Sequence
atgc intronic sequence ATGC exonic sequencegtaagtaaagctccttgtatcaacttcttagtaccatttcgttgttttgatctttgtggtaatcctttggttttgattttgcagCTTGCAAGGCTAGAGGATCCGATCTTAGGGTTCACTTCAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G67430.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G67430.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G10910.2 (Glycine max), 3'ss of exon 2
------------------------------------------gtaagtaaagctccttgtatcaac----ttcttagtaccatttcgttgttttgatctttgtggtaatcctttggttttgattttgcagCTTGCAAGGCTAGAGGATCCGATCTTAGGGTTCACTTCAAG
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gtaggttttattcacacttttcttttttactttttgatatcgatacttgttattcgctaaaacgacggcgtttgtggtctctttcaatctgagccccccacttttttttcttatcgtttttcatttgcagCTTGCAAGGCTAGAGGCGCCGACCTTAGGGTTCATTTTAAG
upper sequence: AT1G67430.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA05G27940.1 (Glycine max), 3'ss of exon 2
---------------------------------gtaagtaaagctccttgtatcaacttcttagtaccatttcgttgttttgatctttgtggtaatcctttggttttgattttgcagCTTGCAAGGCTAGAGGATCCGATCTTAGGGTTCACTTCAAG
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gtaggtttcattagtaatcacttttttgtgtttgtagaatcgacacttattctctaaacgacgacgtttataatctctctcaatctgagcatttttttaatcgtctttcatatgcagCTTGCAAGGCTAGAGGCGCCGACCTTAGGGTTCATTTTAAG
upper sequence: AT1G67430.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ26852 (Selaginella moellendorffii), 3'ss of exon 1
gtaagtaaagctccttgtatcaacttcttagtaccatttcgttgttttgatctttgtggtaatcctttggttttgattttgcagCTTGCAAGGCTAGAGGATCCGATCTTAGGGTTCACTTCAAG
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--------------gtgagtgaaattcgcaa-gcgctctcgttgacctcagcttgga---------------ttgatc--gcagCTTGCAAGGCGAGAGGCTCCGATCTCCGGGTCCACTTCAAG
upper sequence: AT1G67430.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ21308 (Selaginella moellendorffii), 3'ss of exon 1
gtaagtaaagctccttgtatcaacttcttagtaccatttcgttgttttgatctttgtggtaatcctttggttttgattttgcagCTTGCAAGGCTAGAGGATCCGATCTTAGGGTTCACTTCAAG
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--------------gtgagtgaaattcgcaa-gcgctctcgttg-----acctctgc---------ttggattga---tcgcagCTTGCAAGGCGAGAGGCTCCGATCTCCGGGTCCACTTCAAGMapped 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|152035881|gb|BP863620.2|BP863620EST: GTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGT CTTGCAAGGCTAGAGGATCCGATCTTAGGGTTCACTTCAAG
genomic: GTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGTgtaagtaaag ... gattttgcagCTTGCAAGGCTAGAGGATCCGATCTTAGGGTTCACTTCAAG
EST:
gi|125021887|gb|EL094156.1|EL094156EST: GTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGT CTTGCAAGGCTAGAGGATCCGATCTTAGGGTTCACTTCAAGAATAC
genomic: GTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGTgtaagtaaag ... gattttgcagCTTGCAAGGCTAGAGGATCCGATCTTAGGGTTCACTTCAAGAATAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtaccatttcgttgttttgatctttgtggtaatcctttggttttgattttgcagCTTGCAAGGCTAGAGGATCCGATCTTAGGGTTCACTTCAAG
ttttgat putative branch site (score: 4)
ttttgatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtaaagctccttgtatcaacttcttagtaccatttcgttgttttgatctttgtggtaatcctttggttttgattttgcagCTTGCAAGGCTAGAGGATCCGATCTTAGGGTTCACTTCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT