Sequence
atgc intronic sequence ATGC exonic sequence...tggaataattaaccaaatacatttgaaagtctagatctttggtactttaagtagtgtgagccattgttgattttgttccgttctaagagtgcttgcgcagGTGTTTATTACGGATTTGTGGACAGATCATACGCCCTGGCCGTTCAACCAGCTTCCCAGGAGCTATAATTTTCTGGTGAAACATGGAACTCTGTGGAAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G31780.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G31780.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os09g25580.1 (Oryza sativa), 3'ss of exon 1
tggaataattaaccaaat--acatttgaaagtctagatctttggtactttaagtagtgtgagccattgttgattttgt-tccgttctaagagtgcttgc-gcagGTGTTTATTACGGATTTGTGGACAGATCATACGCCCTGGCCGTTCAACCAGCTTCCCAGGAGCTATAATTTTCTGGTGAAACATGGAACTCTGTGGAAAA
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--gaatgatcacttgttctggcgttctgccttctcaactagtggttgttga--tattgataatttatgtaatttctgtattcataacaaaggaatttgttgcagGTATTCGTCACTGATTTATGGACTGACCATACCCCATGGCCATTCAACCAACTACCCAGGAGCTACAGTTTCTTGGTGAAACATGGACCCTTGTGGAAGA
upper sequence: AT4G31780.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA14G12120.1 (Glycine max), 3'ss of exon 1
tggaataattaaccaaatacatttgaaagtctagatctttggtactttaagtagtgtgagccattgttgattttgttccgttctaag-----agtgcttg-cgcagGTGTTTATTACGGATTTGTGGACAGATCATACGCCCTGGCCGTTCAACCAGCTTCCCAGGAGCTATAATTTTCTGGTGAAACATGGAACTCTGTGGAAAA
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----taaggtgatcagaagttatagggaatcaaatgaatgggtgtgt--ggttgtgtgtgtttctttttgttgggttgtgttatcagtttggagttcatggtacagGTTTTCGTTACTGATTTGTGGGCTGATCACACGCCTTGGCCATTCAACCAACTTCCCAGGAGCTATAGTTTTCTGGTGAAACATGGGCCGTTGTGGAAGA
upper sequence: AT4G31780.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA17G33780.1 (Glycine max), 3'ss of exon 1
tggaataatt---aaccaaatacatttgaaagtctagatctttggtactttaagtagtgtgagccattgttgattttgttccgttctaagagtgcttg-cgcagGTGTTTATTACGGATTTGTGGACAGATCATACGCCCTGGCCGTTCAACCAGCTTCCCAGGAGCTATAATTTTCTGGTGAAACATGGAACTCTGTGGAAAA
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taaggtgatcggaagttatagggaatcaaatgaatggatgtgtggttatatgtgtgttttttg--gttg--gattgtattctcagtttggagttcatggtacagGTTTTCGTTACTGATTTGTGGGCTGATCACACACCTTGGCCATTCAACCAACTTCCCAGGAGCTATAGCTTTTTGGTGAAACATGGGCCATTGTGGAAGAMapped 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|86059933|gb|DR355690.1|DR355690EST: CGGAAGCCATTAGAGCGGCTTTTAATCAGGAGTTTGGAGATGAGTACCAG GTGTTTATTACGGATTTGTGGACAGATCATACGCCCTGGCCGTTCAACCAG
genomic: CGGAAGCCATTAGAGCTGCTTTTAATCAGGAGTTTGGAGATGAGTACCAGgttcgtcttg ... gcttgcgcagGTGTTTATTACGGATTTGTGGACAGATCATACGCCCTGGCCGTTCAACCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttaagtagtgtgagccattgttgattttgttccgttctaagagtgcttgcgcagGTGTTTATTACGGATTTGTGGACAGATCATACGCCCTGGCCGTTCAACCAGCTTCCCAGGAGCTATAATTTTCTGGTGAAACATGGAACTCTGTGGAAAA
tgttgat putative branch site (score: 4)
ttgatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tggaataattaaccaaatacatttgaaagtctagatctttggtactttaagtagtgtgagccattgttgattttgttccgttctaagagtgcttgcgcagGTGTTTATTACGGATTTGTGGACAGATCATACGCCCTGGCCGTTCAACCAGCTTCCCAGGAGCTATAATTTTCTGGTGAAACATGGAACTCTGTGGAAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA