Sequence
atgc intronic sequence ATGC exonic sequencegtaaaggaaaacaactaaatcaatttttaactgttgaaagtagttggagatgtttgaggtctttagtcctaaaacttgtgttgtttgtgttgtatttcttacagAGTCCAGATGGTTGTACCGTAGCTTCAGCAGCAGGAGATGAGACTCTGAGGTTCTGGAATGTTTTTGGAGTACCAGAGACCGCCAAAAAAGCTGCTCCAA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G33270.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G33270.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os02g47180.2 (Oryza sativa), 3'ss of exon 4
gtaaaggaaaacaactaaatcaatttttaactgttgaaagtagttggagatgtttgaggtctttagtcctaaaacttg-tgttgtttgtgttgtattt--cttacagAGTCCAGATGGTTGTACCGTAGCTTCAGCAGCAGGAGATGAGACTCTGAGGTTCTGGAATGTTTTTGGAGTACCAGAGACCGCCAAAAAAGCTGCTCCAA
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------------------gtgagtttcttcttgattagtagttttgcagtcactgcctataagttaatctgttatttgctgatcgtcttactgtgattgaactacagAGTCCTGATGGTTGCACAGTAGCATCGGCTGCTGCAGATGAGACCCTGCGGTTCTGGAATGTGTTTGGTAGTCCTGAAGCCCCCAAGCCTGCAGCCAAGG
upper sequence: AT4G33270.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G01450.1 (Glycine max), 3'ss of exon 3
gtaaaggaaaacaactaaatcaatttttaactgttgaaagtagttggagatgtttgaggtctttagtcctaaaacttgtgttgtt---tgtgttgt--atttcttacagAGTCCAGATGGTTGTACCGTAGCTTCAGCAGCAGGAGATGAGACTCTGAGGTTCTGGAATGTTTTTGGAGTACCAGAGACCGCCAAAAAAGCTGCTCCAA
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-------------------gtaattttt---tctcgagcacaaacctgattgatttgattgtcttattatgaggcttttcctgattagtgtgatgtcaacttccttcagAGTCCAGATGGTTGCACAGTAGCATCAGCAGCAGCAGATGAAACATTGAGGTTCTGGAATGTGTTTGGAGCTCCAGAAGCAGCATCTAAGGCTGCACCGA
upper sequence: AT4G33270.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv05s0102g00640.t01 (Vitis vinifera), 3'ss of exon 3
gtaaaggaaaacaactaaatcaatttttaactgttgaaagtagttggagatgtttgaggtctttagtcctaaaacttgtgttgtttgtgttgtatttcttacagAGTCCAGATGGTTGTACCGTAGCTTCAGCAGCAGGAGATGAGACTCTGAGGTTCTGGAATGTTTTTGGAGTACCAGAGACCGCCAAAAAAGCTGCTCCAA---
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----------gtaataaaatggaccttagtttagtgaatgtttctga----gtaccaaatcttta----tatgttctaatattcttgatcaactcatttggcagAGTCCAGATGGGCGTACAGTGGCAACTGCTGCAGGAGATGAGACTCTCAAGTTCTGGAATGCTTTTGGCACGCCAGAA---GTGAAAAAGGCTGCACCAAAAG
upper sequence: AT4G33270.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv05s0102g00680.t01 (Vitis vinifera), 3'ss of exon 3
gtaaaggaaaacaactaaatcaatttttaactgttgaaagtagttggagatgtttgaggtctttagtcctaaaacttgtgttgtttgtgttgtatttcttacagAGTCCAGATGGTTGTACCGTAGCTTCAGCAGCAGGAGATGAGACTCTGAGGTTCTGGAATGTTTTTGGAGTACCAGAGACCGCCAAAAAAGCTGCTCCAA---
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----------gtaataaaatggaccttagtttagtgaatgtttttga----gtagcaaatcttta----tatgttctaatattcttgatcaactcatttggcagAGTCCAGATGGGCGTATAGTGGCAACTGCTGCAGGAGATGAGACTCTCAAGTTCTGGAATGCTTTTGGCACGCCAGAA---GTGAAAAAGGCTGCACCAAAAGMapped 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|19877894|gb|AU238725.1|AU238725EST: AAATGGCTGAGCTCACTGGTCATACATCAAGAGTTCTATATATGGCCCAG AGTCCAGATGGTTGTACCGTAGCTTCAGCAGCAG
genomic: AAATGGCTGAGCTCACTGGTCATACATCAAGAGTTCTATATATGGCCCAGgtaaaggaaa ... tttcttacagAGTCCAGATGGTTGTACCGTAGCTTCAGCAGCAG
EST:
gi|164060315|gb|EL998839.1|EL998839EST: AATGGCTGAGCTCACTGGTCATACATCAAGAGTTCTATATATGGCCCAG AGTCCAGATGGTTGTACTGTAGCTTCAGCAGCAG
genomic: AATGGCTGAGCTCACTGGTCATACATCAAGAGTTCTATATATGGCCCAGgtaaaggaaa ... tttcttacagAGTCCAGATGGTTGTACCGTAGCTTCAGCAGCAG
EST:
gi|164014960|gb|ES190195.1|ES190195EST: ATACATCAAGAGTTCTATATATGG-CCAG AGTCCAGATGGTTGTACCGTAGCTTCAGCAGCAGGAGATGAGACTCTGAGG
genomic: ATACATCAAGAGTTCTATATATGGCCCAGgtaaaggaaa ... tttcttacagAGTCCAGATGGTTGTACCGTAGCTTCAGCAGCAGGAGATGAGACTCTGAGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgtttgaggtctttagtcctaaaacttgtgttgtttgtgttgtatttcttacagAGTCCAGATGGTTGTACCGTAGCTTCAGCAGCAGGAGATGAGACTCTGAGGTTCTGGAATGTTTTTGGAGTACCAGAGACCGCCAAAAAAGCTGCTCCAA
tcctaaa putative branch site (score: 2)
tatttctt putative PPT
tatttctta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaggaaaacaactaaatcaatttttaactgttgaaagtagttggagatgtttgaggtctttagtcctaaaacttgtgttgtttgtgttgtatttcttacagAGTCCAGATGGTTGTACCGTAGCTTCAGCAGCAGGAGATGAGACTCTGAGGTTCTGGAATGTTTTTGGAGTACCAGAGACCGCCAAAAAAGCTGCTCCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT