Sequence
atgc intronic sequence ATGC exonic sequencegtccgttctgttcttgttccatctctactgtgctatcctttcatttgaactattcgttttgtatctctttatttgttctttttttaataataagatatctagatggataataagactaagaggtgattccataccccttgtacagGATTTTGGAATCAAATACAATATGGAAAATGGAGGACCTGCTCCTGAATCAATCACTGATAAAATTTACGAGAACACTAAGACAATCAAGGAGTACCCAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G23190.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G23190.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os03g50480.1 (Oryza sativa), 3'ss of exon 5
gtccgttctgttcttgttccatctctactgtgctatcctttcatttgaactattcgttttgtatctct-ttatt-tgttctttttttaataataagatatctagatggataataagactaagaggtgattccataccccttgtacagGATTTTGGAATCAAATACAATATGGAAAATGGAGGACCTGCTCCTGAATCAATCACTGATAAAATTTACGAGAACACTAAGACAATCAAGGAGTACCCAA
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------------------------------------------------------------gtatcacagttatgatgtatctctgctgctaatcaagtggcacgattttctgtgtttatcagcaacttttcatttgatcttg-gcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCGGTTACTGATAAGATCTTCTCTAATACAACGACAATTACTGAATATCTCA
upper sequence: AT1G23190.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 5
gtccgttctgttcttgttccatctctactgtgctatcctttcatttgaactattcgttttgtatctctttatttgttctttttttaataataagatatc-tagatggataataagactaagaggtgattccataccccttgtacagGATTTTGGAATCAAATACAATATGGAAAATGGAGGACCTGCTCCTGAATCAATCACTGATAAAATTTACGAGAACACTAAGACAATCAAGGAGTACCCAA
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-------------------------------------------------------gtaccaagtttact-gctagtgtctttgttgcaaatcaagtgccacacatgctctatgttattga-atacgcctcactgaactttc--cagGACTTTGGTATCAAATACAATATGGGAAATGGTGGACCTGCCCCTGAATCCGTTACCGACAAGATTTTCTCTAATACAACGACAATCTCTGAATACCTCA
upper sequence: AT1G23190.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G109383_T01 (Zea mays), 3'ss of exon 5
gtccgttctgttcttgttccatctctactgtgctatcctttcatttgaactattcgttttgtatctctttatttgttctttttttaataataagatatctagatggataataagactaagaggtgattccataccccttgtacagGATTTTGGAATCAAATACAATATGGAAAATGGAGGACCTGCTCCTGAATCAATCACTGATAAAATTTACGAGAACACTAAGACAATCAAGGAGTACCCAA
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--------------------------------------------------------gtacctattttactgctagtatctctgatgcaaatcaagtg-ctggtcatgctctatgttattgaatacatctcatcgaactt-tccagGACTTCGGGATCAAATACAACATGGGAAATGGTGGGCCTGCTCCTGAATCTGTTACCGACAAGATTTTCTCTAATACAACGACAATCTCTGAATACCTCA
upper sequence: AT1G23190.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA05G34790.1 (Glycine max), 3'ss of exon 5
gtccgttctgttcttgttccatctctactgtgctatcctttcatttgaactattcgttttgtatctctttat-ttgttctttttttaataataagatatctagatggataataagactaagaggtgattccataccccttgtacagGATTTTGGAATCAAATACAATATGGAAAATGGAGGACCTGCTCCTGAATCAATCACTGATAAAATTTACGAGAACACTAAGACAATCAAGGAGTACCCAA
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-----------------------------------------ggagtagatgggtgttcccctatgatattatgctgagatcttgttggttgtaaaat---taactcggaaagatcgttact--gtcatttggtttccatgtttcagGATTTTGGAATTAAATATAATATGGAAAACGGTGGACCTGCACCAGAGGGAATTACTGACAAGATATATGAAAACACAACAACAATTAATGAGTACTTGA
upper sequence: AT1G23190.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv01s0011g05370.t01 (Vitis vinifera), 3'ss of exon 6
gtccgttctgttcttgttccatctctactgtgctatcctttcatttgaactattcgttttgtatctctttatttgttctttttttaataataagatatctagatggataataagactaagaggtgattccataccccttgtacagGATTTTGGAATCAAATACAATATGGAAAATGGAGGACCTGCTCCTGAATCAATCACTGATAAAATTTACGAGAACACTAAGACAATCAAGGAGTACCCAA
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-------------------------------------tgaacgtttgaagcagataaaatttat---tttatttgattcggattta-tggtagtgcatgattcttgttctttattttt----ttccctgtgttcttcccttgcagGATTTTGGAATTAAGTACAACATGGAAAATGGTGGACCTGCTCAAGAGGCAATTACTGATAAGATCTATGAGAACACAAAATCCATAAAGGAGTATATAAMapped 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|124711940|gb|EH803342.1|EH803342EST: AACAGCAAGCCACAATCCTGGTGGCCCTACTGAG GATTTTGGAATCAAATACAATATGGAAAATGGAGGACCTGCTCCTGAATCA
genomic: AACAGCAAGCCACAATCCTGGTGGCCCTACTGAGgtccgttctg ... ccttgtacagGATTTTGGAATCAAATACAATATGGAAAATGGAGGACCTGCTCCTGAATCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taagatatctagatggataataagactaagaggtgattccataccccttgtacagGATTTTGGAATCAAATACAATATGGAAAATGGAGGACCTGCTCCTGAATCAATCACTGATAAAATTTACGAGAACACTAAGACAATCAAGGAGTACCCAA
tacccctt CT-rich tract
ataataaga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtccgttctgttcttgttccatctctactgtgctatcctttcatttgaactattcgttttgtatctctttatttgttctttttttaataataagatatctagatggataataagactaagaggtgattccataccccttgtacagGATTTTGGAATCAAATACAATATGGAAAATGGAGGACCTGCTCCTGAATCAATCACTGATAAAATTTACGAGAACACTAAGACAATCAAGGAGTACCCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG