Sequence
atgc intronic sequence ATGC exonic sequencegtaagtcctatttgctcaatgtagatgatattttagatacataatgaacctacttatgttatcttcacaagaagacaatggtgagagctaaagagtaaactttctgatcaatttggtgagaatatagatttttttttgtataacagcaagacgagtaaactgttgtttgaatgaatggcatagGTTGCAGAATATTTCGATGCAGTCATTGGTAAGGGTGCTGAAGTGAAGTTGGCAGCAAATTGGATAATGAGTGATATTGCTGCTTACTTGAAAAATGAGA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G48520.3 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G48520.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G05190.2 (Glycine max), 3'ss of exon 4
gtaagtcctatttgctcaatgtagatgatattttagatacataatgaacctacttatgttatcttcacaagaagacaatggtgagagctaaagagtaaactttctgatcaatttggtgagaatatagatttttttttgtataacagcaagacgagtaaactgttgtttgaatgaatggcatagGTTGCAGAATATTTCGATGCAGTCATTGGTAAGGGTGCTGAAGTGAAGTTGGCAGCAAATTGGATAATGAGTGATATTGCTGCTTACTTGAAAAATGAGA
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--------------------------------------------------------------------------agaacagtacatattagaaagctaaat---------agtagatgtcaatataaagtgtattagcacaaatgatctaacatgaattttattttctggatcgatgtattagATTGCAGAATTTTTTGATGCAACTCTTGCAAAAGGTGCTGACTCAAAGCTGGTTGCCAACTGGATAATGAGTGATATTGCTGCCTTCATGAAAAATGAAA
upper sequence: AT1G48520.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA05G34500.1 (Glycine max), 3'ss of exon 4
gtaagtcctatttgctcaatgtagatgatattttagatacataatgaacctacttatgttatcttcacaagaagacaatggtgagagctaaagagtaaactttctgatcaatttggtgagaatatagatttttttttgtataacagcaagacgagtaaactgttgtttgaatgaatggcatagGTTGCAGAATATTTCGATGCAGTCATTGGTAAGGGTGCTGAAGTGAAGTTGGCAGCAAATTGGATAATGAGTGATATTGCTGCTTACTTGAAAAATGAGA
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--------------------------------------------------------------------------agaacagtacatattagaaagctaaat---------agtagatgtcaatataaagtgtattaccacaaatggtctaatgcgatttttattttctgaatcgatgtattagATTGCAGATTTTTTTGATGCAACTCTTGCAAAAGGTGCTGACCCAAAGCTGGTTGCCAACTGGATAATGAGTGATATTGCTGCCTTCATGAAAAATGAAA
upper sequence: AT1G48520.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv05s0049g02140.t01 (Vitis vinifera), 3'ss of exon 5
gtaagtcctatttgctcaatgtagatgatattttagatacataatgaacctacttatgttatcttcacaagaagacaatggtgagagctaaagagtaaactttctgatcaatttggtgagaatatagatttttttttgtataacagcaagac-gagtaaactgttgtttgaatgaatggcatagGTTGCAGAATATTTCGATGCAGTCATTGGTAAGGGTGCTGAAGTGAAGTTGGCAGCAAATTGGATAATGAGTGATATTGCTGCTTACTTGAAAAATGAGA
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------------------------------------------------------------------------------ctatgcttgccttaccct--acctttggttc--ttcagtattttcttcaaacaattctcatgc--ttgaaagactgatttttcctcttgctggatgaatgattcagGTTGCAGGTTTTTTTGATGCAACTATTGGAAAGGGTGCTGATGTGAAGCTGGCTGCCAATTGGATAATGGGTGATATTGCTGCCTACATGAAAAATGAAAMapped 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|124822997|gb|EH907863.1|EH907863EST: GTGCTTTTCCTCGCGAATGACGTCAGT GTTGCAGAATATTTCGATGCAGTCATTGGTAAGGGTG
genomic: GTGCTTTTCCTCGCGAATGACGTCAGTgtaagtccta ... aatggcatagGTTGCAGAATATTTCGATGCAGTCATTGGTAAGGGTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttttttgtataacagcaagacgagtaaactgttgtttgaatgaatggcatagGTTGCAGAATATTTCGATGCAGTCATTGGTAAGGGTGCTGAAGTGAAGTTGGCAGCAAATTGGATAATGAGTGATATTGCTGCTTACTTGAAAAATGAGA
gtataac putative branch site (score: 3)
ttttgtataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtcctatttgctcaatgtagatgatattttagatacataatgaacctacttatgttatcttcacaagaagacaatggtgagagctaaagagtaaactttctgatcaatttggtgagaatatagatttttttttgtataacagcaagacgagtaaactgttgtttgaatgaatggcatagGTTGCAGAATATTTCGATGCAGTCATTGGTAAGGGTGCTGAAGTGAAGTTGGCAGCAAATTGGATAATGAGTGATATTGCTGCTTACTTGAAAAATGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT