Sequence
atgc intronic sequence ATGC exonic sequencegtaagttcatggcgtgttaaggaaacacatttgtcttaccaaaaaatgaccatttgcattattacatctactttgattttactcttttcagGTGGGACATAATTGCAGAGAGACTAGGCTTCATGCTAGTGTTTGGAGATCTCCTGTGGATTCCTTTCACTTTTAGCATTCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G52940.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G52940.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G473533_T06 (Zea mays), 3'ss of exon 8
-----------------------------------------gtaagttcatggcgtgttaaggaaacacatttgtcttaccaaaaa--atgaccat-ttgcattattacatctactttgatttt-actcttttcagGTGGGACATAATTGCAGAGAGACTAGGCTTCATGCTAGTGTTTGGAGATCTCCTGTGGATTCCTTTCACTTTTAGCATTCAG
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gtaagtatatcacatgctctcattggcaaataacttactatccctgaacaaaatatgttgag-atattctgtgggatgattaaagatgatgaacatactattctcctgaacaaaatatcgttgagacctcttccagGTGGGACATTATTGCTGAAAGACTGGGTTTCATGCTGGTGTTTGGTGATCTAGTTTTCATCCCTTTCACCTTCACTATTCAG
upper sequence: AT3G52940.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA13G21450.2 (Glycine max), 3'ss of exon 8
----gtaagttc----atggcgtgttaaggaaacacatttgtcttaccaaaaaatgacc--atttgcattattacatctactttgattttactcttttcagGTGGGACATAATTGCAGAGAGACTAGGCTTCATGCTAGTGTTTGGAGATCTCCTGTGGATTCCTTTCACTTTTAGCATTCAG
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tcctgaaattttcgctaaattatggtcaggatatccacttga-tcatttacatatgatctaattctcttttctaaccttatctttgttttgtcttttgcagCTGGGACATAATTGCAGAGAGACTGGGCTTCATGTTGGTCTTTGGAGATTTAGTGTGGATTCCTTTCTCTTTCAGCATACAG
upper sequence: AT3G52940.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv08s0007g03930.t01 (Vitis vinifera), 3'ss of exon 8
--------gtaagttcatggcgtgttaaggaaacacatttgtcttaccaaaaaatgaccatttgcattattacatctactttgatt--ttactcttttcagGTGGGACATAATTGCAGAGAGACTAGGCTTCATGCTAGTGTTTGGAGATCTCCTGTGGATTCCTTTCACTTTTAGCATTCAG
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cttgcttcttgtctttctatcagtcgataatagtaatgttgtcacactttatgatt-taatttacaaatctgactcagctgtatgtggttatcttttatagATGGGATATCATTGCGGAGAGATTGGGCTTCATGTTGGTGTTTGGGGATCTAGTGTGGATCCCTTTTACTTTTAGCATCCAGMapped 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|125037273|gb|EL109542.1|EL109542EST: ACATGACCTCTAC GTGGGACATAATTGCAGAGAGACTAGGCTTCATGCTAGTGTTTGGAGATCT
genomic: ACATGACCTCTACgtaagttcat ... ctcttttcagGTGGGACATAATTGCAGAGAGACTAGGCTTCATGCTAGTGTTTGGAGATCT
EST:
gi|125266648|gb|EL280733.1|EL280733EST: GCGTTATATATATTGGACTACTTTGTTCATGAAGAATACATGACCTCTAC GTGGGACATAATTGCAGAGAGACTAGGCTT
genomic: GCGTTATATATATTGGACTACTTTGTTCATGAAGAATACATGACCTCTACgtaagttcat ... ctcttttcagGTGGGACATAATTGCAGAGAGACTAGGCTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taccaaaaaatgaccatttgcattattacatctactttgattttactcttttcagGTGGGACATAATTGCAGAGAGACTAGGCTTCATGCTAGTGTTTGGAGATCTCCTGTGGATTCCTTTCACTTTTAGCATTCAG
ttttactcttttc CT-rich tract
attattacat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttcatggcgtgttaaggaaacacatttgtcttaccaaaaaatgaccatttgcattattacatctactttgattttactcttttcagGTGGGACATAATTGCAGAGAGACTAGGCTTCATGCTAGTGTTTGGAGATCTCCTGTGGATTCCTTTCACTTTTAGCATTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC