Sequence
atgc intronic sequence ATGC exonic sequencegtatttcaacttctgtccttttctcactttgagtaatggttatatgctttgtttagtatagttccagttgcttgctcattataggtctatactatgctttgcatttttgccaatagtgtatcacgcttgaactgatcatatatattaatgtatgtgactgaaacagTGAGACCGTCAAGTTTGGGCATGTCACCTTCTTCTGGAATGGAAATCGATCTGGATATTTCAACGAGAAATTGGAGGAGTATGTTGAAATCCCAAGTGAC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G09780.1 |
intron # | 3 |
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 3
lower sequence: LOC_Os01g60190.1 (Oryza sativa), 3'ss of exon 6
gtatttcaacttctgtccttttctcactttgagtaatggttatatgctttgtttagtatagttccagttgcttgctcattataggtctatactatgctttgcatttttg--ccaatagtgtatcacgcttgaactgatcatatatattaatgtatgtgactgaaacagTGAGACCGTCAAGTTTGGGCATGTCACCTTCTTCTGGAATGGAAATCGATCTGGATATTTCAACGAGAAATTGGAGGAGTATGTTGAAATCCCAAGTGAC
| || |||| | ||| ||| | | |||| || | | | | || ||| | || | | | ||| |||| ||| || | | | | |||||||||| || |||||||| |||||||| || |||||||| ||||| ||||||||||| || | || | ||| ||||| |||||||| || |||||
----------------------------------------------------attgtggagttta---tagttgtctattgtgcttatataaaataatattctgtcttagtccatttgtat-ttatgctgtaact---------cattgatttgttttttt---acagTGAGACAGTGAAGTTTGGCCATGTCACATTTTTCTGGAACGGAAACCGATCTGGATACTTTGATGAAACTAAGGAAGAGTACGTTGAAATTCCTAGTGAT
upper sequence: AT1G09780.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os05g40420.1 (Oryza sativa), 3'ss of exon 6
gtatttcaacttctgtccttttctcactttgagtaatggttatatgctttgtttagtatagttccagttgcttgctcattataggtctatactatgctttgcatttttgccaatagtgtatcacgcttgaactgatcatatatattaatgtatgtgactgaaacagTGAGACCGTCAAGTTTGGGCATGTCACCTTCTTCTGGAATGGAAATCGATCTGGATATTTCAACGAGAAATTGGAGGAGTATGTTGAAATCCCAAGTGAC
|| ||| || | | || || | | || || | | |||| | | | ||||| | || ||| | | | | ||| | || || |||||| || || ||||| || |||||||| || |||||||||||||| || |||||||| ||| | || | | ||| |||||||| |||||||| ||||||
---------------------------------------------------agtaacataattggaa--aataacttatagttgcactgtaattt-ctttctaactctaccaatt---tgtccaactttacttactga-----attgactcatttgttc----cagTGAAACTGTGAAGTTCGGCCATGTCACATTTTTCTGGAATGGAAACCGCTCTGGATACTTCGATGAAACAAAGGAAGAGTATGTGGAAATCCCTAGTGAC
upper sequence: AT1G09780.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G40690.1 (Glycine max), 3'ss of exon 5
gtatttcaacttctgtccttttctcactttgagtaatggttatatgctttgtttagtatagttccagttgcttgctcattataggtctatactatgctttgcatttttgccaatagtgtatcacgcttgaactgatcatatatattaatgtatgtgactgaaacagTGAGACCGTCAAGTTTGGGCATGTCACCTTCTTCTGGAATGGAAATCGATCTGGATATTTCAACGAGAAATTGGAGGAGTATGTTGAAATCCCAAGTGAC
|| | | || || | | | | | ||| | ||| | | | | || || || | | | ||| | ||| ||| | | || | ||||||||||| || || ||||| || ||||| ||||||||||||||||| || ||||| ||||| || |||||||||||||||| ||||| || ||||||
----------------------------------------------------tttgcaacattttgtttacct-----taagaactcttcattatctagtacttatctgttaa------atgatggccatcatagtcacttgtatgaatttctttgtc---aacagTGAGACTGTTAAATTTGGTCACGTCACATTCTTCTGGAATGGAAACCGCTCTGGGTATTTTAATTCAGAATTGGAGGAGTATGTGGAAATTCCCAGTGAC
upper sequence: AT1G09780.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv08s0056g00200.t01 (Vitis vinifera), 3'ss of exon 5
gtatttcaacttctgtccttttctcactttgagtaatggttatatgctttgtttagtatagttccagttgcttgctcattata-ggtctatactatgctttgcatttttg--ccaatagtgtatcacgcttgaactgatcatatatattaatgtatgtgactgaaacagTGAGACCGTCAAGTTTGGGCATGTCACCTTCTTCTGGAATGGAAATCGATCTGGATATTTCAACGAGAAATTGGAGGAGTATGTTGAAATCCCAAGTGAC
| | | ||| | ||| | || | | | | || || ||| | | | | | || | | | | | || ||||||||||| ||||| ||||| ||||| ||||| ||||||||||||||||| || || ||||| | | ||||||| ||||| ||||| || |||||
---------------------------------------------------------------------gagggtttatttcatggttagtgataggttctttttcttcaattcaccagtttttaataccattctctgctgtctaactctctttttctttctttaacagTGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTCAGGGTATTTTGATCCAAGTATGGAGGAATATGTAGAAATTCCCAGTGATMapped 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|163966568|gb|ES085227.1|ES085227EST: AATGGCGTCAGTACTTTTGCTTGCAG TGAGACCGTCAAGTTTGGGCATGTCACCTTCTTCTGGAATGGAAACCGATC
genomic: AATGGCGTCAGTACTTTTGCTTGCAGgtatttcaac ... actgaaacagTGAGACCGTCAAGTTTGGGCATGTCACCTTCTTCTGGAATGGAAATCGATC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatagtgtatcacgcttgaactgatcatatatattaatgtatgtgactgaaacagTGAGACCGTCAAGTTTGGGCATGTCACCTTCTTCTGGAATGGAAATCGATCTGGATATTTCAACGAGAAATTGGAGGAGTATGTTGAAATCCCAAGTGAC
tattaat putative branch site (score: 2)
tgatcatatatattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttcaacttctgtccttttctcactttgagtaatggttatatgctttgtttagtatagttccagttgcttgctcattataggtctatactatgctttgcatttttgccaatagtgtatcacgcttgaactgatcatatatattaatgtatgtgactgaaacagTGAGACCGTCAAGTTTGGGCATGTCACCTTCTTCTGGAATGGAAATCGATCTGGATATTTCAACGAGAAATTGGAGGAGTATGTTGAAATCCCAAGTGAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG