Sequence
atgc intronic sequence ATGC exonic sequencegtatggcttcaagatttgatttttcagtcaattgagcttctaccagaatcgtattttctgactaaaactctgtttcttgcagATGCGTGTTAGATCCTGGGGAGAAGATTATAGATTGTCCTCCAACTTTCTCAATGTATGTGTTTGATGCGGCTGTGAATGGAGCAGGTGTCATTAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G71920.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G10330.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ04408 (Selaginella moellendorffii), 3'ss of exon 2
gtatggcttcaagatttgatttttcagtcaattgagcttctaccagaatcgtattttctgactaaaactctgtttcttgcagATGCGTGTTAGATCCTGGGGAGAAGATTATAGATTGTCCTCCAACTTTCTCAATGTATGTGTTTGATGCGGCTGTGAATGG-AGCAGGTGTCATTAAAG-
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gtaagtgaccaactcctagcgtgttttttcttttttcttcttttg-----ctcttcacgagatggttcttcatctctt-tagTTGTACATTGGAAGGTGGTGACAAGATTGTGGATTGTCCTCCCACTTTGACAATGTATGCGTTTGATGCCGCTGTAAGCGTCATCAAAGGTCTTGTTTGT
upper sequence: AT5G10330.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ31551 (Selaginella moellendorffii), 3'ss of exon 3
gtatggcttcaagatttgatttttcagtcaattgagcttctaccagaatcgtattttctgactaaaactctgtttcttgcagATGCGTGTTAGATCCTGGGGAGAAGATTATAGATTGTCCTCCAACTTTCTCAATGTATGTGTTTGATGCGGCTGTGAATGGAGCAGGTGTCATTAAAG
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-------gtaagtgaacgactcctagcgtgcttttttttttcttttgctc---ttcacgagatggttcttcatctctt-tagTTGTACATTGGAAGTTGGTGACAAGATTGTGGATTGTCCTCCCACTTTCACAATGTATGCGTTTGATGCCGCTGTCAACGGAGCAAGCGTCATCAAAG
upper sequence: AT5G10330.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ04411 (Selaginella moellendorffii), 3'ss of exon 3
gtatggcttcaagatttgatttttcagtcaattgagcttctaccagaatcgtattttctgactaaaactctgtttcttgcagATGCGTGTTAGATCCTGGGGAGAAGATTATAGATTGTCCTCCAACTTTCTCAATGTATGTGTTTGATGCGGCTGTGAATGGAGCAGGTGTCATTAAAG
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gtaagtgaccgactccttgcgtttttttttttt---ttcttttccttttgctcttcacgagatggttcttcatctctt-tagTTGTACATTGGAAGTTGGTGACAAGATTGTGGATTGTCCTCCCACTTTCACAATGTATGCGTTTGATGCCGCTGTCAACGGAGCAAGCGTCATCAAAG
upper sequence: AT5G10330.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ38596 (Selaginella moellendorffii), 3'ss of exon 3
gtatggcttcaagatttgatttttcagtcaattgagcttctaccagaatcgtattttctgactaaaactctgtttcttgcagATGCGTGTTAGATCCTGGGGAGAAGATTATAGATTGTCCTCCAACTTTCTCAATGTATGTGTTTGATGCGGCTGTGAATGGAGCAGGTGTCATTAAAG
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gtaagtgaccaactcctagcgtgttttttcttttttcttcttttg-----ctcttcacgagatggttcttcatctctt-tagTTGTACATTGGAAGGTGGTGACAAGATTGTGGATTGTCCTCCCACTTTGACAATGTATGCGTTTGATGCCGCTGTAAGC-------------------Mapped 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|86072940|gb|DR368697.1|DR368697EST: TACATACTTGTAGGCTGTGGTGCTGACGAACTTATTGATTTGATCATGAG ATGCGTGTTAGATCCTGGGGAGAAGATTATAGATTGTCCTCCAACTTTCTC
genomic: TACATACTTGTAGGCTGTGGTGCTGACGAACTTATTGATTTGATCATGAGgtatggcttc ... tttcttgcagATGCGTGTTAGATCCTGGGGAGAAGATTATAGATTGTCCTCCAACTTTCTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaattgagcttctaccagaatcgtattttctgactaaaactctgtttcttgcagATGCGTGTTAGATCCTGGGGAGAAGATTATAGATTGTCCTCCAACTTTCTCAATGTATGTGTTTGATGCGGCTGTGAATGGAGCAGGTGTCATTAAAG
gactaaa putative branch site (score: 2)
ctctgtttctt CT-rich tract
tattttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatggcttcaagatttgatttttcagtcaattgagcttctaccagaatcgtattttctgactaaaactctgtttcttgcagATGCGTGTTAGATCCTGGGGAGAAGATTATAGATTGTCCTCCAACTTTCTCAATGTATGTGTTTGATGCGGCTGTGAATGGAGCAGGTGTCATTAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG