Sequence
atgc intronic sequence ATGC exonic sequencegcaagttccttagaagttttaaatttgaaaccgtttagttttctttaaaattatgctcttcttgagatgtaagaacaacataaacattgtgagacgatatgtagGTTGTATGCAATGCAAACAAGCTGGCCGATTTGGTGAAAAAGAAGAAAAAGCTGCAGAATTGGCTTGATTACTACCAGCTCAAATACGCTAGGAATAACT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G22120.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G22120.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os05g51630.2 (Oryza sativa), 3'ss of exon 4
gcaagttccttagaagttttaaatttgaaaccgtttagttttctttaaaattatgctcttcttgagatgtaagaacaacataaacattgtgagacgatatgtagGTTGTATGCAATGCAAACAAGCTGGCCGATTTGGTGAAAAAGAAGAAAAAGCTGCAGAATTGGCTTGATTACTACCAGCTCAAATACGCTAGGAATAACT
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ttgggttttctaccctgacttcatt--gatttttttattcttccttatactaattactgtatttattccgtcctttttctggccgattgtctat--atctatagGTGGTTTACAATGCAAATAAACTTGCTGATCTGGTTGAGAAGAAGAAGAAACTGCAAAATTGGCTTGATTACTACCAGCTCAAGTATGAAAGAAATCCAT
upper sequence: AT4G22120.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os01g35050.3 (Oryza sativa), 3'ss of exon 5
gcaagttccttagaagttttaaatttgaaaccgtttagttttctttaaaattatgctcttcttgagatgtaagaacaacataaacattgtgagacgatatgtagGTTGTATGCAATGCAAACAAGCTGGCCGATTTGGTGAAAAAGAAGAAAAAGCTGCAGAATTGGCTTGATTACTACCAGCTCAAATACGCTAGGAATAACT
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-ttagttttaactgcttatcgttactaaaaaaaaaaaatctatgctctgat-atggcttaccactaccatgttcttatcattcatttcatggactggtat--agGTTGTCTATAATGCAAATAAGCTTGATAAGATGGTCAAAGAGAAGAAGAAAATGCAGAATTGGCTTGATTACTATCAGCTGAAATATGAAAGAAATACAT
upper sequence: AT4G22120.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G01400.1 (Glycine max), 3'ss of exon 4
gcaagttccttagaagttttaaatttgaaaccgtttagtttt---ctttaaaattatgctcttcttga-gatgtaagaaca-acataaacattgtgagacgatatgtagGTTGTATGCAATGCAAACAAGCTGGCCGATTTGGTGAAAAAGAAGAAAAAGCTGCAGAATTGGCTTGATTACTACCAGCTCAAATACGCTAGGAATAACT----
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-----ttattgcgacaatgtcattttt---ccctttcatttgggactttgaggggggggggggggggataatgtttcagcatattttattgttgtgacatta-atgcagGTTGTTTATAATGCAAACAAACTTGCAAAGTTGGTTAAAAAGAAGAAGAAGTTGCAGAATTGGCTTGTATATTATCA----AAACAAAGTTGAAAGAACTTCAG
upper sequence: AT4G22120.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA07G39320.1 (Glycine max), 3'ss of exon 5
gcaagttccttagaagttttaaatttgaaaccgtttagttttctttaaaattatgctcttcttgagatgtaagaacaacataaacattgtgagacgatatgtagGTTGTATGCAATGCAAACAAGCTGGCCGATTTGGTGAAAAAGAAGAAAAAGCTGCAGAATTGGCTTGATTACTACCAGCTCAAATACGCTAGGAATAACT----
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---gatctatctattattacgacaatgtaattttcccctttcatttgggactttgagaggggggaaataatgtttcagcatatttattgtgacatta-atgcagGTTGTTTATAATGCAAACAAACTTGCAAAGTTGGTTAAAAAGAAGAAGAAGTTGCAGAATTGGCTTGTATATTATCA----AAACAAAGTTGAAAGAACTTCAGMapped 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|116414733|gb|EG457325.1|EG457325EST: TTTTTTCCTGGTCAATCATCCTGATCACTACCTAACACATCAG GTTGTATGCAATGCAAACAAGCTGGCCGATTTGGTGAAAAAGAAGAAAAAG
genomic: TTTTTTCCTGGTCAATCATCCTGATCACTACCTAACACATCAGgcaagttcct ... cgatatgtagGTTGTATGCAATGCAAACAAGCTGGCCGATTTGGTGAAAAAGAAGAAAAAG
EST:
gi|164007091|gb|ES076324.1|ES076324EST: CTGGTCAATCATCCTGATCACTACCTGACACATCAG GTTGTATGCAATGCAAACAAGC
genomic: CTGGTCAATCATCCTGATCACTACCTAACACATCAGgcaagttcct ... cgatatgtagGTTGTATGCAATGCAAACAAGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attatgctcttcttgagatgtaagaacaacataaacattgtgagacgatatgtagGTTGTATGCAATGCAAACAAGCTGGCCGATTTGGTGAAAAAGAAGAAAAAGCTGCAGAATTGGCTTGATTACTACCAGCTCAAATACGCTAGGAATAACT
ataaacatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcaagttccttagaagttttaaatttgaaaccgtttagttttctttaaaattatgctcttcttgagatgtaagaacaacataaacattgtgagacgatatgtagGTTGTATGCAATGCAAACAAGCTGGCCGATTTGGTGAAAAAGAAGAAAAAGCTGCAGAATTGGCTTGATTACTACCAGCTCAAATACGCTAGGAATAACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA