Sequence
atgc intronic sequence ATGC exonic sequencegtgagccaatcgtttcattttcttcattttacgacctatggagtaattatggattcagagaataacggaaaatgtgtttactaacttaatttctttggattcagATATGTTTTGGAGTCTGACCATGTGAAGAAATTCTTTGATTACATACAGCTTCCAAATTTCGACATTGCTGCCGATGCTGCTGCTACTTTTAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G47540.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G47540.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os07g39630.1 (Oryza sativa), 3'ss of exon 4
gtgagccaatcgtttcattttcttcattttacgaccta-tggagtaattatggattcagagaataacggaaaatgtgtttactaacttaatttctttggattcagATATGTTTTGGAGTCTGACCATGTGAAGAAATTCTTTGATTACATACAGCTTCCAAATTTCGACATTGCTGCCGATGCTGCTGCTACTTTTAAG
| | || || |||| | | | || || || ||||| |||| || || | | | | | | ||| | ||| || ||||| ||||||||||| ||||||| |||||||| || ||||| ||||||||||| |||||||| | |||||| |||| || ||||||
--caactaaggattctgttttacataaaccataaaatactgtagaaattagaaattcctgtcggaatggtgcttatttatcttggtaaatgttcactca---cagGTACGTTTTAGAGTCTGACCACATGAAGAAGTTCTTTGACTATATACAACTTCCAAATTTTGACATTGCATCAGATGCTTCTGCGACCTTTAAG
upper sequence: AT5G47540.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G066051_T01 (Zea mays), 3'ss of exon 4
gtgagccaatcgtttcattttcttcattttacgacctatggagtaattatggattca-gagaataacggaaaatgtgtttactaacttaatttctttggattcagATATGTTTTGGAGTCTGACCATGTGAAGAAATTCTTTGATTACATACAGCTTCCAAATTTCGACATTGCTGCCGATGCTGCTGCTACTTTTAAG
||| | | | | | | | | | | | || | | || || | | | | | | || || | || || || ||| |||||||| |||||||| || ||||||| |||||||| || ||||||||||||||||| ||||| ||| | |||||| | ||||| ||||||
---agctagacatccatgatccataagtgcaaaatttttgttggagttggaagctcctgtggacttttggtgctatttt--cttatagaacttgttcattgacagGTATGTTTTAGAGTCTGAACACATGAAGAAGTTCTTTGACTATATACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCGGCTACCTTTAAG
upper sequence: AT5G47540.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G351417_T02 (Zea mays), 3'ss of exon 3
gtgagccaatcgtttcattttcttcattttacgacctatggagtaattatggattca-gagaataacggaaaatgtgtttactaacttaatttctttggattcagATATGTTTTGGAGTCTGACCATGTGAAGAAATTCTTTGATTACATACAGCTTCCAAATTTCGACATTGCTGCCGATGCTGCTGCTACTTTTAAG
| | | || ||| | | | | | | | | || | || || | ||| | | | | | | || || | ||| |||| ||| |||||||| ||||| || ||| ||||||| ||||| || || ||||||||||||||||| ||||| ||| | |||||| ||||||| ||||||
atta-ctaa--gttggacatccataagtgcaaaaatattgtcgaaactagaggctcatgtggacttttggtgctatttt--cttatagaatgtcttcattgacagGTATGTTTTAGAGTCCGAACATATGAAGAAGTTCTTCGACTATATACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCTGCTACCTTTAAG
upper sequence: AT5G47540.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA17G01180.1 (Glycine max), 3'ss of exon 3
gtgagccaatcgtttcattttcttcattttacgacctatggagtaattatggattcagagaataacggaaaatgtgtttactaacttaatttctttggattcagATATGTTTTGGAGTCTGACCATGTGAAGAAATTCTTTGATTACATACAGCTTCCAAATTTCGACATTGCTGCCGATGCTGCTGCTACTTTTAAG
| | | | || || || | | |||| || | || | | || | | | ||| || ||||||||||| |||| || ||| ||||||| || ||||| ||||| |||||||||||||| ||||| ||||| ||||| || || |||||||||
----gttgtagaataaaagacagcctaggtatgatctttctttctagtatgacttttgtgagttgtgacttgtgatgctgtaattattattggctttatatcagATATGTTCTGGACTCACCTCATATGAAGAAGTTTTTTGACTACATTCAGCTTCCAAATTTTGACATAGCTGCAGATGCCGCAGCAACTTTTAAG
upper sequence: AT5G47540.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G01370.2 (Glycine max), 3'ss of exon 4
gtgagccaatcgtttcattttcttcatttt--acgacctatggagtaattatggattcagagaataacggaaaatgtgtttactaacttaatttctttggattcagATATGTTTTGGAGTCTGACCATGTGAAGAAATTCTTTGATTACATACAGCTTCCAAATTTCGACATTGCTGCCGATGCTGCTGCTACTTTTAAG
| | | | | || | | |||||| | || | ||| | ||||| | || | ||| || |||| || ||||||||| || | || | | ||||||| || ||||| || || || ||||||||||| ||||||||||| |||||||| || || ||||||
-----ctgaacactggaattagaaaagggaaaatgacctaggtcttataatttttttcccatcataactaatgtgttgctgtaattcttcatgattttgtat-cagATATGTCCTGAACTCACCTCGTATGAAGAAGTTTTTTGACTATATCCAACTTCCAAATTTTGACATTGCTGCAGATGCTGCAGCAACCTTTAAG
upper sequence: AT5G47540.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA15G12220.2 (Glycine max), 3'ss of exon 2
gtgagccaatcgtttcattttcttcattttacgacctatggagta-attatggattcagagaataacggaaaatgtgtttactaacttaatttctttggattcagATATGTTTTGGAGTCTGACCATGTGAAGAAATTCTTTGATTACATACAGCTTCCAAATTTCGACATTGCTGCCGATGCTGCTGCTACTTTTAAG
||| | | | | | | | | | |||| | || | | | | | | ||||| || | ||| || |||| || ||||||||| || | || | | ||||||| || ||||| || || || ||||||||||| ||||||||||| |||||||| || || ||||||
-tgaac-actagaattagaaaagggaaa--atggcctaggtcttataatttttttccccatcataactattgtgttgctgtaattcttcatggttttgtat-cagATATGTGCTGAACTCACCTCGTATGAAGAAGTTTTTTGACTATATCCAACTTCCAAATTTTGACATTGCTGCGGATGCTGCAGCAACCTTTAAG
upper sequence: AT5G47540.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv10s0405g00020.t01 (Vitis vinifera), 3'ss of exon 4
gtgagccaatcgtttcattttcttcattttacgacctatggagtaattatggattcagagaataacggaaaatgtgtttactaactta--atttctttggattcagATATGTTTTGGAGTCTGACCATGTGAAGAAATTCTTTGATTACATACAGCTTCCAAATTTCGACATTGCTGCCGATGCTGCTGCTACTTTTAAG
|||| | || ||| || | ||| | ||||| | | | | | | || ||| |||| ||| ||| ||| ||| || || |||| || | || ||||||| || |||||||| || || ||||||||||| ||||||||||| ||||||||||| |||||||||
-ctgtccaaagg---cagtttgacaatatcttttattatt--attattattattatatgggtttaactgagttgaattttctaatttatggtttttttcctgacagGTACGTCCTGGAATCAGCGCACATGAAGAAGTTTTTTGATTATATTCAACTTCCAAATTTTGACATTGCTGCAGATGCTGCTGCAACTTTTAAGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|164166206|gb|ES170443.1|ES170443EST: CACTATGGTGCTATGTTTAGGGAGTGTATCCGTCATCAGATTGTGGCTAA ATATGTTTTGGAGTCTGACCATGTGAAGAAATTCTTTGATTACA
genomic: CACTATGGTGCTATGTTTAGGGAGTGTATCCGTCATCAGATTGTGGCTAAgtgagccaat ... ttggattcagATATGTTTTGGAGTCTGACCATGTGAAGAAATTCTTTGATTACA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggattcagagaataacggaaaatgtgtttactaacttaatttctttggattcagATATGTTTTGGAGTCTGACCATGTGAAGAAATTCTTTGATTACATACAGCTTCCAAATTTCGACATTGCTGCCGATGCTGCTGCTACTTTTAAG
tttcttt CT-rich tract
tttactaacttaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagccaatcgtttcattttcttcattttacgacctatggagtaattatggattcagagaataacggaaaatgtgtttactaacttaatttctttggattcagATATGTTTTGGAGTCTGACCATGTGAAGAAATTCTTTGATTACATACAGCTTCCAAATTTCGACATTGCTGCCGATGCTGCTGCTACTTTTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT