Sequence
atgc intronic sequence ATGC exonic sequencegtaaaactataattctaataattataattgatgatataaagttataaaacactccataatctttgacgtataatttaactgtagaattttacttaaagttattaatttgatttatgttggtcgatgggtgaatagTGGACATGGGCTGCGACCATACTGCAAAGTTCAAACGTAGCATGGCAGTATGGGGTTAGTGGACCGTTTTGGTACGCTAGTGGAGCCACCATACAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G45380.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G45380.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA04G14790.1 (Glycine max), 3'ss of exon 2
gtaaaactataattctaataattataattgatgatataaagttataaaacactccataatctttgacgtataatttaactgtagaattttacttaaagttattaatttgatttatgttggtcgatgggtgaatagTGGACATGGGCTGCGACCATACTGCAAAGTTCAAACGTAGCATGGCAGTATGGGGTTAGTGGACCGTTTTGGTACGCTAGTGGAGCCACCATACAG
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-----------------------------------gtaatggattcaaatagcc--tcatagttaatactttgatgaacc-tgagattccattttttcacgtctcttttctttattacgatgattttgtg--cagTGGACATGGGCTGCTACAATCCTGCAAAGCTCTAATGTTGCATGGGAGTATGGAGTTAGTGGACCTTTCTGGTATGCTA-----------------
upper sequence: AT5G45380.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv02s0033g01370.t01 (Vitis vinifera), 3'ss of exon 2
gtaaaactataattctaataattataattgatgatataaagttataaaacactccataatctttgacgtataatttaactgtagaattttacttaaagttattaatttgatttatgttggtcgatgggtgaatagTGGACATGGGCTGCGACCATACTGCAAAGTTCAAACGTAGCATGGCAGTATGGGGTTAGTGGACCGTTTTGGTACGCTAGTGGAGCCACCATACAG
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---------------------------------------------gtaatgtctaatatcgcttcctttgtagttctac-atggaatt-----cagattcaataagcttatattttcgagtaccggtctgtacagTGGACTTGGGCTGCCACAATCTTGCAAAGCTCCAATGTAGCATGGCAGTATGGAGTTAGCGGCCCTTTCTGGTATGCCAGTGGAGCTACCATCCAG
upper sequence: AT5G45380.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S409_42V6.1 (Physcomitrella patens), 3'ss of exon 2
gta-aaactataattctaataattataattgatgatataaagttataaaacactccataatctttgacgtataatttaactgta--gaattttacttaaagtt-attaatttgatttatgttggtcgatgggtgaatagTGGACATGGGCTGCGACCATACTGCAAAGTTCAAACGTAGCATGGCAGTATGGGGTTAGTGGACCGTTTTGGTACGCTAGTGGAGCCACCATACAG----
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gtatggatcatgtgcacgaggaatcgaatgtgtaat-tgtgcctttgcag--tctagcagttctcaaattgcaactgtgttgtaatgaattttcgtgattctccgttgtgatggtggcctggggtggatgtg-gtgcagTGGACATGGGCTGCAACCATTTTACAGAGCTCCAACGTGGCGTGGCAGTACGGAGTTAGTGGGCCTTTCTGGTACGCTAGTGGCGCCACTGTGCAGGTGCMapped 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|116459873|gb|EG502465.1|EG502465EST: CGGGAAGAAACGTTAAGACAGGACTTATTGCAAGTGTCATTGTATCACAG TGGACATGGGCTGCGACCATACTGCAAAGTTCAAACGTAGCATGGCAGTAT
genomic: CGGGAAGAAACGTTAAGACAGGACTTATTGCAAGTGTCATTGTATCACAGgtaaaactat ... gggtgaatagTGGACATGGGCTGCGACCATACTGCAAAGTTCAAACGTAGCATGGCAGTAT
EST:
gi|116412044|gb|EG454636.1|EG454636EST: CGGGAAGAAACGTTAAGACAGGACTTATTGCAAGTGTCATTGTATCACAG TGGACATGGGCTGCGACCATACTGCAAAGTTCAAACGTAGCATGGCAGTAT
genomic: CGGGAAGAAACGTTAAGACAGGACTTATTGCAAGTGTCATTGTATCACAGgtaaaactat ... gggtgaatagTGGACATGGGCTGCGACCATACTGCAAAGTTCAAACGTAGCATGGCAGTAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtagaattttacttaaagttattaatttgatttatgttggtcgatgggtgaatagTGGACATGGGCTGCGACCATACTGCAAAGTTCAAACGTAGCATGGCAGTATGGGGTTAGTGGACCGTTTTGGTACGCTAGTGGAGCCACCATACAG
attttacttaaagtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaactataattctaataattataattgatgatataaagttataaaacactccataatctttgacgtataatttaactgtagaattttacttaaagttattaatttgatttatgttggtcgatgggtgaatagTGGACATGGGCTGCGACCATACTGCAAAGTTCAAACGTAGCATGGCAGTATGGGGTTAGTGGACCGTTTTGGTACGCTAGTGGAGCCACCATACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG