Sequence
atgc intronic sequence ATGC exonic sequencegtacaatcctcctttcatttcagttcattcaacgaaaagaagattctaccggtaacatttttgtggctccatgaattgttttagGCCTGATTGTGGATACGGTTGTAATGAACCCTCCATTTGGTACACGGAAGAAAGGAGCTGACATGGAGTTTCTCTCTGCGGCAATGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G28830.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G28830.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G113640_T05 (Zea mays), 3'ss of exon 5
-gtacaatcctcctttcatttcagttcattcaacgaaaagaaga-ttctaccggtaac---atttt----tgtggctccatgaa-------ttgttttagGCCTGATTGTGGATACGGTTGTAATGAACCCTCCATTTGGTACACGGAAGAAAGGAGCTGACATGGAGTTTCTCTCTGCGGCAATGAAG-----------
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gaaacagcgtcacacagagcaaatggaacacttctaaaagcattcttcttcccctaattgaactttaccttgtggctgaatagaaagcaatttagtgcagGCGTCCATGTTGATACTGTTGTCATGAATCCTCCCTTTGGTACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGCAGGTCAGAACCGG
upper sequence: AT4G28830.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G113640_T03 (Zea mays), 3'ss of exon 4
-gtacaatcctcctttcatttcagttcattcaacgaaaag-aagattctaccggtaac---atttt----tgtggctccatgaa-------ttgttttagGCCTGATTGTGGATACGGTTGTAATGAACCCTCCATTTGGTACACGGAAGAAAGGAGCTGACATGGAGTTTCTCTCTGCGGCAATGAAG
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gaaacagcgtcacacagagcaaatggaacacttctaaaagcattcttcttcccctaattgaactttaccttgtggctgaatagaaagcaatttagtgcagGCGTCCATGTTGATACTGTTGTCATGAATCCTCCCTTTGGTACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGCAG
upper sequence: AT4G28830.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA01G34690.3 (Glycine max), 3'ss of exon 5
-----------gtacaatcct--cctttcatttcag--ttcattcaacgaaaagaagattctaccggtaacatttttgtggctccatgaattgttt-tagGCCTGATTGTGGATACGGTTGTAATGAACCCTCCATTTGGTACACGGAAGAAAGGAGCTGACATGGAGTTTCTCTCTGCGGCAATGAAG
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agctggctgaaaatcaattctaagttctaactctagattttatatgttgttgaaatttttctataacaaactcgtatgattatctgggtattgtctctagGTCGAATTGTTGATACAGTTATAATGAATCCTCCATTTGGTACTCGGAAAAAAGGTGCAGATTTGGATTTTCTCTCCGTTGCTTTGAAG
upper sequence: AT4G28830.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv11s0016g03520.t01 (Vitis vinifera), 3'ss of exon 5
-----gtacaatcctcctttcatttcagttcattcaacgaaaa-----gaagat-tctaccggtaacatttttgtggctccatga--attgttt---tagGCCTGATTGTGGATACGGTTGTAATGAACCCTCCATTTGGTACACGGAAGAAAGGAGCTGACATGGAGTTTCTCTCTGCGGCAATGAAG
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taattgtatatatgttctctgtatacatgctcttcaacatatattactgcacttgtcttttaattttatgtccatgtaacaatgattatctcttatgtagGTCAAATTGTTGATACTGTTGTAATGAATCCTCCATTTGGAACACGGAAGAAGGGGGCTGACATGGATTTTCTCGCTGTGGCTTTGAAGMapped 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|19874619|gb|AU235450.1|AU235450EST: GTCGAGATAGATTTCGTTCAGTGTGACATCACAAAGCTAGAGTTAAAAG GCCTGATTGTGGATACGGTTGTAATGAACCCTCCATTTGGTACACGGAAGA
genomic: GTCGAGATAGATTTCGTTCAGTGTGACATCACAAAGCTAGAGTTAAAAGgtacaatcct ... attgttttagGCCTGATTGTGGATACGGTTGTAATGAACCCTCCATTTGGTACACGGAAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caacgaaaagaagattctaccggtaacatttttgtggctccatgaattgttttagGCCTGATTGTGGATACGGTTGTAATGAACCCTCCATTTGGTACACGGAAGAAAGGAGCTGACATGGAGTTTCTCTCTGCGGCAATGAAG
cggtaac putative branch site (score: 3)
ttgtttt putative PPT
taacattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacaatcctcctttcatttcagttcattcaacgaaaagaagattctaccggtaacatttttgtggctccatgaattgttttagGCCTGATTGTGGATACGGTTGTAATGAACCCTCCATTTGGTACACGGAAGAAAGGAGCTGACATGGAGTTTCTCTCTGCGGCAATGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA