Sequence
atgc intronic sequence ATGC exonic sequencegtgagatggatgcatagtcttatgatcttataatcgaacatcccaggaaataagcagtgatcatcttatgtttcaatattgattttcagGTGCGAGTTAACATTCCAAATGGAGATATGGTGGGTCATACAGGTGATATTGAAGCCACGGTTGTTGCATGCGAGGCTGCTGATCTTGCTGTGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G09780.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G09780.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os05g40420.1 (Oryza sativa), 3'ss of exon 7
gtgagatggatgcatagtcttatgatcttataatcgaacatcccaggaaataagcagtgatcatcttatgtttcaatattgattttcagGTGCGAGTTAACATTCCAAATGGAGATATGGTGGGTCATACAGGTGATATTGAAGCCACGGTTGTTGCATGCGAGGCTGCTGATCTTGCTGTGAAG
|| | | | | | | || | | || | | | | | | | | ||||| ||| | || || ||||| || |||||| | |||||||| |||||||||||||| || ||||| ||||| ||||| || ||||| ||| | ||||||||| ||||| |||
gtaaaaaaca---gcacttgtgtgcgactttgataggtttgttaaattatttacccctaaaattcttaacattc--tgtt--cttacagGTCCGCGTTAACCTCCCAAATGGTGATATGGTGGGTCACACTGGTGACATTGAGGCCACAGTGGTTGCTTGCAAAGCTGCTGATGAGGCTGTCAAG
upper sequence: AT1G09780.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os01g60190.1 (Oryza sativa), 3'ss of exon 7
gtgagatggatgcatagtcttatgatcttataatcgaacatcccaggaaataagcagtgatcatcttatgtttcaatattgattttcagGTGCGAGTTAACATTCCAAATGGAGATATGGTGGGTCATACAGGTGATATTGAAGCCACGGTTGTTGCATGCGAGGCTGCTGATCTTGCTGTGAAG
| | | || || | | | || | | |||| | || | | | ||| | || | ||| |||| || || ||| | || ||||| || ||||| ||||| || |||||||||||||||||||| ||||| ||| |||| ||||| || || |||
-----gtaggta-attgtttcgtcggtgctcagatgactgtttgcctatataa--aatgttgcttaaaatttttattact--cttttagGTACGTGTCAACCTGCCGAATGGTGACATGGTTGGTCACACTGGTGATATTGAAGCCACGGTAGTTGCTTGCAAGGCAGCTGACGAAGCCGTTAAG
upper sequence: AT1G09780.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM5G833389_T02 (Zea mays), 3'ss of exon 7
gtgagatggatgcatagtcttatgatcttataatcgaacatcccaggaaataagcagtgatcatcttatgtttcaatattgattttcagGTGCGAGTTAACATTCCAAATGGAGATATGGTGGGTCATACAGGTGATATTGAAGCCACGGTTGTTGCATGCGAGGCTGCTGATCTTGCTGTGAAG
| ||| | | | | | ||| | | || || | | || | | | || ||| || ||||| || || ||| | |||||||| || ||||| ||||| || ||||||||||| ||||| || ||||| ||| |||| |||||| ||||| |||
---------gtaaataatttgaagtttctattagagcac-tctttcggtttccctgttgcttagccta-------gcgttg--ttacagGTACGTGTCAACCTGCCAAATGGTGACATGGTTGGTCACACTGGTGATATTGAGGCCACCGTAGTTGCTTGCAAGGCAGCTGATGAAGCTGTTAAG
upper sequence: AT1G09780.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G40690.1 (Glycine max), 3'ss of exon 6
gtgagatggatgcatagtc--ttatgatcttataatcgaacatcccaggaaataagcagtgatcatcttatgtttcaatattgattttcagGTGCGAGTTAACATTCCAAATGGAGATATGGTGGGTCATACAGGTGATATTGAAGCCACGGTTGTTGCATGCGAGGCTGCTGATCTTGCTGTGAAG
| | || || |||| || | ||| | ||| | | | |||||| || || | | |||| || || ||| |||||||||| || |||||||| ||||||||||| |||||||| || ||||| || ||| |||| |||||| ||||||||||
-----gtaactaaatggttcaccgtgattttgggaatcgtgatctaattaaacttttatttactctcttattttgt----ctgttgtatagGTACGCGTCAACCTTCCAAATGGTGACATGGTGGGGCATACAGGTGACATTGAAGCAACAGTTGTGGCTTGCAAGGCAGCTGATGCTGCTGTGAAGMapped 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|86081556|gb|DR377313.1|DR377313EST: GATGCAATCCTTAGTGGCAAGTTTGATCAG GTGCGAGTTAACATTCCAAATGGAGATATGGTGGGTCATACAGGTGATATT
genomic: GATGCAATCCTTAGTGGCAAGTTTGATCAGgtgagatgga ... tgattttcagGTGCGAGTTAACATTCCAAATGGAGATATGGTGGGTCATACAGGTGATATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgaacatcccaggaaataagcagtgatcatcttatgtttcaatattgattttcagGTGCGAGTTAACATTCCAAATGGAGATATGGTGGGTCATACAGGTGATATTGAAGCCACGGTTGTTGCATGCGAGGCTGCTGATCTTGCTGTGAAG
tattgat putative branch site (score: 3)
ttttc CT-rich tract
ttatgtttcaatattg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagatggatgcatagtcttatgatcttataatcgaacatcccaggaaataagcagtgatcatcttatgtttcaatattgattttcagGTGCGAGTTAACATTCCAAATGGAGATATGGTGGGTCATACAGGTGATATTGAAGCCACGGTTGTTGCATGCGAGGCTGCTGATCTTGCTGTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT