Sequence
atgc intronic sequence ATGC exonic sequence...tgctccttgacatctctagtactatgctccctgtaaggatttattttctttgtgattgttaattagaagctgacttgttcttgttatcaatcttttgcagATTTGGACTTTTTGTTCCATATGTTTTTTCTAGCTCGATACTGCAAACTGCTCGAAGAAAACTCCTTCAGGGGAAAGACCGCGGATTTCCTTTACATGCT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G21810.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G21810.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os03g63520.1 (Oryza sativa), 3'ss of exon 2
tgctccttgacatctctagtactatgctccctgtaaggatttattttctttgtg-attgttaattagaagctgacttgttcttgttatcaatcttttg-------cagATTTGGACTTTTTGTTCCATATGTTTTTTCTAGCTCGATACTGCAAACTGCTCGAAGAAAACTCCTTCAGGGGAAAGACCGCGGATTTCCTTTACATGCT
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------agaacatgta-agcgctgttattctagcattattgaataatttttatgcataatttaatccctttactcttattcctga-atccatcttttgttgtttccagATTTGGACTTTCTGTTCCACATGTTTTTTCTTGCACGATACTGCAAGCTTCTTGAGGAGAACTCATTCAGAGGAAGAACTGCTGACTTTTTCTACATGCT
upper sequence: AT4G21810.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G082976_T01 (Zea mays), 3'ss of exon 2
-tgctccttgac-atctctagtactatgctccctg-taaggatttattttctttgtgattgttaattagaa-gctgacttgttcttgttatcaatcttttgcagATTTGGACTTTTTGTTCCATATGTTTTTTCTAGCTCGATACTGCAAACTGCTCGAAGAAAACTCCTTCAGGGGAAAGACCGCGGATTTCCTTTACATGCT
||||| || || || || | | | || | |||| | ||| || ||| || |||| ||| || | |||| |||||||||| ||| ||||||| ||||||||||| || ||||||||||| || || || || ||||| || || |||| || || || || ||||||||||
tcgctccagacttataattactattaggttgcatgctgtttatttgcatctcaagtgcttcacccttataataaaaacttactctctttctt----ttttccagATTTGGATTTTCTGTTCCACATGTTTTTTCTCGCACGATACTGCAAGCTTCTGGAGGAGAACTCATTTAGAGGAAGAACTGCCGACTTTTTTTACATGCT
upper sequence: AT4G21810.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G27600.1 (Glycine max), 3'ss of exon 2
--tgctccttgacatctctagtactatgctccctgtaaggatttattttctttgtgattgttaattagaagctgacttgttcttgttatcaatcttttgcagATTTGGACTTTTTGTTCCATATGTTTTTTCTAGCTCGATACTGCAAACTGCTCGAAGAAAACTCCTTCAGGGGAAAGACCGCGGATTTCCTTTACATGCT
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aataacccttattcttatttgtttcataatcgtttgat--atttaattagaaagttatgcatcttctaaatttgacatggtattttcttattgaatgggcagACTTGGATTTCCTGTTTCATATGTTTTTTCTTGCTCGTTACTGCAAGCTTCTTGAGGAGAACTCGTTCAGGGGGAGGACTGCTGATTTCTTTTACATGCT
upper sequence: AT4G21810.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA15G11350.2 (Glycine max), 3'ss of exon 2
---tgctccttgacatctctagtactatgctccctgtaaggatttattttctttgtgattgttaattagaagctgacttgttcttgttatcaatcttttgcagATTTGGACTTTTTGTTCCATATGTTTTTTCTAGCTCGATACTGCAAACTGCTCGAAGAAAACTCCTTCAGGGGAAAGACCGCGGATTTCCTTTACATGCT
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atattctctttgctctcttt-gtttcatcatcgtttgatg--tttaattagaaaattgtgcatcttctaaatttgacatggtattttcttattgaatgggcagACTTGGATTTCCTGTTTCATATGTTTTTTCTTGCCCGTTACTGCAAGCTTCTTGAGGAGAACTCGTTCAGGGGGAGGACTGCTGATTTCTTTTACATGCTMapped 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|124778326|gb|EH868269.1|EH868269EST: ATACCAGTTCTGGCGTCTTGTCACAAATTTCCTTTATTTCCGAAAGATGG ATTTGGACTTTTTGTTCCATATGTTTTTTCTAGCTCGATACT
genomic: ATACCAGTTCTGGCGTCTTGTCACAAATTTCCTTTATTTCCGAAAGATGGgtaaaattat ... tcttttgcagATTTGGACTTTTTGTTCCATATGTTTTTTCTAGCTCGATACT
EST:
gi|125141485|gb|EL178986.1|EL178986EST: CGTCTTGTCACAAATTTCCTTTATTTCCGAAAGATGG ATTTGGACTTTTTGTTCCATATGTTTTT-CTAGCTCGATACTGCAAACTGC
genomic: CGTCTTGTCACAAATTTCCTTTATTTCCGAAAGATGGgtaaaattat ... tcttttgcagATTTGGACTTTTTGTTCCATATGTTTTTTCTAGCTCGATACTGCAAACTGC
EST:
gi|125009280|gb|EL081549.1|EL081549EST: CTTTATTTCCGAAAGATGG ATTTGGACTTTTTGTTTCCATATGTTTTTTCTTAGCTCGATACTGCAAACT
genomic: CTTTATTTCCGAAAGATGGgtaaaattat ... tcttttgcagATTTGGACTTTTTG-TTCCATATGTTTTTTC-TAGCTCGATACTGCAAACT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctttgtgattgttaattagaagctgacttgttcttgttatcaatcttttgcagATTTGGACTTTTTGTTCCATATGTTTTTTCTAGCTCGATACTGCAAACTGCTCGAAGAAAACTCCTTCAGGGGAAAGACCGCGGATTTCCTTTACATGCT
agctgac putative branch site (score: 3)
tcttttgc putative PPT
attgttaattagaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgctccttgacatctctagtactatgctccctgtaaggatttattttctttgtgattgttaattagaagctgacttgttcttgttatcaatcttttgcagATTTGGACTTTTTGTTCCATATGTTTTTTCTAGCTCGATACTGCAAACTGCTCGAAGAAAACTCCTTCAGGGGAAAGACCGCGGATTTCCTTTACATGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - catctct
- - - - - - - - - - - -atgctcc