Sequence
atgc intronic sequence ATGC exonic sequencegtaattcatctcgatctcgatcttgagcatatagaatcaaattgctttgatttgagcatatatagactttgattttggtttagtggattcacatttttttgtgttgattagATCTCGAAGCTGAGCATGATTCCTGTGGTATGTGTAATGGAATGGATTCTACATAGCAAGAGATACTCAAGAGAAGTGAAAATATCTGTTGTGGTTGTTG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G42420.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G42420.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA01G45700.1 (Glycine max), 3'ss of exon 2
gtaattcatctcgatctcgatcttgagcatatagaatcaaattgctttgatttgagcatatatagact-ttgattttggtttagtggattcacatttttttgtgttgattagATCTCGAAGCTGAGCATGATTCCTGTGGTATGTGTAATGGAATGGATTCTACATAGCAAGAGATACTCAAGAGAAGTGAAAATATCTGTTGTGGTTGTTG
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-------cttttaatgt--atcataaatgatagccaccttctcattttcat--aactgaattttcactgctgcttttcagttgttaattttctcgttatgtatggtcac-agATATCAAAACTGAGCATGATTCCAGTGGTTTGTGTGATGGAATGGATACTTCACAACAAGCACTACTCAAGGGAAGTGAAAATGTCAGTGGTGGTTGTGG
upper sequence: AT5G42420.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G00210.2 (Glycine max), 3'ss of exon 2
gtaattcatctcgatctcgatcttgagcatatagaatcaaattgctttgatttgagcatatatagactttgattttggtttagtggattcacatttttttgtgttgattagATCTCGAAGCTGAGCATGATTCCTGTGGTATGTGTAATGGAATGGATTCTACATAGCAAGAGATACTCAAGAGAAGTGAAAATATCTGTTGTGGTTGTTG
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atcataaatgatagccacgttctcattctcatat----------cttcactttgaattttcactgcttctgctttttagttgttaattttctcgttatttatggtc-ccagATATCAAAACTGAGCATGATTCCTGTGGTTTGTGTGATGGAATGGATACTTCACAACAAACACTACTCAAGGGAAGTGAAAATGTCAGTGGTGGTTGTGG
upper sequence: AT5G42420.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv18s0122g00090.t01 (Vitis vinifera), 3'ss of exon 2
gtaattcatctcgatctcgatcttgagcatatagaatcaaattgctttgatttgagcatatatagactttgattttggtttagtggattcacatttttttgt--gttgattagATCTCGAAGCTGAGCATGATTCCTGTGGTATGTGTAATGGAATGGATTCTACATAGCAAGAGATACTCAAGAGAAGTGAAAATATCTGTTGTGGTTGTTG
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-----------ctgtttcagaagc-agcacttaatgt-aatttgttcaaagaagtgcaagaatttgatgctaactctccatgtaaaacttgccttgttctatctgtggtgcagATTTCAAAACTGAGCATGATTCCAGTGGTATGTGTGATGGAATGGATCCTTCATAACAAACACTACTCTAGGGAAGTGAAGATTTCTGTGGTGGTTGTGGMapped 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|125004539|gb|EL076808.1|EL076808EST: TGAACTTCAGTCTCATGCTCAATTCCGTTGGCTTCTACCAA ATCTCGAAGCTGAGCATGATTCCTGTGGTATGTGTAATGGAATGGATTCTA
genomic: TGAACTTCAGTCTCATGCTCAATTCCGTTGGCTTCTACCAAgtaattcatc ... tgttgattagATCTCGAAGCTGAGCATGATTCCTGTGGTATGTGTAATGGAATGGATTCTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catatatagactttgattttggtttagtggattcacatttttttgtgttgattagATCTCGAAGCTGAGCATGATTCCTGTGGTATGTGTAATGGAATGGATTCTACATAGCAAGAGATACTCAAGAGAAGTGAAAATATCTGTTGTGGTTGTTG
ctttgat putative branch site (score: 5)
tttttttgt putative PPT
attcacattttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattcatctcgatctcgatcttgagcatatagaatcaaattgctttgatttgagcatatatagactttgattttggtttagtggattcacatttttttgtgttgattagATCTCGAAGCTGAGCATGATTCCTGTGGTATGTGTAATGGAATGGATTCTACATAGCAAGAGATACTCAAGAGAAGTGAAAATATCTGTTGTGGTTGTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT