Sequence
atgc intronic sequence ATGC exonic sequence...tgtattgagattatgtaaaccagccttgggataatgagttggttgtttgagcaatgtttcataaccatgaagctgagtgaactttttcttttggtgccagCTGCACCAGTTGATGCCATCTGTTGTAACATGCCTTGTATCAAGAAAGCTTGGAAATAGATTTGCTGACAACCACTGGGAACTCAGAGATTTTGCGGCAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G04950.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G04950.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA18G52720.1 (Glycine max), 3'ss of exon 3
----tgtattgagattatgtaaaccagccttgggataatgagttggttgtttgagcaatgtttcataaccatgaagctgagtgaactttttcttttggtgccagCTGCACCAGTTGATGCCATCTGTTGTAACATGCCTTGTATCAAGAAAGCTTGGAAATAGATTTGCTGACAACCACTGGGAACTCAGAGATTTTGCGGCAA
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aaaggccatttagatcttagtatgttacttggttcacatgaatgagttaatgtgaaaccatctctttacctc----tttttctttctgtttttgcatgcttcagCTACACCAGTTGATGCCATCTGTTGTGACCTGCCTTGTTGCTAAAAGGTTGGGCAGTAGGTTGGCAGACAACCACTGGGAACTTAGAGACTCTACGGCTA
upper sequence: AT1G04950.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA02G10220.1 (Glycine max), 3'ss of exon 7
----tgtattgagattatgtaaaccagccttgggataatgagttggttgtttgagcaatgtttcataaccatgaagctgagtgaactttttcttttggtgccagCTGCACCAGTTGATGCCATCTGTTGTAACATGCCTTGTATCAAGAAAGCTTGGAAATAGATTTGCTGACAACCACTGGGAACTCAGAGATTTTGCGGCAA
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aaagcccatttagatttcagtatgttacttgcttcacatgaatgagttaatgtgaaaccatctctttacccc----tttttctttctgtttttgcatgcttcagCTACACCAGTTGATGCCATCTGTTGTGACTTGCCTTGTTGCTAAAAGGTTGGGCACTAGGTTGGCAGACAACCACTGGGAACTTAGAGACTTTACGGCTC
upper sequence: AT1G04950.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv12s0059g00300.t01 (Vitis vinifera), 3'ss of exon 7
tgtattg-agattatgt---aaaccagccttgggataatgagttggttgtttgagcaatgtttcataaccatgaagctgagtgaactttttcttttggtgccagCTGCACCAGTTGATGCCATCTGTTGTAACATGCCTTGTATCAAGAAAGCTTGGAAATAGATTTGCTGACAACCACTGGGAACTCAGAGATTTTGCGGCAA
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gatactctagcttatgtgttaaagtgacagacatgtattgatgtcctt-tttgggaagtgtctaacttctgtacatctaatggggcatctttccttg---tcagCTGCACCAATTAATGCCATCTGTGGTTACCTGCCTTGTTGCAAAACGAATTGGAAATAGACTTGCAGACAACCACTGGGAACTTCGAGACTTCACAGCAAMapped 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|125239785|gb|EL253870.1|EL253870EST: CATACACATAGAACCTTAT CTGCACCAGTTGATGCCATCTGTTGTAACATGCCTTGTATCAAGAAAGCTT
genomic: CATACACATAGAACCTTATgtaagttttc ... ttggtgccagCTGCACCAGTTGATGCCATCTGTTGTAACATGCCTTGTATCAAGAAAGCTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgagcaatgtttcataaccatgaagctgagtgaactttttcttttggtgccagCTGCACCAGTTGATGCCATCTGTTGTAACATGCCTTGTATCAAGAAAGCTTGGAAATAGATTTGCTGACAACCACTGGGAACTCAGAGATTTTGCGGCAA
tcataac putative branch site (score: 2)
ctttttcttttggt putative PPT
tttttctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtattgagattatgtaaaccagccttgggataatgagttggttgtttgagcaatgtttcataaccatgaagctgagtgaactttttcttttggtgccagCTGCACCAGTTGATGCCATCTGTTGTAACATGCCTTGTATCAAGAAAGCTTGGAAATAGATTTGCTGACAACCACTGGGAACTCAGAGATTTTGCGGCAA
- - - - - - - - aaaccag
- - - - - - - - - - - - - - - - - - - - - -tgtttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ataacca