Sequence
atgc intronic sequence ATGC exonic sequence...ttgcaatcaatctactatgattcttatttttgaaagccttctcttttagtttattgtatttcttggtgggctaattatgtgtttgggtttggttttatagATTGGGAACAGAATCATAAGGAAGAGGATACATGTGCGTGTGGAGCATGTGCAACAGTCAAGGTGTGCTGAGGAGTTTAAACTCAGAAAGAAGCAGAACG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G57660.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G57660.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os10g32820.1 (Oryza sativa), 3'ss of exon 1
------ttgcaatcaatctactatgattcttatttttgaaagccttctcttttagtttattgtatttcttggtgggctaattatgtgtttgggtttggttttatagATTGGGAACAGAATCATAAGGAAGAGGATACATGTGCGTGTGGAGCATGTGCAACAGTCAAGGTGTGCTGAGGAGTTTAAACTCAGAAAGAAGCAGAACG
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catgtgtaatgttcagtcatgtggatatgtagtcttcgggattatttaatttttgaa-atcatgtatct-gttttactgattgtttgtt--aatct--cttggtagGTTGGGAACCGCATTATCAGGAAGAGGATCCATGTCCGTGTGGAGCATGTGCAGCCATCCAGGTGCACTGAGGAGTTCCGCCTGAGGAAGATCAAGAACG
upper sequence: AT1G57660.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os03g04750.1 (Oryza sativa), 3'ss of exon 1
---ttgcaatcaatctactatgattcttatttttgaaagccttctcttttagtttattgtatttcttggtgggctaattatgt-gtttgggtttggttttat-agATTGGGAACAGAATCATAAGGAAGAGGATACATGTGCGTGTGGAGCATGTGCAACAGTCAAGGTGTGCTGAGGAGTTTAAACTCAGAAAGAAGCAGAACG
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attttagaatggaacatcaa--atattgagtattgaa---catcaaatagggctcgctacttgatgtggcaacttcacattgaagactctgttttctgtcatcagGTCGGTAACCGCATCATCAGGAAGAGGATCCATGTCCGTGTGGAGCATGTCCAGCCATCCAGGTGCACCGAGGAGCTCCGCCTGAGGAAAATCAAGAACG
upper sequence: AT1G57660.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA03G36560.1 (Glycine max), 3'ss of exon 1
ttgcaatcaatctactatgattcttatttttgaaagccttctcttttagtttattgtatttcttggtgggctaattatgtgtttgggtttg--gttttat--agATTGGGAACAGAATCATAAGGAAGAGGATACATGTGCGTGTGGAGCATGTGCAACAGTCAAGGTGTGCTGAGGAGTTTAAACTCAGAAAGAAGCAGAACG
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-ttctgcccgtgtgtta--attttagtttctagggttttatgtgtatgcctcgttgattttgggaatggttttattgaa-attactttttgatgtttcattcagGTCGGCAACAGAATCATAAGGAAGAGGATTCACGTGCGTGTGGAGCATGTTATGCCATCAAGGTGCACTGAGGAGTTCCGCCTTAGGAAGATCAAGAATG
upper sequence: AT1G57660.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA06G22900.1 (Glycine max), 3'ss of exon 2
-ttgcaatcaatctactatgattcttat--ttttgaaagccttctcttttagtttattgtatttcttggtgggctaattatgtgtttgggtttggttttatagATTGGGAACAGAATCATAAGGAAGAGGATACATGTGCGTGTGGAGCATGTGCAACAGTCAAGGTGTGCTGAGGAGTTTAAACTCAGAAAGAAGCAGAACG
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ctgcccgtgtgttaattttagtttctagggttttatgtgtatgcctcattgatttggggatttggtgtttattgaaattaccttttgatgtttcattc---agGTCGGCAACAGAATCATAAGGAAGAGGATTCACGTGCGTGTGGAGCATGTTATGCCATCGAGGTGCACTGAGGAGTTCCGCCTTAGGAAAATCAAGAATG
upper sequence: AT1G57660.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA19G39240.1 (Glycine max), 3'ss of exon 1
-----ttgcaatcaatctactat--gattcttatttttgaaagccttctcttttagtttattgtatttcttggtgggctaattatgtgtttgggtttggttttatagATTGGGAACAGAATCATAAGGAAGAGGATACATGTGCGTGTGGAGCATGTGCAACAGTCAAGGTGTGCTGAGGAGTTTAAACTCAGAAAGAAGCAGAACG
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tttagtttctagggtttttatgtcaaactcttgtgtatgccaaccttattgatttggggattatgttt--tgttgaaattactttgtgtga-----tgttcattcagGTTGGCAACAGAATTATAAGGAAGAGGATTCATGTGCGGGTAGAGCATGTTATGCCTTCAAGGTGCACTGAGGAGTTCCGCCTCAGGAAGATTAAGAATGMapped 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|116437489|gb|EG480081.1|EG480081EST: GCATCTAGAATGTCACTAAGCGTGCCGTTGGTGTTGAAGTCAACAAACAG ATTGGGAACAGAATCATAAGGAAGAGGATACATGTGCGTGTGG
genomic: GCATCTGGAATGTCACTAAGCGTGCCGTTGGTGTTGAAGTCAACAAACAGgtgttgatta ... ggttttatagATTGGGAACAGAATCATAAGGAAGAGGATACATGTGCGTGTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttagtttattgtatttcttggtgggctaattatgtgtttgggtttggttttatagATTGGGAACAGAATCATAAGGAAGAGGATACATGTGCGTGTGGAGCATGTGCAACAGTCAAGGTGTGCTGAGGAGTTTAAACTCAGAAAGAAGCAGAACG
ggctaat putative branch site (score: 3)
ttattgtatttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgcaatcaatctactatgattcttatttttgaaagccttctcttttagtttattgtatttcttggtgggctaattatgtgtttgggtttggttttatagATTGGGAACAGAATCATAAGGAAGAGGATACATGTGCGTGTGGAGCATGTGCAACAGTCAAGGTGTGCTGAGGAGTTTAAACTCAGAAAGAAGCAGAACG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- -caatcaa
- - - - - - - - - - - - - - - tgaaagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttgg