Sequence
atgc intronic sequence ATGC exonic sequenceGGAGAAGGAATTTGAGATGGCTTTGCAAGACAGAGTTATGGAAGAGACCAAGGACCGGAAGAATGCTGTTGAGTCTTATGTTTATGATATGCGGAACAAAgtgagaatctttatttcgtcttttcattggcagtatgcatatgtaaagttgtgagtattgggtactaacgtgtcttgttttcag
Basic information
species | Arabidopsis thaliana |
transcript | AT1G79930.1 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G79930.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os05g08840.1 (Oryza sativa), 5'ss of exon 5
GGAGAAGGAATTTGAGATGGCTTTGCAAGACAGAGTTATGGAAGAGACCAAGGACCGGAAGAATGCTGTTGAGTCTTATGTTTATGATATGCGGAACAAAgtgagaatctttatttcgtcttttcattggcagtatgcatatgtaaagttgtgagtattgggtactaacgtgtcttgttttcag
||||| || | ||| |||||| | || |||||||| |||||||| |||||||| ||||||||||| ||| ||||||||||||| ||||| ||||| || | | ||| | || | || |||| | || | ||| | | | | | || ||||| |||||
TGAGAATGAGTATGAAATGGCTCTTCAGGACAGAGTAATGGAAGAAACCAAGGAGAAAAAGAATGCTGTCGAGGCTTATGTTTATGACATGCGTAACAAGgtatg---ccgagtttaattttgtgatg----------atatatgaacatttgaacagtacctgatga-gtttcttgcgttcag
upper sequence: AT1G79930.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os01g08560.2 (Oryza sativa), 5'ss of exon 6
GGAGAAGGAATTTGAGATGGCTTTGCAAGACAGAGTTATGGAAGAGACCAAGGACCGGAAGAATGCTGTTGAGTCTTATGTTTATGATATGCGGAACAAAgtgagaatctttatttcgtcttttcattggcagtatgcatatgtaaagttgtgagtattgggtactaacgtgtcttgttttcag
||| || || | ||| |||||| | || ||||| || ||||||||||| || || ||||||||| || ||||||||||||||||| ||||| ||||| || || | ||| | |||| || | || || || || | | || ||| ||| | |||||||
GGAAAAAGAGTATGAAATGGCTCTTCAGGACAGGGTGATGGAAGAGACAAAAGATAAGAAGAATGCCGTGGAGTCTTATGTTTATGACATGCGAAACAAGgtttga---tcgattccactctttc-ctgacttcatctttagttagag--gcagaaactga----taatatgttat-ttttcag
upper sequence: AT1G79930.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G023232_T01 (Zea mays), 5'ss of exon 6
GGAGAAGGAATTTGAGATGGCTTTGCAAGACAGAGTTATGGAAGAGACCAAGGACCGGAAGAATGCTGTTGAGTCTTATGTTTATGATATGCGGAACAAAgtgagaatctttatttcgtcttttcattggcagtatgcatatgtaaagttgtgagtattgggtactaacgtgtcttgttttcag
||||| || | |||||||||| | ||||||||||| |||||||| || ||||| ||||||||||||||| ||||||| ||||| ||||| ||||| || |||| ||| | | | | | | |||||||||| | | | | | |||| | || ||
AGAGAAAGAGTATGAGATGGCTCTTCAAGACAGAGTAATGGAAGAAACAAAGGAGAAGAAGAATGCTGTTGAAGCTTATGTGTATGACATGCGTAACAAGgta--------tattgagtcacgca--tactaatgttgtcttatgaagttgtgagcct--gattttgt--tctcttctatttag
upper sequence: AT1G79930.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G361605_T02 (Zea mays), 5'ss of exon 8
GGAGAAGGAATTTGAGATGGCTTTGCAAGACAGAGTTATGGAAGAGACCAAGGACCGGAAGAATGCTGTTGAGTCTTATGTTTATGATATGCGGAACAAAgtgagaatctttatttcgtcttttcattggcagtatgcatatgtaaagttgtgagtattgggtactaacgtgtcttgttttcag
||||| || | |||||||||| |||| |||||||| |||||||||||||| || ||| |||||||| || ||||||| ||||| ||||| ||||| || | | | || | || | || | || ||| || || ||| | | | ||||| || ||
AGAGAAAGAGTATGAGATGGCTCTGCAGGACAGAGTAATGGAAGAGACCAAAGAAAAGAAAAATGCTGTGGAAGCTTATGTCTATGACATGCGTAACAAGgtatgtggagatgcatgccctgatggtttttcttgtgaacat---aagcagtatctaatggtttttc---ttccttgtatttag
upper sequence: AT1G79930.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA13G43630.2 (Glycine max), 5'ss of exon 6
GGAGAAGGAATTTGAGATGGCTTTGCAAGACAGAGTTATGGAAGAGACCAAGGACCGGAAGAATGCTGTTGAGTCTTATGTTTATGATATGCGGAACAAAgtgagaatctttatt-tcgtcttttcattgg----cagtatgcatatgtaaagttgtgagtattgggtactaacgtgtcttgttttcag
|||||||| ||||| |||||||||||||| ||||| ||||| || || || || ||| ||||| |||||| ||||||||||||| ||| | ||||| ||||| || || | |||| | ||| | || | | ||| | | || | | || || | | || | ||| ||
AGAGAAGGAGTTTGAAATGGCTTTGCAAGATAGAGTCATGGAGGAAACGAAAGATAAGAAAAATGCAGTTGAGGCTTATGTTTATGACATGAGAAACAAGgtgaggattgccatggttttcttgttatttgaggtcaatttttttatttttaattattactaa-aactaatttcttgatatcattttag
upper sequence: AT1G79930.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA15G01750.1 (Glycine max), 5'ss of exon 6
GGAGAAGGAATTTGAGATGGCTTTGCAAGACAGAGTTATGGAAGAGACCAAGGACCGGAAGAATGCTGTTGAGTCTTATGTTTATGATATGCGGAACAAAgtgagaatctttatt-tcgtcttttcattggcagtatgcatat-gtaaagttgtgagtattgggtactaacgtgtcttgttttcag
|||||||| ||||| |||||||||||||| ||||| ||||| || || ||||| ||| ||||| || ||| ||||||||||||| | | | ||||| ||||| || || | |||| | ||| || ||| || | ||| || | | | | || | | | ||||||
AGAGAAGGAGTTTGAAATGGCTTTGCAAGATAGAGTGATGGAGGAAACAAAGGATAAGAAAAATGCAGTAGAGGCTTATGTTTATGACACGAGAAACAAGgtgaggattgccatggttttcttgttattta-aggatgaattttgtattattactaaaactaatttctca----ttatcatttcag
upper sequence: AT1G79930.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA08G22100.1 (Glycine max), 5'ss of exon 5
GGAGAAGGAATTTGAGATGGCTTTGCAAGACAGAGTTATGGAAGAGACCAAGGACCGGAAGAATGCTGTTGAGTCTTATGTTTATGATATGCGGAACAAAgtgagaatc-tttatttcgtcttttcattggcagtatgcatatgtaaagtt---gtgagtattgggtactaac--gtgtcttgttttcag------------
|| ||||| ||||| |||||||||||||| | || |||||||| || || ||| ||| ||||| |||||| ||||||||||||| ||| | ||||| ||| | | | | |||| |||| || | ||| | | | | || | || | | || | | | || ||||| |
AGAAAAGGAGTTTGAAATGGCTTTGCAAGATCGTGTGATGGAAGAAACAAAAGACAAGAAAAATGCAGTTGAGGCTTATGTTTATGACATGAGAAACAAGgtgggtgttatctttttcttcttctcttactcagggtcta-acatcaactacaaatgcctgtcatataattgttgatttttttttttccgttatcatttcag
upper sequence: AT1G79930.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA07G00820.1 (Glycine max), 5'ss of exon 5
GGAGAAGGAATTTGAGATGGCTTTGCAAGACAGAGTTATGGAAGAGACCAAGGACCGGAAGAATGCTGTTGAGTCTTATGTTTATGATATGCGGAACAAAgtgag-aatctttatttcgtcttttcattggcagtatg----catatgtaaag--ttgtga-gtattgggtactaacgtgtcttgttttcag--------
|||||||| ||||| |||||||||||||| | || |||||||| || || ||| ||| || || |||||| ||||||||||||| ||| | ||||| ||| | | | | | | || | | | || | || || ||| ||| | || | | | | | | || | | |
AGAGAAGGAGTTTGAAATGGCTTTGCAAGATCGTGTGATGGAAGAAACAAAAGACAAGAAAAACGCAGTTGAGGCTTATGTTTATGACATGAGAAACAAGgtgggcgctatctttcttgttctcttacccagggtctaacatcacatacaaatgcctgtcatataataattgttgattttttttcctgttatcatttcag
upper sequence: AT1G79930.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv09s0002g04680.t01 (Vitis vinifera), 5'ss of exon 5
GGAGAAGGAATTTGAGATGGCTTTGCAAGACAGAGTTATGGAAGAGACCAAGGACCGGAAGAATGCTGTTGAGTCTTATGTTTATGATATGCGGAACAAAgtgagaatctttatttcgtcttttcat-tggcagtat-gcatatgtaaagttgtgagtattgggtacta-acgtgtcttgttttcag------
|| ||||| ||||| |||||||||||||| |||| |||||||| || || ||| ||||||||| || ||| | ||||||||||| ||| | ||||| || || | | ||| | | | | | || |||| ||||| || || || ||| || || || | ||| |
AGAAAAGGAGTTTGAAATGGCTTTGCAAGATCGAGTCATGGAAGAAACAAAAGACAAGAAGAATGCCGTGGAGGCATATGTTTATGACATGAGAAACAAGgtaagtgtttctatcctattggctaagacagaattacagcatttgtaacctt-cacctactgatatctacacatga-ttatcttctgccccagMapped 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|47829967|gb|CK119651.1|CK119651EST: AGGACCGGAAGAATGCTGTTGAGTCTTATGTTTATGATATGCGGAACAAA CTGAGTGACAAATACCAGGAATATATCACTGACTCGGAGAGGGAAGCATTC
genomic: AGGACCGGAAGAATGCTGTTGAGTCTTATGTTTATGATATGCGGAACAAAgtgagaatct ... ttgttttcagCTGAGTGACAAATACCAGGAATATATCACTGACTCGGAGAGGGAAGCATTC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GGAGAAGGAATTTGAGATGGCTTTGCAAGACAGAGTTATGGAAGAGACCAAGGACCGGAAGAATGCTGTTGAGTCTTATGTTTATGATATGCGGAACAAAgtgagaatctttatttcgtcttttcattggcagtatgcatatgtaaagttgtgagtattgggtactaacgtgtcttgttttcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT