Sequence
atgc intronic sequence ATGC exonic sequencegtgacatgtccatctctgtagataagatcactgtttttattcagccaatttataatctctttttgtttccttatattttgatccatagACTCTTCGTAGGCTTGCTCAAAACCGTGAGGCAGCAAGGAAAAGCAGATTGAGGAAGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G06950.3 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G06950.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os07g48820.2 (Oryza sativa), 3'ss of exon 4
gtgacatgtccatctc-tgtagataagatcactgtttttattcagccaattta--taatctctttttgtttccttatattttgatccatagACTCTTCGTAGGCTTGCTCAAAACCGTGAGGCAGCAAGGAAAAGCAGATTGAGGAAGAAG
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gtgacattttagttccgtttcttttcgtatacaatgtcacttaatcttgtgtgattaatttcatattgtattttggcatg-----caatagACAATTCGGCGGCTTGCTCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAG
upper sequence: AT5G06950.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G174284_T01 (Zea mays), 3'ss of exon 4
---gtgacatgtc-catctctgtagataagatcactgtttttattcagccaatttataatctctttttgtttccttatattttgatccatagACTCTTCGTAGGCTTGCTCAAAACCGTGAGGCAGCAAGGAAAAGCAGATTGAGGAAGAAG
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gtttttttatctcatatgtcttctgtactctttagtgtttgttaccatttcaca-atgatggaatctagataatgcatttgatattctttagGTTTTACGACGGCTTGCCCAAAATCGTGAGGCAGCAAGGAAAAGTCGGCTGAGGAAAAAG
upper sequence: AT5G06950.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA20G39050.2 (Glycine max), 3'ss of exon 4
--gtgacatgtccatctc--tgtagataagatca--ctgtttttattcag----ccaatttataatctctttttgtttccttatattttgatc--catagACTCTTCGTAGGCTTGCTCAAAACCGTGAGGCAGCAAGGAAAAGCAGATTGAGGAAGAAG
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aaaacaaatgtttactctattttaaatttggttatgcggttaatatctaaaattttaaatggtatttgttacgtgattattgattttttaattattgcagACTCTCCGAAGGCTTGCTCAGAATCGTGAGGCAGCAAGAAAAAGTCGGTTGAGAAAGAAA
upper sequence: AT5G06950.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv13s0084g00660.t01 (Vitis vinifera), 3'ss of exon 6
------gtgacatgtccatctctgtagataagatcactgtttttattcagccaatttataatctctttttgtttccttatattttgatccatagACTCTTCGTAGGCTTGCTCAAAACCGTGAGGCAGCAAGGAAAAGCAGATTGAGGAAGAAG
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gtcatatagatcaaactaattgcgtgtatatcatctcaactga-atgcagt-aacatttgatgatcttttgtttgtttgtattt-----cacagACTCTTCGTAGGCTTGCTCAAAATCGTGAAGCTGCACGAAAAAGCCGATTGAGAAAGAAAMapped 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|125190194|gb|EL205148.1|EL205148EST: CTGCTGCTTCTGATTCGAGTGACCGATCGAAGGGAAAGATGGATCAAAAG ACTCTTCGTAGGCTTGCTCAAAA
genomic: CTGCTGCTTCTGATTCGAGTGACCGATCGAAGGGAAAGATGGATCAAAAGgtgacatgtc ... tgatccatagACTCTTCGTAGGCTTGCTCAAAA
EST:
gi|19877697|gb|AU238528.1|AU238528EST: CTGCTGCTTCTGATTCGAGTGACCGATCGAAGGGAAAGATGGATCAAAAG ACTCTTCGTAGGCTTGCTCAAAACCGTGAGGCAGCAAGGAAAAGCAGATTG
genomic: CTGCTGCTTCTGATTCGAGTGACCGATCGAAGGGAAAGATGGATCAAAAGgtgacatgtc ... tgatccatagACTCTTCGTAGGCTTGCTCAAAACCGTGAGGCAGCAAGGAAAAGCAGATTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttattcagccaatttataatctctttttgtttccttatattttgatccatagACTCTTCGTAGGCTTGCTCAAAACCGTGAGGCAGCAAGGAAAAGCAGATTGAGGAAGAAG
ttttgat putative branch site (score: 4)
tctctttttgtttcct CT-rich tract
aatttataatctcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgacatgtccatctctgtagataagatcactgtttttattcagccaatttataatctctttttgtttccttatattttgatccatagACTCTTCGTAGGCTTGCTCAAAACCGTGAGGCAGCAAGGAAAAGCAGATTGAGGAAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG