Sequence
atgc intronic sequence ATGC exonic sequencegtatgtatcaaatccttgaatgtaaaaagtggcttctttggaatctattttttgtatattggctgattttatgtcattctggttgaatttgcagGGAAGAGTACGCTCTTGAATCATTTGTTTGGAACCAACTTTAGAGAAATGGATGCATTTAGAGGAAGGCAT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G13870.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G13870.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA07G01230.1 (Glycine max), 3'ss of exon 2
-----gtatgtatcaaatccttgaatgtaaaaag----tggcttctttggaatctattttttgtatattggctgattttatgtcattctggttgaatttgcagGGAAGAGTACGCTCTTGAATCATTTGTTTGGAACCAACTTTAGAGAAATGGATGCATTTAGAGGAAGGCAT
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tttgcgtttgt-ttaaatttgttagcataatgagatgattactattcccaataaaaggatctttatattatctagttctttgttttctttgctc--tggacagGCAAGAGCACACTGTTAAATCATTTGTTTGGTACCAACTTCAGAGAGATGGATGCTTTTAAGGGAAG----
upper sequence: AT3G13870.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv09s0002g02200.t01 (Vitis vinifera), 3'ss of exon 2
gtatgtatcaaatccttgaatgtaaaaagtggcttctttggaatctattttttgtatattggctgattttatg---tcattctggttg----aatttg--cagGGAAGAGTACGCTCTTGAATCATTTGTTTGGAACCAACTTTAGAGAAATGGATGCATTTAGAGGAAGGCAT
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--atttggtatctgttcatttgcatatattg-ctgtgtcaaaaattctttccgtcatactgttttatctcaaggtttgatactgttttctataattcgaacagGGAAGAGCACACTATTAAATCATTTGTTTGGTACCAACTTCAGGGAGATGGATGCTTTTAGAGGAAG----
upper sequence: AT3G13870.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ31796 (Selaginella moellendorffii), 3'ss of exon 2
gtatgtatcaaatccttgaatgtaaaaagtggcttctttggaatctattttttgtatat---tggctgattttatgtcattctggttga-atttgcagGGAAGAGTACGCTCTTGAATCATTTGTTTGGAACCAACTTTAGAGAAATGGATGCATTTAGAGGAAGGCAT
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---------------------------gtaggtgtgtttagatcatatccaaaaaaaatctctctctctctctctctcttttcttttgatgtgaacagGGAAGAGCACGCTCTTGAACCATTTGTTTCGTACGAGGTTTCGAGAAATGGATGCTTTCAAGGGAAG----
upper sequence: AT3G13870.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ38064 (Selaginella moellendorffii), 3'ss of exon 1
gtatgtatcaaatccttgaatgtaaaaagtggcttctttggaatctattttttgtatattggctgattttatgtcattctggttga-atttgcagGGAAGAGTACGCTCTTGAATCATTTGTTTGGAACCAACTTTAGAGAAATGGATGCATTTAGAGGAAGGCAT
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---------------------------gttggtgtgtttagatcatatccaaaaaaatctctctctctctctctcctttcttttgatgtgaacagGGAAGAGCACGCTCTTGAACCATTTGTTTCGTACGAGGTTTCGAGAAATGGATGCTTTCAAGGGAAG----Mapped 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|164227580|gb|ES178450.1|ES178450EST: CTTTCATACGCGGTTGTCTCGATTATGGGTCCACAAAGTAGTG GGAAGAGTACGCTCTTGAATCATTTGTTTGGAACCAACTTTAGAGAAATGG
genomic: CTTTCATACGCGGTTGTCTCGATTATGGGTCCACAAAGTAGTGgtatgtatca ... gaatttgcagGGAAGAGTACGCTCTTGAATCATTTGTTTGGAACCAACTTTAGAGAAATGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggaatctattttttgtatattggctgattttatgtcattctggttgaatttgcagGGAAGAGTACGCTCTTGAATCATTTGTTTGGAACCAACTTTAGAGAAATGGATGCATTTAGAGGAAGGCAT
ggctgat putative branch site (score: 4)
tattttttgtatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtatcaaatccttgaatgtaaaaagtggcttctttggaatctattttttgtatattggctgattttatgtcattctggttgaatttgcagGGAAGAGTACGCTCTTGAATCATTTGTTTGGAACCAACTTTAGAGAAATGGATGCATTTAGAGGAAGGCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA