Sequence
atgc intronic sequence ATGC exonic sequencegttgttacccctcatattacccctgcaaatgtctatttatttagtgaaaggcatgaaaaactcataattttacaaacttagGTTATTGCAGCGACAAATCGTGCTGATATACTAGATCCTGCCCTTATGCGTTCTGGTCGTTTGGATCGTAAAATCGAGTTTCCGCACCCCACTGAAGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G09100.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os06g07630.1 (Oryza sativa), 3'ss of exon 7
gttgttacc--cctcatattacccctgcaaatgtctat---ttatttagtga-----------aaggcatgaaaaactcataattttaca----aacttagGTTATTGCAGCGACAAATCGTGCTGATATACTAGATCCTGCCCTTATGCGTTCTGGTCGTTTGGATCGTAAAATCGAGTTTCCGCACCCCACTGAAGAAG
| || | | | |||| | || | ||| ||||| || |||| | || ||| | | || || | | |||| || || || || ||||||||||| || || |||||||| | ||||| |||||||||||||| || || || |||||||| || || |||||||||
-tcaatatcatcttgatatcattgcttcgaatctctatgttttgattagcaatgttttctttttagtcatttcatctgtttgatggtatattattggtcagGTCATAGCGGCAACGAATCGTGCTGACATTCTTGATCCTGCTTTGATGCGATCTGGTCGTTTGGACCGAAAGATTGAGTTTCCTCATCCATCTGAAGAAG
upper sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G027282_T01 (Zea mays), 3'ss of exon 7
-------------------------------------------------------------------------------------------------------------------gttgttacccctcatattacccctgcaaatgtctatttatttagtgaaaggcatgaaaaactcataatt-ttaca-aactt--agGTTATTGCAGCGACAAATCGTGCTGATATACTAGATCCTGCCCTTATGCGTTCTGGTCGTTTGGATCGTAAAATCGAGTTTCCGCACCCCACTGAAGAAG
| | || ||||| | | ||||||| |||||| | || | |||| | ||| || ||| |||| || || || ||||||||||||||||| || |||||||| || ||| | ||||||||| |||| || || || ||||| || || || | || ||||
gtcagcattcaacctcaaacctattagttattacagtcttgatgctttgtctcaggttttgttcagttgcaggttgagaaggtataaagttacctctattgatcatgatatgagagatagatgaactgatattttttc--ccaatgtct---tatttaatatctggtgtactaaacgtttgattgttgtgtggcttacagGTGATAGCTGCAACAAATCGTGCTGATATTCTTGATCCTGCTCTGATGAGATCTGGTCGTCTGGACCGGAAGATTGAGTTCCCTCATCCATCAGAGGAAG
upper sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA03G39500.1 (Glycine max), 3'ss of exon 7
------gttgttacccctcatattacccctgcaa--------atgtctatttatttagtga--aaggcatgaaaaactcataatt--ttacaaact-tagGTTATTGCAGCGACAAATCGTGCTGATATACTAGATCCTGCCCTTATGCGTTCTGGTCGTTTGGATCGTAAAATCGAGTTTCCGCACCCCACTGAAGAAG
| | | || || | | || || | |||| | |||| | | | || ||| ||| | || ||| | |||| |||||||| ||||| |||||||| || || |||||||||||||||||||||||||| |||||||| ||||| ||||| || ||||| ||||||||||
ctcaaaacaaacatacatgatgttgacacaaaaatgtgttagatttttattcagttagaaattaggtgattgaaatgccattttcacttgtaaattacagGTGATTGCAGCAACAAACCGTGCTGACATTCTTGATCCTGCCCTTATGCGTTCTGGTCGATTGGATCGAAAAATTGAGTTCCCACACCCAACTGAAGAAG
upper sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA10G29250.1 (Glycine max), 3'ss of exon 7
-------gttgttacccctcatattacccctgcaaatgtctatttat--------ttagtgaaaggca---tgaaaaactcataattttacaaact-tagGTTATTGCAGCGACAAATCGTGCTGATATACTAGATCCTGCCCTTATGCGTTCTGGTCGTTTGGATCGTAAAATCGAGTTTCCGCACCCCACTGAAGAAG
|| | | || |||| | ||| | ||| ||| |||| || | | | | | || ||| | |||| || ||||| || || ||||| ||||| || ||||||||||| ||||||||||||||||||||||||||||| |||||||| ||||| | ||||||||
tagatttgtaagttggcaccaaattaactggatttttgttcagttaggctataggttattgaagtgccatttttttcattttttttcttgtaaattgcagGTGATAGCAGCAACTAACCGTGCAGATATTCTTGATCCTGCCCTGATGCGTTCTGGTCGTTTGGATCGTAAAATTGAGTTTCCACACCCAAGTGAAGAAG
upper sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 7
-------------gttgttacccctcatattacccctgcaaatgtctatttat----ttagtgaaaggcatgaaaaactcat--aattttacaaact-tagGTTATTGCAGCGACAAATCGTGCTGATATACTAGATCCTGCCCTTATGCGTTCTGGTCGTTTGGATCGTAAAATCGAGTTTCCGCACCCCACTGAAGAAG
| ||| | | || |||| | ||| | ||| | || | || | |||| | | || ||| | |||| || ||||| ||||| ||||| ||||| || || ||||||||||||||||||||||| || ||||||||||| |||||||| ||||| | ||||||||
gtggctagatttagaagttggcac-caaattaactggatttttgttcagttaggctataggttgttgaagtgccattttcatttattcttgtaaattgcagGTGATAGCAGCAACAAACCGTGCAGATATTCTTGACCCTGCCCTTATGCGTTCTGGTCGATTAGATCGTAAAATTGAGTTTCCACACCCAAGTGAAGAAG
upper sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 7
---gttgttacccct-catattacccctgcaaatgtctatttatttagtgaaaggcatgaaaaactcata----------attttac--------aaacttagGTTATTGCAGCGACAAATCGTGCTGATATACTAGATCCTGCCCTTATGCGTTCTGGTCGTTTGGATCGTAAAATCGAGTTTCCGCACCCCACTGAAGAAG
| | | ||| |||| | | ||| | |||| || | | || |||| ||| || ||| || | | ||||| || ||||| ||||| || |||||||| || || ||||| |||||||| |||||||| |||||||||||||| |||||||| || |||||||||||||
gcagctagaatgcctatgtatt-cagttacaatattttattccctt--ttaggatcaagaaattctcctatctaatgtttattctatttatggtaacatgtagGTGATAGCAGCAACAAACCGAGCTGATATTCTGGACCCTGCACTTATGCGATCTGGTCGATTGGATCGTAAAATTGAGTTTCCACATCCCACTGAAGAAGMapped 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|124990657|gb|EL062926.1|EL062926EST: ATTCAGCAGCGATGATCGCATTAAG GTTATTGCAGCGACAAATCGTGCTGATATACTAGAATCCTGCCCTTATGCG
genomic: ATTCAGCAGCGATGATCGCATTAAGgttgttaccc ... acaaacttagGTTATTGCAGCGACAAATCGTGCTGATATACTAGA-TCCTGCCCTTATGCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaatgtctatttatttagtgaaaggcatgaaaaactcataattttacaaacttagGTTATTGCAGCGACAAATCGTGCTGATATACTAGATCCTGCCCTTATGCGTTCTGGTCGTTTGGATCGTAAAATCGAGTTTCCGCACCCCACTGAAGAAG
aaaaactcataatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgttacccctcatattacccctgcaaatgtctatttatttagtgaaaggcatgaaaaactcataattttacaaacttagGTTATTGCAGCGACAAATCGTGCTGATATACTAGATCCTGCCCTTATGCGTTCTGGTCGTTTGGATCGTAAAATCGAGTTTCCGCACCCCACTGAAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG