Sequence
atgc intronic sequence ATGC exonic sequencegcaagtctgaagagtctcttaacatcttcatctttcacattccattaatctttgactgtctaactgacaaattttacttgttcaactttagGTGGTACGAAGGAGTACAAGATTCTAATGGACCAATTTCACCATGTTTCTGCAGCTTTTTTGGAACTTGAAAAAGG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G34640.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G34640.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA12G04220.3 (Glycine max), 3'ss of exon 3
-------gcaagtctgaagagtctcttaacatcttcatctttcacattc-cattaatctttgactgtctaactg---acaaatt-ttacttgttcaactttagGTGGTACGAAGGAGTACAAGATTCTAATGGACCAATTTCACCATGTTTCTGCAGCTTTTTTGGAACTTGAAAAAGG
| | | | | | || || | || || | || | ||| | || | ||| || |||| || || | ||| |||||| || ||||||||||| ||||||||||||| ||||| |||||||| | |||||| ||||||||| |||
atctagcttgtttttcagaaattggattggattttaaacta-catactcatagcaattgcttgatgctgatctgcacactaattgtttctaatgtgact--agGTGGCACAAAGGAGTACAAAGTTCTAATGGACCAGTTTCATCATGTTTCAACTGCTTTTCTGGAACTTGGAAAGAA
upper sequence: AT4G34640.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA11G11960.3 (Glycine max), 3'ss of exon 3
------------gcaa--gtctgaagagtc-tcttaacatcttcatctttcacattccattaatctttgactgtctaactgacaaattttacttgttcaactttagGTGGTACGAAGGAGTACAAGATTCTAATGGACCAATTTCACCATGTTTCTGCAGCTTTTTTGGAACTTGAAAAAGG
||| || | ||| | | ||| | | | ||| | | ||| || | ||| | || | || || | ||| |||||| || ||||||||||| ||||||||||||| ||||| |||||||| | |||||| ||||||||| ||
agacaacctttatcaatcatcaggagaatggttttattgtatatgtgcctcaaaatttattgatgctgatctgcacatt----aattgtttctaatgtgact--agGTGGCACAAAGGAGTACAAAGTTCTAATGGACCAGTTTCATCATGTTTCAACTGCTTTTCTGGAACTTGGGAAGAA
upper sequence: AT4G34640.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv03s0038g00450.t01 (Vitis vinifera), 3'ss of exon 3
-------gcaagtctgaagagtctctta-acatcttcatct-ttcacattccattaatctttgactgtctaactgacaaattttacttgttcaactttagGTGGTACGAAGGAGTACAAGATTCTAATGGACCAATTTCACCATGTTTCTGCAGCTTTTTTGGAACTTGAAAAAGG
| |||| ||||| | | || || || | || |||| ||| || | || | | | || || ||||||||| ||||| |||||| |||| ||||||||||| || |||||||| | |||||| |||| ||||||| |||
ttgcaaaatatttctgtagagtacatggtatatatttatgtgttgacatgtatacaattttagtttgctccctaatcgtgcctctttcttttctgttaagGTGGTACAAAGGACTACAAGGTTCTCATGGACCAATTCCATCATGTTTCAACTGCTTTTCTGGAGCTTGAAAGAGGMapped 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|124863686|gb|EH948123.1|EH948123EST: CACCGGCACATATACGATACTGATTGGCATTATTCAT GTGGTACGAAGGAGTACAAGATTCTAATGGACCAATT-CACCATGTTTCTG
genomic: CACCGGCACATATACGATACTGATTGGCATTATTCATgcaagtctga ... tcaactttagGTGGTACGAAGGAGTACAAGATTCTAATGGACCAATTTCACCATGTTTCTG
EST:
gi|164100665|gb|ES135390.1|ES135390EST: CCTGATAGCTTTTCACCGGCACATATACGATACTGATTGGCATTATTCAT GTGGTACGAAGGAGTACAAGATTCTAA
genomic: CCTGATAGCTTTTCACCGGCACATATACGATACTGATTGGCATTATTCATgcaagtctga ... tcaactttagGTGGTACGAAGGAGTACAAGATTCTAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acattccattaatctttgactgtctaactgacaaattttacttgttcaactttagGTGGTACGAAGGAGTACAAGATTCTAATGGACCAATTTCACCATGTTTCTGCAGCTTTTTTGGAACTTGAAAAAGG
aactgac putative branch site (score: 2)
cttgttc putative PPT
aaattttacttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcaagtctgaagagtctcttaacatcttcatctttcacattccattaatctttgactgtctaactgacaaattttacttgttcaactttagGTGGTACGAAGGAGTACAAGATTCTAATGGACCAATTTCACCATGTTTCTGCAGCTTTTTTGGAACTTGAAAAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT