Sequence
atgc intronic sequence ATGC exonic sequencegtattcaggtttacatcatctttcagtatctgtcagaatggtcttgtgtacttaacactgttgtttctcagAAAATTGCATTGGCATGGATGTTTCAGAAGGAAACTAATAGTTTGCACTGTATGGGAGGGATATTAGCTGATGATCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G50410.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G50410.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA20G23390.1 (Glycine max), 3'ss of exon 3
gtattcaggtttacatcat------ctttcagtatctgtcagaatggtcttgtgtac-ttaacactgttgtttctcagAAAATTGCATTGGCATGGATGTTTCAGAAGGAAACTAATAGTTTGCACTGTATGGGAGGGATATTAGCTGATGATCAG
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gtattaaggcttgtctattaaattgcttttatcatttctgttctgggccatttatttgttatcact-ttgtatttcagAAAATTGCATTGGCTTGGATGCTTCAGAAGGAAACCAAGAGTTTGCATTGCTTGGGGGGGATTTTGGCTGATGATCAG
upper sequence: AT1G50410.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G43430.1 (Glycine max), 3'ss of exon 5
gtattcaggtttacatcat------ctttcagtatctgtcagaatggtcttgtgtac-ttaacactgttgtttctcagAAAATTGCATTGGCATGGATGTTTCAGAAGGAAACTAATAGTTTGCACTGTATGGGAGGGATATTAGCTGATGATCAG
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gtattatggcttgtctattaaattgcttctattatttctgttctgggccatttatttgttatcact-ttgtatttcagAAAATTGCATTGGCTTGGATGCTTCAGAAGGAAACCAAGAGTTTGCATTGCTTGGGGGGGATTTTGGCTGATGACCAG
upper sequence: AT1G50410.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv10s0071g00780.t01 (Vitis vinifera), 3'ss of exon 3
--------------------------------------------------------------------------------------gtattcaggt--ttacatcatctttcagtatctgt-cagaatggtc--ttgtgtacttaacac-tgttgtttctcagAAAATTGCATTGGCATGGATGTTTCAGAAGGAAACTAATAGTTTGCACTGTATGGGAGGGATATTAGCTGATGATCAG
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gttgtttttttttttgttttttttctatttttttattttttttctgcatctactttagttgactttggtttgtatgtgaattacttggtttgagatactgtaattatacttcgaattgtgtgtgaaatacttggttttgaccctaaggtattttgtcgtacagAAAATTGCATTGGCATGGATGCATCAGAAGGAAACAAGAAGTTTACATTGTTTGGGCGGGATTCTAGCTGATGATCAGMapped 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|86056954|gb|DR352711.1|DR352711EST: AGGTCGATTTACCTGCTGGTCTTCTTTCGGTTCCCCTTATGAAGCATCAC AAAATTGCATTGGCATGGATGTTTCAGAAGGAAACTAATAGTTTGCACTGT
genomic: AGGTCGATTTACCTGCTGGTCTTCTTTCGGTTCCCCTTATGAAGCATCAGgtattcaggt ... tgtttctcagAAAATTGCATTGGCATGGATGTTTCAGAAGGAAACTAATAGTTTGCACTGT
EST:
gi|86056953|gb|DR352710.1|DR352710EST: AGGTCGATTTACCTGCTGGTCTTCTTTCGGTTCCCCTTATGAAGCATCAG AAAATTGCATTGGCATGGATGTTTCAGAAGGAAACTAATAGTTTGCACTGT
genomic: AGGTCGATTTACCTGCTGGTCTTCTTTCGGTTCCCCTTATGAAGCATCAGgtattcaggt ... tgtttctcagAAAATTGCATTGGCATGGATGTTTCAGAAGGAAACTAATAGTTTGCACTGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catctttcagtatctgtcagaatggtcttgtgtacttaacactgttgtttctcagAAAATTGCATTGGCATGGATGTTTCAGAAGGAAACTAATAGTTTGCACTGTATGGGAGGGATATTAGCTGATGATCAG
acttaac putative branch site (score: 3)
ttgtttctc putative PPT
tacttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattcaggtttacatcatctttcagtatctgtcagaatggtcttgtgtacttaacactgttgtttctcagAAAATTGCATTGGCATGGATGTTTCAGAAGGAAACTAATAGTTTGCACTGTATGGGAGGGATATTAGCTGATGATCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT