Sequence
atgc intronic sequence ATGC exonic sequenceGAAGATGATGCAGAAATATATAGGTTCGGATATTACGTCAATGGTGACTCTTCCTGTTGTTATATTTGAGCCTATGACTATGCTCCAGAAGATGGCTGAGgttagtgttatacatctaattctcctgtgtttgtaagtatttgttgttttttgtgtgtactgtattataacatttgcaaatttctcacag
Basic information
species | Arabidopsis thaliana |
transcript | AT5G59420.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G59420.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G114126_T01 (Zea mays), 5'ss of exon 3
GAAGATGATGCAGAAATATATAGGTTCGGATATTACGTCAATGGTGACTCTTCCTGTTGTTATATTTGAGCCTATGACTATGCTCCAGAAGATGGCTGAGgttagtgttatacatctaatt----ctcctgtgtttg----taagtatttgttgttttt---tgtgtgtactgtattataacatttgcaaatttctcacag
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GAAGATGATGCACAAGTACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAGgtttgtactatgttccgaattagacttcttgagatttacactggccatctacaactgaaggatgtgtctgcaattgtttgatccttgtcgtctttaaaaa-
upper sequence: AT5G59420.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G174644_T01 (Zea mays), 5'ss of exon 3
GAAGATGATGCAGAAATATATAGGTTCGGATATTACGTCAATGGTGACTCTTCCTGTTGTTATATTTGAGCCTATGACTATGCTCCAGAAGATGGCTGAGgttagtgttatacatctaattct--cctgtgtttgtaagtatttgttgttttttgtgtgta-ctgtattataacatttgcaaatttctcacag---------
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GAAGATGATGCACAAATACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCCGAGgtttgtactttgtattatgttctgaattagacttcttgagatttac-actgcccatctacaactgaaggatg-tgtctgcaattgtttgattctcgacggct
upper sequence: AT5G59420.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA12G06690.1 (Glycine max), 5'ss of exon 3
GAAGATGATGCAGAAATATATAGGTTCGGATATTACGTCAATGGTGACTCTTCCTGTTGTTATATTTGAGCCTATGACTATGCTCCAGAAGATGGCTGAGgttagtgttatacatctaattctcctgtgtttgtaagtatttgttgttttttgtgtgtactgtat---tataacatttgcaaatttctcacag---
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GAAGATGATGCAGAAGTATATTGGCTCGGATGTAACATCAATGGTGACATTACCTGTTATTATATTTGAACCAATGACTATGATTCAGAAAATTGCTGAGgtcggctt---actcttagttttgccattgttgatgatacct-taatctgtagtgtcaattgattgaatttgaaaattg-aaattgcttgaaatag
upper sequence: AT5G59420.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA11G14770.1 (Glycine max), 5'ss of exon 3
GAAGATGATGCAGAAATATATAGGTTCGGATATTACGTCAATGGTGACTCTTCCTGTTGTTATATTTGAGCCTATGACTATGCTCCAGAAGATGGCTGAGgttagtgttatacatctaattctcctgtgtttgtaagtatttgttgttttttgtgtgtactgtattataacatttgcaaatttctcacag---
||||||||||||||| ||||| || |||||| | || ||||||||||| || || ||| |||||||||| || ||||||||| | ||||| || |||||||| || || || | || || | | | ||| || || ||| | |||| | || || ||||| ||||| || |
GAAGATGATGCAGAAGTATATTGGCTCGGATGTAACATCAATGGTGACACTACCAGTTATTATATTTGAACCAATGACTATGATTCAGAAAATTGCTGAGgt--atgcta-acttttagttttgccattgttgatgatacctga-atttgtagtgtcaattg----attgaatttg-aaattgcttgaaatag
upper sequence: AT5G59420.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA15G04210.1 (Glycine max), 5'ss of exon 3
GAAGATGATGCAGAAATATATAGGTTCGGATATTACGTCAATGGTGACTCTTCCTGTTGTTATATTTGAGCCTATGACTATGCTCCAGAAGATGGCTGAGgttagtgttatacatctaattctcctgtgtttgtaagtattt---gttgtttt--ttgtgtgtactgtattataac--atttgcaaatttctcacag---
|||||||||||| |||||||| || || ||| | || |||||||| || || || ||| |||| ||||| || ||||||||||| ||||| ||||| |||||| | | | | | ||||||| | | | ||| ||| |||| |||| || | | | | |||| || |
GAAGATGATGCACAAATATATTGGCTCAGATGTAACATCAATGGTAACACTACCAGTTATTATTTTTGAACCAATGACTATGCTTCAGAAAATGGCAGAGgtttgcacagctctattttattttttgtgttttctgctttgttaaattgctttatttgtttgtattggcacttgattgagctttgaattgttcgaactag
upper sequence: AT5G59420.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv06s0004g04930.t01 (Vitis vinifera), 5'ss of exon 3
GAAGATGATGCAGAAATATATAGGTTCGGATATTACGTCAATGGTGACTCTTCCTGTTGTTATATTTGAGCCTATGACTATGCTCCAGAAGATGGCTGAGgttagtgttatacatctaattc---tcctgtgtttgtaagtatttgttgttttttgtgtgtactgtattataacatttgcaaat--ttctcacag
|||||||||||| || ||||||||||| ||| | || ||||||||||| ||||| ||| | || |||||||| ||||| ||||| ||||| ||||| || || ||| || | | | | ||||| | | |||| | | | ||| || | | ||| ||| || | ||||
GAAGATGATGCAAAAGTATATAGGTTCAGATGTCACCTCAATGGTGACACTTCCAGTTCTGATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCAGAAgtatgtgccatctagtttgtataagtttgatgtttatcttggtagattgtctctagcctgtttcaaatgttgcaaattgtgaatgcttgtgacag
upper sequence: AT5G59420.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: PP1S148_87V6.1 (Physcomitrella patens), 5'ss of exon 3
GAAGATGATGCAGAAATATATAGGTTCGGATATTACGTCAATGGTGACTCTTCCTGTTGTTATATTTGAGCCTATGACTATGCTCCAGAAGATGGCTGAGgttagtgttatacatctaattctcctgtgtttgtaag-tatttg---ttgttttttgtgtgtactgt-attataacat--------ttgcaaatttctcacag
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GAAAATGATGCACAAGTACATAGGTTCTGACATTACTTCAATGGTGACACTTCCAGTCATCATATTTGAGCCCATGACTACGCTTCAGAAGATGGCTGAGgt-atttttttactttt--tttgtgcgtggccgcaaaatatttggctttaatctttgagtacaaaatgattctgctatccgtgatgttgcaaattctgtatac
upper sequence: AT5G59420.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: PP1S20_97V6.1 (Physcomitrella patens), 5'ss of exon 3
GAAGATGATGCAGAAATATATAGGTTCGGATATTACGTCAATGGTGACTCTTCCTGTTGTTATATTTGAGCCTATGACTATGCTCCAGAAGATGGCTGAGgttagtg--ttatacatctaattctcctgtgtttgtaagtatttgttgttttttgtgtgtactgtattataacatttgcaaatttctcacag--------
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GACACAGGTTCACAATTATATTGGATCTGATGTATCGTCTTTGATTACCCTGCCAGTTACAATATTTGAGCCTATGTCCATGCTACAGAAGATGGCTGAGgttagttacttacaaatcaacttctctgacacatcacaatatcgaagctttagagtctctaaagctgcctgatgcttagtaattctaaacttaaaccacaMapped 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|47827935|gb|CK117619.1|CK117619EST: TTCCTGTTGTTATATTTGAGCCTATGACTATGCTCCAGAAGATGGCTGAG ATAATGGAGTATTCTCATTTGTTGGATCAAGCAGATGAATGCGAAGATCCA
genomic: TTCCTGTTGTTATATTTGAGCCTATGACTATGCTCCAGAAGATGGCTGAGgttagtgtta ... tttctcacagATAATGGAGTATTCTCATTTGTTGGATCAAGCAGATGAATGCGAAGATCCA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GAAGATGATGCAGAAATATATAGGTTCGGATATTACGTCAATGGTGACTCTTCCTGTTGTTATATTTGAGCCTATGACTATGCTCCAGAAGATGGCTGAGgttagtgttatacatctaattctcctgtgtttgtaagtatttgttgttttttgtgtgtactgtattataacatttgcaaatttctcacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG