Sequence
atgc intronic sequence ATGC exonic sequencegtgagatttaaattatttactacaaaccagggtgcattgattccactaggattctggtaaatgtaactggttttgtcatcagGTTTTCACGAGTCACCATTGGATGGTTCGGCTATACAAGCTGAAACCTCCCAGGAACAGGATTCGTGGTAAAGCAAAGAAACTGAAATCG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G19690.1 |
intron # | 21 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G19690.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GRMZM2G154165_T03 (Zea mays), 3'ss of exon 19
---gtgagatttaaat----tatttactacaaaccagggtgcattgattccactaggattctggtaa-atgtaactggttttgtcat-----------cagGTTTTCACGAGTCACCATTGGATGGTTCGGCTATACAAGCTGAAACCTCCCAGGAACAGGATTCGTGGTAAAGCAAAGAAACTGAAATCG
| | | ||| | | | ||| || | || || || | ||| ||| | ||| | || || || ||| ||||||||||| | |||||||||| |||||||| | ||||| |||||||||| | |||||| | | || ||| |||| | |||||
gtggagtgcttttattctttttttttcttccaatttggatgtgaaaagtcccctattgcttgaataatgcattccttgtgtttccatgctgctggatacagGTTTTCACAACTCACCATTGGCTGGTTCGGATTTACAAACTGAAACCTCAGAAGAACAGAGTCAGAGGGAAACT---GAAATTTAAATCT
upper sequence: AT5G19690.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GLYMA16G08410.1 (Glycine max), 3'ss of exon 21
------------------gtgagatttaaattatttactacaaaccagggtgcattgattccactaggattctggtaaatgtaactggttt-tgtcatcagGTTTTCACGAGTCACCATTGGATGGTTCGGCTATACAAGCTGAAACCTCCCAGGAACAGGATTCGTGGTAAAGCAAAGAAACTGAAATCG
| | || | ||| || | ||| ||| | | | | | | || || | || |||||| ||||| | ||||||||||||||||||| | |||||| ||||||| || | |||||||||||| || || || ||| ||||
caacatctgttaattgttaccatgtgtatgtgttttgata-gtgttattctgcgttgttccttcctaatctactatgtgtttaccttactaatgctttcagGTGTTCACAACTCACCATTGGATGGTTCGGATTTACAAGTTGAAACCACCAAAGAACAGGATTCGAGGAAAGATTAAAAAATCAAAATTT
upper sequence: AT5G19690.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GLYMA01G01270.1 (Glycine max), 3'ss of exon 21
-------------------gtgagatttaaattatttactacaaaccagggtgcattgattccactaggattctggtaaatgtaactggttttgtcatcagGTTTTCACGAGTCACCATTGGATGGTTCGGCTATACAAGCTGAAACCTCCCAGGAACAGGATTCGTGGTAAAGCAAAGAAACTGAAATCG
| | || | ||| || | ||| ||| | | | | | | | | || |||||| ||||| | ||||||||||||||||||| | |||||| ||||||| || | |||| ||||||| || || || ||| |||||
actacatcttttaattgttaccatgtgtatgtgttttgata-gtgttattctgctttgttccttactaatctaccatgtgtttccttactaatgcattcagGTGTTCACAACTCACCATTGGATGGTTCGGATTTACAAGTTGAAACCACCAAAGAACCGGATTCGAGGAAAGATTAAAAAATCAAAATCT
upper sequence: AT5G19690.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: Vv03s0088g00210.t01 (Vitis vinifera), 3'ss of exon 7
gtgagatttaaattatttactacaaaccagggtgcattgattccactaggattctggtaaatgtaactggttttgtcatcagGTTTTCACGAGTCACCATTGGATGGTTCGGCTATACAAGCTGAAACCTCCCAGGAACAGGATTCGTGGTAAAGCAAAGAAACTGAAATCG
| | ||| || ||| ||| || || | | || | | | ||| | |||| ||||| | ||||||||||||||||||| ||||||| | |||||||| | |||||||||||||| ||| ||||||| ||||||
-----gtctttatt-ttccctataaagtcccatgt-ctgttctgattaacttcccatggtttataatcaatga-------agGTGTTCACTACTCACCATTGGATGGTTCGGATATACAAATTAAAACCTCCGAAGAACAGGATTCGTGTAAAAATAAAGAAATCAAAATCG
upper sequence: AT5G19690.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: Vv11s0016g03320.t01 (Vitis vinifera), 3'ss of exon 21
-----------gtgagatttaaattatttact---acaaaccagggtgcattgattccactaggattctggtaaatgtaactggttttgtcatca-----gGTTTTCACGAGTCACCATTGGATGGTTCGGCTATACAAGCTGAAACCTCCCAGGAACAGGATTCGTGGTAAAGCAAAGAAACTGAAATCG
|||||| | | || | | || | | | | ||| ||||| | || | | | ||| | ||| ||| ||||| | ||||||||||||||||||| ||||||| || || ||||| | ||||||||| |||| ||| |||||||| ||||||
caccaacccttccgagattaggaattttcgtttgaataattttccctataacg-tcccatgtctgttctgattaactttccatggtttatactcaatgaagGTGTTCACTACTCACCATTGGATGGTTCGGATATACAAACTAAAGCCTCCGAAGAACAGGATCCGTGTAAAAACAAAGAAATCAAAATCGMapped 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|125267589|gb|EL281674.1|EL281674EST: GGCGGACAGAGATTGGGAAGAAGCATTTTAAGCTTACACATTTCGAAGAG GTTTTCACGAGT
genomic: GGCGGACAGAGATTGGGAAGAAGCATTTTAAGCTTACACATTTCGAAGAGgtgagattta ... ttgtcatcagGTTTTCACGAGT
EST:
gi|164165011|gb|ES025990.1|ES025990EST: GCGGACAGAGATTGGGAAGAAGCATTTTAAGCTTACACATTTCGAAGAG GTTTTCACGAGTCACCATTGGATGGTTCGGCTATACAAGCTGAAACCTCCC
genomic: GCGGACAGAGATTGGGAAGAAGCATTTTAAGCTTACACATTTCGAAGAGgtgagattta ... ttgtcatcagGTTTTCACGAGTCACCATTGGATGGTTCGGCTATACAAGCTGAAACCTCCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagggtgcattgattccactaggattctggtaaatgtaactggttttgtcatcagGTTTTCACGAGTCACCATTGGATGGTTCGGCTATACAAGCTGAAACCTCCCAGGAACAGGATTCGTGGTAAAGCAAAGAAACTGAAATCG
atgtaac putative branch site (score: 3)
ttttgtc putative PPT
taaatgtaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagatttaaattatttactacaaaccagggtgcattgattccactaggattctggtaaatgtaactggttttgtcatcagGTTTTCACGAGTCACCATTGGATGGTTCGGCTATACAAGCTGAAACCTCCCAGGAACAGGATTCGTGGTAAAGCAAAGAAACTGAAATCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA