Sequence
atgc intronic sequence ATGC exonic sequencegtgaggagattataacaactttctctcttttaaaagctttcactgtgattcttgtcccttaatgaaatctttgttccttaaagATGCTTGATCCTGGAGGAATCTCGAACTGGTCAGTCACATATGTTGATTGGTCTGAGCGTAGATGGCATCCAAAGACATATAGAGCACGCGATGTCTCAC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G57270.2 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G57270.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os02g07880.1 (Oryza sativa), 3'ss of exon 8
gtgaggagattataacaactttctctcttttaaaagctttcactgtgattc-ttgtcccttaatgaaatctttgttccttaa-----agATGCTTGATCCTGGAGGAATCTCGAACTGGTCAGTCACATATGTTGATTGGTCTGAGCGTAGATGGCATCCAAAGACATATAGAGCACGCGATGTCTCAC
|| || | || ||| | | ||| ||||||| || | | ||| | | | || || | || | ||||| | |||||||| |||||||| || |||||||| ||| |||||||||||||||| | | ||||||||||| | | |||||||| ||||| |
gtcagtaaataatattttgaattgatattt----agctttcttcttggtcccttgcttttctttcatatgctttcactttcatcttcagATGGTAGATCCTGGTGGAATCTCTAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCAAGGTCGTATAGAGCTATTGATGTTACCT
upper sequence: AT5G57270.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os06g45110.1 (Oryza sativa), 3'ss of exon 8
gtgaggagattataacaactttctctctt----ttaaaagctttcactgtgattcttgtccctta-atgaaatctttgttccttaaagATGCTTGATCCTGGAGGAATCTCGAACTGGTCAGTCACATATGTTGATTGGTCTGAGCGTAGATGGCATCCAAAGACATATAGAGCACGCGATGTCTCAC
|| || | | | |||| | | | || | |||| | | |||| || || || || | | ||||| | |||||||| ||||| | || |||||||| ||| ||||||||||||||||| | | ||||||||| | | |||||||||| |||||| |
gtcagtatttatttacaatatattgaagtgacatttgattcttttgggggcttacttgctaaatacatatcattttgcatatcttcagATGGTAGATCCTGGTGGAATTGCTAATTGGTCAGTTACACATGTTGATTGGTCTGAGGGAAAATGGCATCCGAGGTCATATAGAGCTGCAGATGTCACCT
upper sequence: AT5G57270.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G138505_T01 (Zea mays), 3'ss of exon 8
gtgaggagattataacaactttctc-----tcttttaaaagctttcactgtgattcttgtcccttaatgaaatc---tttgttccttaaagATGCTTGATCCTGGAGGAATCTCGAACTGGTCAGTCACATATGTTGATTGGTCTGAGCGTAGATGGCATCCAAAGACATATAGAGCACGCGATGTCTCAC
|| || | | | |||| | | ||||| | | || ||| | ||| | | | ||| ||| ||| |||| |||| ||||| ||||| | ||||||||||| || ||||||||||||| ||| | | ||||||||||| | |||||||||| ||||| ||
gttagtaattatttttaactctgttatttaccttttttccctcgaccccttgcttccctttttttagtacagttgtgtttattcttta--gATGGTTGACCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGGTCCGAGGGAAAATGGCATCCAAGGTCATATAGAGCTGCAGATGTTACAT
upper sequence: AT5G57270.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G124151_T01 (Zea mays), 3'ss of exon 8
gtgaggagattataacaactttctct--cttttaaaagctttcactgtgattcttgtcccttaatgaaatctttgttcc---ttaaagATGCTTGATCCTGGAGGAATCTCGAACTGGTCAGTCACATATGTTGATTGGTCTGAGCGTAGATGGCATCCAAAGACATATAGAGCACGCGATGTCTCAC
|| || | | ||||| | | | ||||| | | | || | |||| | | | |||| | ||||| | |||||||| ||||| | ||||||||||| || ||||||||||||| ||| | | ||||||||||| | |||||||||| ||||| |
gttagtaatccttttcaactgttatttgcctttaatttcctcgatcccttgctttcttttttaagtatagttatgttttgatcttcagATGGTCGATCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGGTCCGAGGGAAAATGGCATCCAAGGTCATATAGAGCTGCAGATGTTACCT
upper sequence: AT5G57270.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G103805_T02 (Zea mays), 3'ss of exon 8
gtgaggagattataacaactttctctcttttaaaagctttcactgtgatt--cttgtcccttaatgaaatct--ttgttccttaaagATGCTTGATCCTGGAGGAATCTCGAACTGGTCAGTCACATATGTTGATTGGTCTGAGCGTAGATGGCATCCAAAGACATATAGAGCACGCGATGTCTCAC
| || ||| ||| | | || || | || || | ||| | || || | || | ||||| | |||||||| || ||||| || ||||| || ||| |||| |||||||||||| | | ||||||||||| | ||||||| || |||||| |
-------gtcggtattcactatctattgaagtgacatttagcctttatttagctgggtgcttgcttaattcatgtccttggcttcagATGGTAGATCCTGGTGGGATCTCTAATTGGTCTGTTACACATGTGGATTGGTCTGAGGGAAAATGGCATCCAAGGTCATATAGCGCTGATGATGTCACCTMapped 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|116472907|gb|EG515499.1|EG515499EST: AACTGGATCGCGGATGAACATTACCTGCCAACATTCTTTCAT ATGCTTGATCCTGGAGGAATCTCGAACTGGTCAGTCACATATGTTGATTGG
genomic: AACTGCATCGCGGATGAACATTACCTGCCAACATTCTTTCATgtgaggagat ... ttccttaaagATGCTTGATCCTGGAGGAATCTCGAACTGGTCAGTCACATATGTTGATTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttaaaagctttcactgtgattcttgtcccttaatgaaatctttgttccttaaagATGCTTGATCCTGGAGGAATCTCGAACTGGTCAGTCACATATGTTGATTGGTCTGAGCGTAGATGGCATCCAAAGACATATAGAGCACGCGATGTCTCAC
ccttaat putative branch site (score: 4)
tctttgttcctt putative PPT
ttaatgaaatcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaggagattataacaactttctctcttttaaaagctttcactgtgattcttgtcccttaatgaaatctttgttccttaaagATGCTTGATCCTGGAGGAATCTCGAACTGGTCAGTCACATATGTTGATTGGTCTGAGCGTAGATGGCATCCAAAGACATATAGAGCACGCGATGTCTCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA