Sequence
atgc intronic sequence ATGC exonic sequencegtattatttgatatatgtgtatgctacctttttgcttttgaactgtgtttggtagaagagccaatattttgtttatttctttgacagCTATCTGTTGAAAGACTGAGTTCCATGAAGAAATATGTTTTTGGATTAGGCTCAGCTCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G01790.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G01790.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA07G08030.1 (Glycine max), 3'ss of exon 4
gtattatttgatatatgtgtatgctacctttttgcttttgaactgtgtttggtagaa---gagccaatattttgtttatttctttgacagCTATCTGTTGAAAGACTGAGTTCCATGAAGAAATATGTTTTTGGATTAGGCTCAGCTCAG
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gtggagcttcctataagatcttgttctgccttagctttgatcatctctgtagtaagaaataaactgaagctctgaactgtatttttatagCTCTCTGTTGAAAGGCTTAGTTCAATGAAGAAATATGTCTTTGGATTAGGCTCTGCTCAG
upper sequence: AT1G01790.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA09G39770.1 (Glycine max), 3'ss of exon 8
----------gtatta--tttgatatatgtgt---atgctacctttttgcttttgaactgtgtttggtagaagagccaatattttgtttatttctttgac--agCTATCTGTTGAAAGACTGAGTTCCATGAAGAAATATGTTTTTGGATTAGGCTCAGCTCAG
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gtggggattcctattagttctggttcagttgttctatgttaactttgtccatcaccattatctaaggagctgaattgaggctcttatttgctttgttgttttagCTCTCTGTTGAAAGGCTTAGTTCAATGAAGAAATATGTCTTTGGATTAGGCTCTGCACAG
upper sequence: AT1G01790.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA18G46420.1 (Glycine max), 3'ss of exon 12
----------gtatta--tttgatatatgtgt---atgctacctttttgcttttgaactgtgtttggtagaagagccaatattttgtttatttctttgac--agCTATCTGTTGAAAGACTGAGTTCCATGAAGAAATATGTTTTTGGATTAGGCTCAGCTCAG
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gtggggattcttattagttctggttcagttgttctatgttaactttgtccatcaccattatcgaaagagctaaattgaggctcttatttgcttttttgttttagCTCTCGGTTGAAAGGCTTAGTTCAATGAAGAAATATGTCTTTGGATTTGGCTCTGCACAG
upper sequence: AT1G01790.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv15s0046g03390.t01 (Vitis vinifera), 3'ss of exon 3
----------------------gtattatttgatatatgtgtatgctacctttttgcttttgaactgtgtttggtagaagagccaatattttgtttatttctttgacagCTATCTGTTGAAAGACTGAGTTCCATGAAGAAATATGTTTTTGGATTAGGCTCAGCTCAG
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gtggactccataaaatctttatttctttttttatttgttaatctaagacaatgatgttctttataaatgaataaaaaaaaaattgaaccttc---tgtctgcattgcagCTATCTGTTGAAAGGCTGAGTTCCATGAAGAAATATGTTTTTGGATTGGGCACTGCTCAG
upper sequence: AT1G01790.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S2_217V6.1 (Physcomitrella patens), 3'ss of exon 7
----------gtattatttgatatatgtgtatgctacctttttgcttttga-actgtgtttggtagaagagccaatatt---ttgtttatttctttgacagCTATCTGTTGAAAGACTGAGTTCCATGAAGAAATATGTTTTTGGATTAGGCTCAGCTCAG
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tctgattgctttgcaagtcttttttgttttatgtttccaatttttttatgataccacaataaggggattgacctctgttcgatcggttgtatttttg-cagTTGTCGGTGGAGAGACTGAGCTCCATGAAGAAGTATGTATTTGGATTTGGCTCAGCTCAGMapped 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|164010817|gb|ES076347.1|ES076347EST: CCATCGCAGAATTTGGAGTAGTTTTCTTGCTTTTCAACATCGGCCTTGAG CTATCTGTTGAAAGACTGTAGTTCCAT
genomic: CCATCGCAGAATTTGGAGTAGTTTTCTTGCTTTTCAACATCGGCCTTGAGgtattatttg ... tctttgacagCTATCTGTTGAAAGACTG-AGTTCCAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcttttgaactgtgtttggtagaagagccaatattttgtttatttctttgacagCTATCTGTTGAAAGACTGAGTTCCATGAAGAAATATGTTTTTGGATTAGGCTCAGCTCAG
ttttgtttatttcttt CT-rich tract
aatattttgtttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattatttgatatatgtgtatgctacctttttgcttttgaactgtgtttggtagaagagccaatattttgtttatttctttgacagCTATCTGTTGAAAGACTGAGTTCCATGAAGAAATATGTTTTTGGATTAGGCTCAGCTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA