Sequence
atgc intronic sequence ATGC exonic sequencegtaaataacaacatttcttcttcttcttcgtgtacccgcaaatatgacgaaaatcagcaaactcatatgttcttttattttctgatgttgtacagTTCCTCCAGCGTATTATGCTCATCTTGCAGCATTTCGAGCACGTTTCTACCTGGAACCGGAGATAATGCAAGACAACGGATCACCGGGTAAAAAGAACAC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G43810.2 |
intron # | 20 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA10G38770.1 (Glycine max), 3'ss of exon 21
-------------------------------------------------------------------------------------gtaaataacaac-atttcttcttcttcttcgtgtacccgcaaatatgacgaaaatcagcaaactcatatgttcttttatt---ttctgatgttgtacagTTCCTCCAGCGTATTATGCTCATCTTGCAGCATTTCGAGCACGTTTCTACCTGGAACCGGAGATAATGCAAGACAACGGATCACCGGGTAAAAAGAACAC---
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gtaagcccgtgcttcaattaatatgtagtttttcggttgtttggtcccagttatgactcacccatgtccttaccctcaacactagttgaacagctatgatatttttaacatgattgaactttaacctttat-acttgtcttggatagtttaaaacttaattgactggaaattgttgttatgcagTTCCTCCAGCATATTATGCACATTTAGCAGCGTTTCGAGCACGTTTCTATATGGAACCAGATAT---GCAAGACAATGGCTCTGCAGGTGACGGTAATGGTCA
upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA10G00530.1 (Glycine max), 3'ss of exon 12
------gtaaataacaacatttcttcttcttcttcgtgtacccgcaaatatgacgaaaatcagcaaactcatatgttcttttattttctgatgttgtacagTTCCTCCAGCGTATTATGCTCATCTTGCAGCATTTCGAGCACGTTTCTACCTGGAACCGGAGATAATGCAAGACAACGGATCACCGGGTAAAAAGAACAC
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tctatattttatatttatatctttatatcatatttgtcatgattgaggtttcagcttgttttgcaaaat-ataaatcttaatggacttcattcatgtgcagTTCCTCCAGCGTATTACGCACATTTAGCAGCTTTTCGAGCACGTTTCTATATGGAGCCAGACCTGCAGCAGGAGAATGGCTCCTCAGGTGGTGGCTCCAG
upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA20G28970.1 (Glycine max), 3'ss of exon 21
------------------------------------------------------------------------------------gtaaataacaacatttcttcttcttcttcgt-gtacccgcaaatatg---acgaaaatcagcaaactcatatgttcttttatttt---ctgatgttgtacagTTCCTCCAGCGTATTATGCTCATCTTGCAGCATTTCGAGCACGTTTCTACCTGGAACCGGAGATAATGCAAGACAACGGATCACCGGGTAAAAAGAACAC---
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gtaagcctgtgcttcaattaatatgttgtttttcagttgtttggtcccagttatgactcaccatgtccttaccctcaagactagttgaacagctatgctattttaatgacatggttgaacttttaaccctttatacttgtcttggatagtttaaaacttaattgactggaaattgttgttgtgcagTTCCTCCAGCATATTATGCACATTTAGCAGCGTTCCGAGCACGTTTCTATATGGAGCCAGATAT---GCAAGACAATGGCTCTGCAGGTGATGGCAATGGTTA
upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA02G00510.1 (Glycine max), 3'ss of exon 20
----------gtaaataacaacatttcttcttcttcttcgtgtacccgcaaatatgacgaaaatcagcaaactcatatgttcttttattttctgatgttgtacagTTCCTCCAGCGTATTATGCTCATCTTGCAGCATTTCGAGCACGTTTCTACCTGGAACCGGAGATAATGCAAGACAACGGATCACCGGGTAAAAAGAACAC
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tgaacacaaaggggacaaagggaaacaaattactt--taatgtactattctatattatctatatttgt---ttcttacaacttagtggacttaattcatgtgcagTTCCTCCAGCGTATTATGCACATTTGGCAGCTTTTCGAGCGCGGTTCTATATGGAGCCAGACCTGCAGCAGGAGAATGGCTCCTCAGGTGGTGGCTCCAA
upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: Vv05s0020g04190.t01 (Vitis vinifera), 3'ss of exon 18
----gtaaataacaacatttc--ttcttcttcttcgtgtac-ccgcaaatatga-cgaaaatcagcaaactcatatgttcttttattttctgatgttgtacagTTCCTCCAGCGTATTATGCTCATCTTGCAGCATTTCGAGCACGTTTCTACCTGGAACCGGAGATAATGCAAGACAACGGATCACCGGGTAAAAAGAACAC
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tcctttgaagttctttgttcaaattgtcctccttgaggagctccatcattttgttctatgagctgcaa-ctgaaatag--ctaaatccatggctcatttgcagTTCCTCCAGCATATTATGCACATTTAGCAGCATTTCGAGCCCGATTCTACATGGAGCCTGACA---TGCAGGAGAATGGTTCAAATGGAGGTGGCAGTG-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|125141945|gb|EL179446.1|EL179446EST: TGCGCGGTGCACTCGGTCGGTCTCTATAG TTCCTCCAGCGTATTATGCTCATCTTGCAGCATTTCGAGCACGTTTCTACC
genomic: TGCGCGGTGCACTCGGTCGGTCTCTATAGgtaaataaca ... tgttgtacagTTCCTCCAGCGTATTATGCTCATCTTGCAGCATTTCGAGCACGTTTCTACC
EST:
gi|164226000|gb|EL986636.1|EL986636EST: GGTCTCTATAG TTCCTCCAGCGTATTATGCTCATCTTGCAGCATTTCGAGCACGTTTCTACC
genomic: GGTCTCTATAGgtaaataaca ... tgttgtacagTTCCTCCAGCGTATTATGCTCATCTTGCAGCATTTCGAGCACGTTTCTACC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatatgacgaaaatcagcaaactcatatgttcttttattttctgatgttgtacagTTCCTCCAGCGTATTATGCTCATCTTGCAGCATTTCGAGCACGTTTCTACCTGGAACCGGAGATAATGCAAGACAACGGATCACCGGGTAAAAAGAACAC
ttctgat putative branch site (score: 3)
atatgttcttttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaataacaacatttcttcttcttcttcgtgtacccgcaaatatgacgaaaatcagcaaactcatatgttcttttattttctgatgttgtacagTTCCTCCAGCGTATTATGCTCATCTTGCAGCATTTCGAGCACGTTTCTACCTGGAACCGGAGATAATGCAAGACAACGGATCACCGGGTAAAAAGAACAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC