Sequence
atgc intronic sequence ATGC exonic sequence...tctaacgatgtcattctgtggggacaattgtgtatgaatttgctgattactttgtcattctgattggtttctttttatatttttgctgtttgcctctcagGTAGCTGTAGGAGATGTAATCTATATCGAAGCAAACAGTGGAGCTGTCAAACGGGTAGGTAGAAGTGATGCTTTTGCCACTGAATTTGATCTGGAAGCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G22330.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G22330.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA07G02170.1 (Glycine max), 3'ss of exon 4
---------------------------------------------------------------------tctaacgatgtcattctg----tggggacaattgtgtatgaatttgctgattactttgtcattctg---attggtttc-tttttatatttttgctgtttgcctct---cagGTAGCTGTAGGAGATGTAATCTATATCGAAGCAAACAGTGGAGCTGTCAAACGGGTAGGTAGAAGTGATGCTTTTGCCACTGAATTTGATCTGGAAGCAG
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gtgaggtttctgaaattatttcctcttgttctttgtgtgcttctgtctttacaagttataaatttcttttcttattattttttttttcttttttgtatgatgctgttttagttttaaagctgtgtgatatttgtgtcaacaaatgtgatgttttgatttgggatttctgccaatgtacagGTAGCTGTTGGGGATGTAATATACATTGAGGCAAATAGTGGGGCTGTAAAAAGGGTGGGTCGAAGCGATGCTTTTGCTACCGAGTTTGACCTTGAAGCAG
upper sequence: AT5G22330.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv06s0004g02910.t01 (Vitis vinifera), 3'ss of exon 4
tctaacgatgtcattctgtggggacaattgtgta--tgaatt--tgctgattactttgtcattctgattggtttct--ttttatatttttgctgtttgcctctcagGTAGCTGTAGGAGATGTAATCTATATCGAAGCAAACAGTGGAGCTGTCAAACGGGTAGGTAGAAGTGATGCTTTTGCCACTGAATTTGATCTGGAAGCAG
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------atcattagtttataggtctacttgcatgcttagattgttatttttttcttttattttttattttgtgtatggtttcattatttttcaatacaatctgcagGTAGCTGTTGGTGATGTTATATATGTTGAAGCCAATAGTGGAGCTGTTAAAAGGGTGGGCAGAAGTGATGCTTTTGCTACAGAATTTGACCTTGAGGCGG
upper sequence: AT5G22330.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ33466 (Selaginella moellendorffii), 3'ss of exon 4
tctaacgatgtcattctgtggggacaattgtgtatgaatttgctgattactttgtcattctgattggtttctttttatatttttgctgtttgcctctcagGTAGCTGTAGGAGATGTAATCTATATCGAAGCAAACAGTGGAGCTGTCAAACGGGTAGGTAGAAGTGATGCTTTTGCCACTGAATTTGATCTGGAAGCAG
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---------------------------------------gtgatggtt--tccgacggttt---tgctctttgctggttttgaaactgttatcgtc--agGTAGCAGTGGGAGATGTCATCTACATTGAAGCCAACAGCGGTGCTGTGAAACGAGTTGGACGAAGTGATGCTTTCGCGACCGAATTCGACCTTGAAGCGG
upper sequence: AT5G22330.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ27201 (Selaginella moellendorffii), 3'ss of exon 4
tctaacgatgtcattctgtggggacaattgtgtatgaatttgctgattactttgtcattctgattggtttctttttatatttttgctgtttgcctctcagGTAGCTGTAGGAGATGTAATCTATATCGAAGCAAACAGTGGAGCTGTCAAACGGGTAGGTAGAAGTGATGCTTTTGCCACTGAATTTGATCTGGAAGCAG
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------------------------------------------gtgatggtttc--caacggttttgctctttgctggttttgaaactgttatcgtc--agGTAGCAGTGGGAGATGTCATCTACATTGAAGCCAACAGCGGTGCTGTGAAACGAGTTGGACGAAGTGATGCTTTCGCGACTGAATTCGACCTTGAAGCGGMapped 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|116443983|gb|EG486575.1|EG486575EST: AACATCTGAAATTGGATCCCACTATCTATGATGCCTTGATTAAGGAAAAG GTAGCTGTAGGAGATGTAATCTATATCGAAGCAAACAGTGGAGCTGTCAAA
genomic: AACATCTGAAATTGGATCCCACTATCTATGATGCCTTGATTAAGGAAAAGgtcagttctt ... tgcctctcagGTAGCTGTAGGAGATGTAATCTATATCGAAGCAAACAGTGGAGCTGTCAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attactttgtcattctgattggtttctttttatatttttgctgtttgcctctcagGTAGCTGTAGGAGATGTAATCTATATCGAAGCAAACAGTGGAGCTGTCAAACGGGTAGGTAGAAGTGATGCTTTTGCCACTGAATTTGATCTGGAAGCAG
ttctgat putative branch site (score: 3)
tttgcctctc putative PPT
attggtttctttttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctaacgatgtcattctgtggggacaattgtgtatgaatttgctgattactttgtcattctgattggtttctttttatatttttgctgtttgcctctcagGTAGCTGTAGGAGATGTAATCTATATCGAAGCAAACAGTGGAGCTGTCAAACGGGTAGGTAGAAGTGATGCTTTTGCCACTGAATTTGATCTGGAAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG