Sequence
atgc intronic sequence ATGC exonic sequence...taatctactgaactaagcctctagtagagaaatttttgtctataaaattaggcttctaggtggttgactactcctattgtttggcattgtgcgtttgcagTGGCAATCCGAAGGAAGAACCCGGCGCAATCGTTTGCAGGGTTTCTCAGTCATTTCTACGCTTTGGGTCATACCAAATACATGCCTCTAGAGGAAAAGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G13030.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G13030.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA20G39090.2 (Glycine max), 3'ss of exon 1
------------------------taatctactgaactaagcctctagtagagaaatttttgtctataaaattaggcttctaggtggttgactactcctattgtttggcattgtgcgtttgcagTGGCAATCCGAAGGAAGAACCCGGCGCAATCGTTTGCAGGGTTTCTCAGTCATTTCTACGCTTTGGGTCATACCAAATACATGCCTCTAGAGGAAAAGAG
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gtatgctattgcttcctctactttcacttttttctatcatctctacctattacatattggtggacttcggatccttggttttatttaccgattacatttcctgtttttaatatcacacgcgcagCGGCAATCCAAAGGAAGAACCTGGCGCAATTGTTTGCAGAGTTGCCCAATCTTTTCTGCGGTTTGGGTCATACCAAATACATGCCTCCAGAAGTGATGAG
upper sequence: AT5G13030.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv06s0004g01360.t01 (Vitis vinifera), 3'ss of exon 4
taatctactgaactaagcctctagtaga--gaaatttttgtctataaaattaggcttctaggt--ggttgactactcctatt-gtttggcattgtgcgtttgcagTGGCAATCCGAAGGAAGAACCCGGCGCAATCGTTTGCAGGGTTTCTCAGTCATTTCTACGCTTTGGGTCATACCAAATACATGCCTCTAGAGGAAAAGAG
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----atatccag-taggtttttaatgggatgggatatccaggaattgggggatagtcatagattaaaataattgtttaacttcgtttttatttgctcatgtacagTGGCAATCCAAAGGAAGAACCTGGTGCAATTGTTTGTAGAGTTGCTCAATCCTTTTTGCGATTTGGTTCTTACCAAATACATGCTGCTAGAGGGAAGGAGMapped 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|164057414|gb|EL967263.1|EL967263EST: CTTTGTCTTCTCACCACAGGTCAAAATGTGACTCGCGACATGTTTTATGA TGGCAATCCGAAGGAAGAACCCGGCG
genomic: CTTTGTCTTCTCACCACAGGTCAAAATGTCACTCGCGACATGTTTTATGAgtatgtccaa ... gcgtttgcagTGGCAATCCGAAGGAAGAACCCGGCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattaggcttctaggtggttgactactcctattgtttggcattgtgcgtttgcagTGGCAATCCGAAGGAAGAACCCGGCGCAATCGTTTGCAGGGTTTCTCAGTCATTTCTACGCTTTGGGTCATACCAAATACATGCCTCTAGAGGAAAAGAG
ggttgac putative branch site (score: 4)
tattgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taatctactgaactaagcctctagtagagaaatttttgtctataaaattaggcttctaggtggttgactactcctattgtttggcattgtgcgtttgcagTGGCAATCCGAAGGAAGAACCCGGCGCAATCGTTTGCAGGGTTTCTCAGTCATTTCTACGCTTTGGGTCATACCAAATACATGCCTCTAGAGGAAAAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - aactaag
- - - - - - - - - - - - -agagaaa
- - - - - - - - - - - - - - - - - - - - -ataaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttgg