Sequence
atgc intronic sequence ATGC exonic sequencegtgcaatatctggcactatatttttaatgttcaccagtttccttttagtgctgcttgtgacatgaactgctgtggtatttcagGGCACTTAAAACACGTGGAAACACTCCCAAGTATGGATTGATTTTCCATTCTTCCTTCATTGGCCGAGCATCTGCTAAGAACAAGGGCCGTATCGCTCGT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G56110.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G56110.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G13770.1 (Glycine max), 3'ss of exon 5
-----------------gtgcaatatctggcactatatttttaatgttcaccagtttccttttagtg-ctgcttgtgacatgaactgctgtggtatttcagGGCACTTAAAACACGTGGAAACACTCCCAAGTATGGATTGATTTTCCATTCTTCCTTCATTGGCCGAGCATCTGCTAAGAACAAGGGCCGTATCGCTCGT
| || | | ||| | | | | | | | || | || | || | | | ||| |||| ||||||| | |||||| | |||||||||||||| ||||| ||||| ||||| ||||| || ||||| || |||||||| || || ||||| | || ||||||
ttgtttaggttgttttgtcaggacctcagctaaaatacagacattactactccttgtgcattcactgacattttataatgtctttgcctgctttatt-cagGGCATTAAAAACAAGAGGAAACACTCCCAAATATGGTTTGATATTCCACTCTTCTTTTATTGGTCGGGCATCTGCCAAAAATAAGGGTAGAATGGCTCGT
upper sequence: AT1G56110.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA05G03150.1 (Glycine max), 3'ss of exon 5
----------------gtgca-atatctggcactatatttttaatgttcaccagtttccttttagtgctgctt-gtgacatgaactgctgtggtatttcagGGCACTTAAAACACGTGGAAACACTCCCAAGTATGGATTGATTTTCCATTCTTCCTTCATTGGCCGAGCATCTGCTAAGAACAAGGGCCGTATCGCTCGT
|| | || | | ||| | | | | | | | | | |||| || | | | ||| ||||| |||||| | |||||| | |||||||||||||| ||||| ||||| ||||| ||||| || ||||| || |||||||| || || |||||| | || |||||
ttgtttaggttgttttgtctggacctcagctaaaatacagacattactattccttgtgcactcactgctattttataatgtctttgcctgctttattt-agGGCATTAAAAACAAGAGGAAACACTCCCAAATATGGTTTGATATTCCACTCTTCTTTTATTGGTCGGGCATCTGCCAAAAATAAGGGCAGAATGGCTCGA
upper sequence: AT1G56110.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA07G11560.1 (Glycine max), 3'ss of exon 5
----------------------gtgcaatatctggcactata-tttttaatgt-tcaccagtttccttttagtgctgcttgtgacatgaactgctgtggtatttcagGGCACTTAAAACACGTGGAAACACTCCCAAGTATGGATTGATTTTCCATTCTTCCTTCATTGGCCGAGCATCTGCTAAGAACAAGGGCCGTATCGCTCGT
|||||| | || | | | | || || ||| | || ||| || | || | | | |||| |||| ||||||| | |||||| | ||||||||||| || ||||| |||| ||||| ||||| || || || ||||||||||| || || |||||||| || |||||
caagaaagcagataattttggtatgcaatgt-tgacgccacaattctttgtgtgctgttacttgacttctaat-----ttataatgtttttgactgttctatt-cagGGCATTAAAAACAAGAGGAAACACTCCTAAATATGGTCTGATATTCCACTCTTCTTTTATCGGTCGAGCATCTGCCAAAAATAAGGGCCGAATAGCTCGCMapped 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|164038361|gb|EL993537.1|EL993537EST: AGAAGGCTCTTTTCAG GGCACTTAAAACACGTGGAAACACTCCCAAGTATGGATTGATTTTCCATTC
genomic: AGAAGGCTCTTTTCAGgtgcaatatc ... ggtatttcagGGCACTTAAAACACGTGGAAACACTCCCAAGTATGGATTGATTTTCCATTC
EST:
gi|125081726|gb|EL142839.1|EL142839EST: TGCCCATCTTCCACCCTCCAGATTCTTGGAGCCGAGAAGGCTC-TTTCAG GGCACTTAAAACACGTGGAAACACTCCCAAGTATGGATTGATTTTCCATTC
genomic: TGCCCATCTTCCACCCTCCAGATTCTTGGAGCCGAGAAGGCTCTTTTCAGgtgcaatatc ... ggtatttcagGGCACTTAAAACACGTGGAAACACTCCCAAGTATGGATTGATTTTCCATTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttcaccagtttccttttagtgctgcttgtgacatgaactgctgtggtatttcagGGCACTTAAAACACGTGGAAACACTCCCAAGTATGGATTGATTTTCCATTCTTCCTTCATTGGCCGAGCATCTGCTAAGAACAAGGGCCGTATCGCTCGT
ttttagt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcaatatctggcactatatttttaatgttcaccagtttccttttagtgctgcttgtgacatgaactgctgtggtatttcagGGCACTTAAAACACGTGGAAACACTCCCAAGTATGGATTGATTTTCCATTCTTCCTTCATTGGCCGAGCATCTGCTAAGAACAAGGGCCGTATCGCTCGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC