Sequence
atgc intronic sequence ATGC exonic sequencegtaacttgtcttggagatttgctctttcggttattcgattgaaagattgttgttttgattttgcttattcattttcactttagATTTCGAAATTGAGCATGATTCCGGTGGTATGCGTGTTGGAATGGATTCTACATAGCAAGCATTATTGTAAAGAAGTGAAAGCTTCTGTAATGGTTGTGG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G76670.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G76670.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os07g39280.1 (Oryza sativa), 3'ss of exon 2
--------------gtaacttgtcttggagatttgctctttcggttattcgat--tgaaagattgttgttttgattttgcttattcattttca--ctttagATTTCGAAATTGAGCATGATTCCGGTGGTATGCGTGTTGGAATGGATTCTACATAGCAAGCATTATTGTAAAGAAGTGAAAGCTTCTGTAATGGTTGTGG
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gtattgtatatttactaggttgcccatttgcctggaatgtttgtatatgccgtcttgtgctcttgtgtggctgaaggtgcgaaacctctgcaaacctgtagATCTCGAAATTGAGCATGATCCCGGTGGTTTGCTTGATGGAATGGGTGCTCAACAGCAAGCACTACACCACCAAGGTTATATCGGCCGTGGTCGTCGTGG
upper sequence: AT1G76670.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv18s0122g00090.t01 (Vitis vinifera), 3'ss of exon 2
-----------gtaacttgtcttggagatttgctct------ttcggttattcgattgaaagattgttgttttgattttgcttattc-attttcactttagATTTCGAAATTGAGCATGATTCCGGTGGTATGCGTGTTGGAATGGATTCTACATAGCAAGCATTATTGTAAAGAAGTGAAAGCTTCTGTAATGGTTGTGG
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ctgtttcagaagcagcacttaatgta-atttgttcaaagaagtgcaagaatttgatgctaactctccatgtaaaacttgccttgttctatctgtggtgcagATTTCAAAACTGAGCATGATTCCAGTGGTATGTGTGATGGAATGGATCCTTCATAACAAACACTACTCTAGGGAAGTGAAGATTTCTGTGGTGGTTGTGG
upper sequence: AT1G76670.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S41_21V6.2 (Physcomitrella patens), 3'ss of exon 3
-----------------------------------gtaacttgtcttggagatttgctctttcggttattcgattgaaag-attg---ttgttttgattttg-cttattcattttcactttagATTTCGAAATTGAGCATGATTCCGGTGGTATGCGTGTTGGAATGGATTCTACATAGCAAGCATTATTGTAAAGAAGTGAAAGCTTCTGTAATGGTTGTGG
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gtgagtgtgtttctaactttggttgtgcgtcgtttgaaggatgacttgggg-tgcttagtttctggtattagatttatgtcattgaatttagactgataaggacgttgtttttgtcatcacagATTGCGAAATTGAGCATGATACCAACCGTATGCGTGTTGGAATGGTTGCTACATGGCAAGACTTACACGAGAGAAATGAAAATATCGGTTTTTGTTGTGAMapped 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|301503208|gb|HO208748.1|HO208748EST: TCGCTGCTATGAACTTTAGTCTTATGCTCAACTCTGTTGGCTTCTATCAG ATTTCGAAATTGAGCATGATTCCGGTGGTATGCGTGTTGGAATGGATTCTA
genomic: TCGCTGCTATGAACTTTAGTCTTATGCTCAACTCTGTTGGCTTCTATCAGgtaacttgtc ... ttcactttagATTTCGAAATTGAGCATGATTCCGGTGGTATGCGTGTTGGAATGGATTCTA
EST:
gi|125166135|gb|EL192077.1|EL192077EST: TCGCTGCTATGAACTTTAGTCTTATGCTCAACTCTGTTGGCTTCTATCAG ATTTCGAAATTGAGCATGATTC
genomic: TCGCTGCTATGAACTTTAGTCTTATGCTCAACTCTGTTGGCTTCTATCAGgtaacttgtc ... ttcactttagATTTCGAAATTGAGCATGATTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggttattcgattgaaagattgttgttttgattttgcttattcattttcactttagATTTCGAAATTGAGCATGATTCCGGTGGTATGCGTGTTGGAATGGATTCTACATAGCAAGCATTATTGTAAAGAAGTGAAAGCTTCTGTAATGGTTGTGG
ttttgat putative branch site (score: 4)
ttcattttcacttt putative PPT
ttattcatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacttgtcttggagatttgctctttcggttattcgattgaaagattgttgttttgattttgcttattcattttcactttagATTTCGAAATTGAGCATGATTCCGGTGGTATGCGTGTTGGAATGGATTCTACATAGCAAGCATTATTGTAAAGAAGTGAAAGCTTCTGTAATGGTTGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT