Sequence
atgc intronic sequence ATGC exonic sequence...catggtggatatctgtgtttttccttgtttagtttacacccagattctctaccttatcccttgatcttatctttaatgtgcactgctccttttattccagGTGTGATTGAAGTTCTCGTGAACAGTGGAAAACAGATTGATGCGGTTAACTTGGCATTTGCGTTTGAACTCACAGAACAGTTCTCACCTGTCTCATTACT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G48385.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G48385.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA03G23760.1 (Glycine max), 3'ss of exon 3
-catggtggatatctgtgtttttccttgtttagtttacacccagattctctaccttatcccttgatcttatctttaatgtgcactgctccttttat---tccagGTGTGATTGAAGTTCTCGTGAACAGTGGAAAACAGATTGATGCGGTTAACTTGGCATTTGCGTTTGAACTCACAGAACAGTTCTCACCTGTCTCATTACT
||| || |||| || | ||| | | | | | || | | | | || | || | | || | || |||| | ||||||| ||||| ||| | ||||||||||| ||| |||||||| ||||||||||| ||||| ||||| || || |||||||| | ||||| || |||||
tcatacatgaaatctagcagttgtatcaatta---cagagtgaagcaataaaactattgcatctgt-ttgttttaatgcttcatttttctttttggatatgcagGTGTAATTGAGGTTTTGGTGAACAGTGGGCGACAAATTGATGCTGTTAACTTGGCTTTTGCATTTGATCTTACTGAACAGTTTTGTCCTGTTTCTTTACT
upper sequence: AT5G48385.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA03G23740.1 (Glycine max), 3'ss of exon 2
catgg--tggatatctgtgtttttccttgtttagtttacacccagattctctaccttatcccttgatcttatctttaatgtgcactgctccttttattccagGTGTGATTGAAGTTCTCGTGAACAGTGGAAAACAGATTGATGCGGTTAACTTGGCATTTGCGTTTGAACTCACAGAACAGTTCTCACCTGTCTCATTACT
||| | |||||| || ||| | | || || | | | || || | || | || | | || | || || | | ||||||| ||||||||| | ||||| ||||| || |||||||| ||||||||||| ||||| ||||| || |||||||| || ||||| | | |||||
aatgactttagcatctgtattattcaaagagtgaggta-actaaagtattttatctgtttattttaattt-ttaatgattcattttactttttcttgtgcagGTGTCATTGAAGTTTTGGTGAATAGTGGGCGGCAAATTGATGCTGTTAACTTGGCTTTTGCATTTGATCTTACAGAACAATTTTCACCCATTCCTTTACT
upper sequence: AT5G48385.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv07s0151g00650.t01 (Vitis vinifera), 3'ss of exon 2
catggtggatatctgtgtttttccttgtttagtttacacccagattctctaccttatcccttgatcttatc---tttaatgtgcactgctccttttattccagGTGTGATTGAAGTTCTCGTGAACAGTGGAAAACAGATTGATGCGGTTAACTTGGCATTTGCGTTTGAACTCACAGAACAGTTCTCACCTGTCTCATTACT
| | | | | ||| || | | | |||| | || | || || | |||| ||||| || | | || |||||| || || | || | |||||||||| || |||||||| |||||| |||| ||||| ||||| |||||||| |||||||||||||| | || ||
-acttttcacgtg-gaatttggaagtgatagaaatggatattccttctgtgttagatttggtcattttttactgtttattgtgctttgttttgactcttt-agGTGTAATCGAGATACTGATAAACAGTGGAAGGCAAATTGATGCTGTTAACCTGGCTTTTGCATTTGAGCTCACAGAGCAGTTCTCACCTGTGCCTTTGCTMapped 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|116437794|gb|EG480386.1|EG480386EST: TCAGGCAGCTGAGCTCTGCCGTTCACTTGGATTAGCTGAAAAAATGCCTG GTGTGATTGAAGTTCTCGTGAACAGTGGAAAACAGATTGATGCGGTTAACT
genomic: TCAGGCAGCTGAGCTCTGCCGTTCACTTGGATTAGCTGAAAAAATGCCTGgtttgttctc ... tttattccagGTGTGATTGAAGTTCTCGTGAACAGTGGAAAACAGATTGATGCGGTTAACT
EST:
gi|47830768|gb|CK120452.1|CK120452EST: TCAGGCAGCTGAGCTCTGCCGTTCACTTGGATTAGCTGAAAAAATGCCTG GTGTGATTGAAGTTCTCGTGAACAGTNGGAAA-CAGATTGATGCGGTTAAC
genomic: TCAGGCAGCTGAGCTCTGCCGTTCACTTGGATTAGCTGAAAAAATGCCTGgtttgttctc ... tttattccagGTGTGATTGAAGTTCTCGTGAACAGT-GGAAAACAGATTGATGCGGTTAAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctctaccttatcccttgatcttatctttaatgtgcactgctccttttattccagGTGTGATTGAAGTTCTCGTGAACAGTGGAAAACAGATTGATGCGGTTAACTTGGCATTTGCGTTTGAACTCACAGAACAGTTCTCACCTGTCTCATTACT
ctttaat putative branch site (score: 4)
ctgctccttttattcc putative PPT
atcttatctttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catggtggatatctgtgtttttccttgtttagtttacacccagattctctaccttatcccttgatcttatctttaatgtgcactgctccttttattccagGTGTGATTGAAGTTCTCGTGAACAGTGGAAAACAGATTGATGCGGTTAACTTGGCATTTGCGTTTGAACTCACAGAACAGTTCTCACCTGTCTCATTACT
- - - - - - - - - - - - -tgtttag
- - - - - - - - - - - - - - - - - - -acccaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgctcc