtgttcccttttctctcgcttgtttgacaatgtgcttactagtgagttctgatgcatgat-agCCGTGAGATATTCAACAAATGGCAAGCGCAAAGATGGTGGGCCGAAAATTATGAGAAAGTCATGGAGCTTTACAATGTTCAGAGGTTCAACCAGCAAACT
upper sequence: AT5G20540.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G066672_T01 (Zea mays), 3'ss of exon 3
-gtaacttaatcatgaccttttcctagtagcagcttgaagaaaattaacatgtttccaaaatgtatttgtgtctcactttt--tgttttgggtttttgattagCCGAGACATGTTCAACAAGTTACAAGCTCAACGATGGTGGGCAGATAACTATGACAAAGTAATGGAACTTTACAATGTTCAAAAACTAAGCCGCCAAGCT
| | || || | | || || | | | | ||| ||| | | | | ||| ||| || | | |||||| || ||||||||||| | |||| ||| |||||||||| || |||||||||||||| ||||||||||||||||| || || | | | |
ccagatatggatgtgcatgcttgcctatctatttatgtagcagttcttcgaataacca---tgtggtcatctgctattttgcatgtaacggtgtgtatgctagCCGTGAGATGTTCAACAAATGGGAAGCACAAAGATGGTGGGCTGAAAACTATGACAAAGTTATGGAACTTTACAATGTGCAGAAGTTTAATCAAACTGTC
upper sequence: AT5G20540.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA15G18980.1 (Glycine max), 3'ss of exon 1
gtaacttaatcatgaccttttccta---gtagcagcttgaagaaaattaacatgtttccaaaatgtatttg-tgtctcactttttgttttgggtttttgattagCCGAGACATGTTCAACAAGTTACAAGCTCAACGATGGTGGGCAGATAACTATGACAAAGTAATGGAACTTTACAATGTTCAAAAACTAAGCCGCCAAGCT
| | | | | || | | || || | | | | || | ||| | | | || || | | ||| |||| ||| || ||| || || || || ||||| | ||||||||| ||||||||||||| ||||||||||| || |||||||||||||||||||||| || |||||||||
-ttgttcatttccaaaattctgatgtacgtgtcaatgttattatagttcatatgatatgatgacttaacaactgaattatggtttatttt---tttatgtatagTCGCGAGATATTTAACAAATGGCAAGCTCAAAGATGGTGGGCAGAGAACTATGACAAGGTGATGGAACTTTACAATGTTCAAAGGCTTGATCGCCAAGCT
upper sequence: AT5G20540.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G16800.1 (Glycine max), 3'ss of exon 3
-gtaacttaatcatgaccttttcctagtagcagcttgaagaaaattaacatgtttcca-aaatgt-atttgtgtctcactttttgttttgggtttttgattagCCGAGACATGTTCAACAAGTTACAAGCTCAACGATGGTGGGCAGATAACTATGACAAAGTAATGGAACTTTACAATGTTCAAAAACTAAGCCGCCAAGCT
|| || || | | ||| | | | || | | | | | | | || | ||| | | ||| | || | || || || ||||| |||||||| || | ||||||||| | ||||||||||| ||||| |||||||| |||||||||||||||||||||| | | |||||||||
gccaatggtgctttgttctaatgcatatagttcatatgatgacatcaggacgactagagagaagtgaattgaattttggtttattttcta---ttatgtacagTCGAGAGATGTTCAATAAATGGCAAGCTCAAAGGTGGTGGGCAGAGAACTACGACAAAGTTATGGAACTTTACAATGTTCAAAGGTTTAACCGCCAAGCA
upper sequence: AT5G20540.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA09G07930.1 (Glycine max), 3'ss of exon 1
gtaacttaatcatgacctt---ttcctagtagcagcttgaagaaaattaacatgtttccaaaatgtatttgtgtctcactttttgttttgggtttt-tgattagCCGAGACATGTTCAACAAGTTACAAGCTCAACGATGGTGGGCAGATAACTATGACAAAGTAATGGAACTTTACAATGTTCAAAAACTAAGCCGCCAAGCT
||||| || | || | |||| | | || ||| | | || | | ||| | || | ||| |||| || |||||| || || || ||||| | ||||||||| ||||||||||||| ||||||||||| || ||||||||||||||||| |||| || | || ||||||
----attaattattagctaggatggttagttacgatagttcatatgatatgatgacttaacaactgagtggtgaactaaattaaggtttatattttatgtatagCCGTGAGATATTTAACAAATGGCAAGCTCAAAGATGGTGGGCAGAGAACTATGACAAGGTGATGGAACTTTACAATGTGCAAAGGCTTAATCGTCAAGCT
upper sequence: AT5G20540.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA17G05900.1 (Glycine max), 3'ss of exon 2
gtaacttaatcatgaccttttcctagta---gcagcttgaagaaaattaacatgtttcca-aaatgt-atttgtgtctcactttttgttttgggtttttgattagCCGAGACATGTTCAACAAGTTACAAGCTCAACGATGGTGGGCAGATAACTATGACAAAGTAATGGAACTTTACAATGTTCAAAAACTAAGCCGCCAAGCT
| ||| || | || | ||| | || | | | | || | | | | | || | ||| | | ||| | || | || || ||| ||||| |||||||| || | ||||||||| | ||||||||||| ||||| ||||| || |||||||||||||||||||||| | | |||||||||
-aatgccaatggtg-ctttgttctaatgcacatagttcatatgatgacatcaggactagagagaagtgaattgaattttggtttattttcta---ttatgtatagTCGAGAGATGTTCAATAAATGGCAAGCTCAAAGGTGGTGGGCAGAGAACTACGACAAGGTTATGGAACTTTACAATGTTCAAAGGTTTAACCGCCAAGCA
upper sequence: AT5G20540.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv11s0016g01460.t01 (Vitis vinifera), 3'ss of exon 3
-gtaacttaatcatgaccttttcctagta-gcagcttgaagaaaattaacatgtttccaaaatgtatttgtgtctcactttttgttttgggtttttgattagCCGAGACATGTTCAACAAGTTACAAGCTCAACGATGGTGGGCAGATAACTATGACAAAGTAATGGAACTTTACAATGTTCAAAAACTAAGCCGCCAAGCT
|||| | || | | | ||| || | || || || | | || | | | | | ||||| | ||||||||| ||||| ||||| ||||| | ||||||||| | ||||||||||| || ||||| | || |||||||| ||||||||||||| | | |||||||||
tgtaagatgcctttgtttaatggcaaaggtgcaatgtgctctag-ttctcactgctcatacaagtgaagggttttgattggttgttgttt-cctttgattagTCGAGAAATGTTTAACAAATGGCAAGCTCAAAGGTGGTGGGCAGAGAATTATGATAGGGTCATGGAACTCTACAATGTTCAAAGGTTTAACCGCCAAGCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacatgtttccaaaatgtatttgtgtctcactttttgttttgggtttttgattagCCGAGACATGTTCAACAAGTTACAAGCTCAACGATGGTGGGCAGATAACTATGACAAAGTAATGGAACTTTACAATGTTCAAAAACTAAGCCGCCAAGCT
ttttt CT-rich tract
aaaatgtattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacttaatcatgaccttttcctagtagcagcttgaagaaaattaacatgtttccaaaatgtatttgtgtctcactttttgttttgggtttttgattagCCGAGACATGTTCAACAAGTTACAAGCTCAACGATGGTGGGCAGATAACTATGACAAAGTAATGGAACTTTACAATGTTCAAAAACTAAGCCGCCAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- aacttaa
- - - - - - - - cttttcc
- - - - - - - - - - - - - - - - - - aagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - ccaaaat