Sequence
atgc intronic sequence ATGC exonic sequenceTCATCAGTGTTACATTCGCAACCAAAATCAACTGTTGGAACTCCTGCTTACATCGCTCCTGAGGTTTTACTAAAGAAAGAATATGATGGAAAGgtactccattttcatagttcccaaactagtatgataaccatatcttatagaaagaacaatctttgtatttttatcctctgattatagataggggaaacat...
Basic information
species | Arabidopsis thaliana |
transcript | AT4G33950.1 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G33950.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os03g41460.1 (Oryza sativa), 5'ss of exon 4
TCATCAGTGTTACATTCGCAACCAAAATCAACTGTTGGAACTCCTGCTTACATCGCTCCTGAGGTTTTACTAAAGAAAGAATATGATGGAAAGgtactccattttcatagttcccaaactagtatgataaccatatcttatagaaagaacaatctt-tgtatttttatcctctgattatag-ataggggaaacat-------------------------------------------------------------------
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TCGTCTGTTCTTCATTCGCAACCAAAATCTACTGTTGGAACTCCGGCATACATCGCTCCTGAGGTTCTGCTGAAGAAGGAATATGATGGAAAGgtactcatatatttgaatttacatgcttgcgtcctgaatatggtgtcatggtgtctcagtctggtatattgatacatcatacatgtaccattttctccacttaagcaattgtactttcttcgcgaggcatcagtgcgattgctgactaaatatttgtttctcaacaaag
upper sequence: AT4G33950.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os12g39630.1 (Oryza sativa), 5'ss of exon 6
TCATCAGTGTTACATTCGCAACCAAAATCAACTGTTGGAACTCCTGCTTACATCGCTCCTGAGGTTTTACTAAAGAAAGAATATGATGGAAAGgtac--tccattttcatagttcccaaactagtatgataaccatatcttatagaaagaacaatctttgtattttta----tcctctgattatagataggggaaacat
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TCATCGGTTCTTCATTCACAACCAAAATCAACAGTTGGAACTCCAGCTTATATTGCTCCAGAAGTTTTGCTCAAGAAAGAATACGATGGAAAGgtattatctatcccctttgtgctttaa--aagttgccatcctgcatgcaaagatacactgataccagcagctgcccaacttctatgccttttgctcgacaat----
upper sequence: AT4G33950.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os03g55600.1 (Oryza sativa), 5'ss of exon 6
TCATCAGTGTTACATTCGCAACCAAAATCAACTGTTGGAACTCCTGCTTACATCGCTCCTGAGGTTTTACTAAAGAAAGAATATGATGGAAAGgtactccattt-tcatagttcccaaactagtat--gataaccatatcttatagaaagaacaatctttgtatttttatcctctgattatagataggggaaacat
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TCTTCAGTTCTCCATTCACAACCAAAATCCACTGTAGGAACCCCTGCTTATATTGCACCTGAAGTTCTGTTGAAGAAAGAATACGATGGCAAGgtacatgacttattaagcttgttgatttaatccccgagagcagtaccttt--gggaggactatagcttttcgtcttgcatcgtattttgacaaacataaaca-
upper sequence: AT4G33950.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G066867_T01 (Zea mays), 5'ss of exon 5
TCATCAGTGTTACATTCGCAACCAAAATCAACTGTTGGAACTCCTGCTTACATCGCTCCTGAGGTTTTACTAAAGAAAGAATATGATGGAAAGgtactccattttcatagttcccaaactagtatgataaccatatcttatagaaagaacaatctttgtatttttatcctctgattatagataggggaaacat---
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TCATCAGTTCTACACTCGCAGCCGAAATCTACAGTGGGAACTCCTGCATACATTGCTCCTGAGGTTCTTCTGAAGAAGGAATACGATGGAAAGgtat--catgtgtattgtcattga-ttattctacataccgtttctattcatgcacacgttattgctctccccttaaacaacatgtttgtgtggcaactggcaa
upper sequence: AT4G33950.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G171435_T02 (Zea mays), 5'ss of exon 6
TCATCAGTGTTACATTCGCAACCAAAATCAACTGTTGGAACTCCTGCTTACATCGCTCCTGAGGTTTTACTAAAGAAAGAATATGATGGAAAGgtactccattttcatagttcccaaactagtatgataaccatatcttatagaaagaacaatctttgtatttttatcctctgatt--atagataggggaaacat-
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TCATCTGTTCTTCATTCCCAACCGAAGTCAACTGTTGGAACACCTGCTTATATTGCACCTGAAGTTCTGTTGAAAAAAGAATATGATGGCAAGgtact---tgtgcgactttccttatttatcttgagatgtgtctttaagagttgtgtatacctctgcatcagtgcactgtagttccataaacatgtgccgcgtg
upper sequence: AT4G33950.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G138861_T01 (Zea mays), 5'ss of exon 7
TCATCAGTGTTACATTCGCAACCAAAATCAACTGTTGGAACTCCTGCTTACATCGCTCCTGAGGTTTTACTAAAGAAAGAATATGATGGAAAGgtactccattttcatagttcccaaactagtatgataaccatatcttatagaaagaaca-atctttgtatttttatcctctgatt--atagataggggaaacat-
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TCATCTGTTCTTCATTCCCAGCCGAAGTCCACTGTTGGAACACCTGCTTATATTGCACCTGAAGTTTTGTTGAAAAAAGAATATGATGGCAAGgtactt-gtgctatcacttttt---ttatcttgagaaatgtgtcttgagagttgtgcatacctctgcatcagtgcactgttgttccatatacatgtgccacatg
upper sequence: AT4G33950.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA02G15330.1 (Glycine max), 5'ss of exon 6
TCATCAGTGTTACATTCGCAACCAAAATCAACTGTTGGAACTCCTGCTTACATCGCTCCTGAGGTTTTACTAAAGAAAGAATATGATGGAAAGgtactccattttcat-------agttc-ccaaactagtatgataaccatatcttatagaaagaacaatctttgtatttttatcctctgattatagataggggaaacat
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TCTTCAGTGCTACATTCACAACCAAAATCTACAGTTGGTACCCCTGCATATATCGCTCCAGAAGTTTTGCTTAAGAAGGAATATGATGGCAAGgtatgtaacttctatcacttggaattcatctaactgaagagactttgataatttctcttaaga-tgttctttattttgcttatgtgtttttatagattatg-------
upper sequence: AT4G33950.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA07G33120.1 (Glycine max), 5'ss of exon 6
TCATCAGTGTTACATTCGCAACCAAAATCAACTGTTGGAACTCCTGCTTACATCGCTCCTGAGGTTTTACTAAAGAAAGAATATGATGGAAAGgtactccat---tttcatagttcccaaactagtatgataaccatatcttatagaaagaacaat----ctttgtatttttatcctctgattatagataggggaaacat
|| |||||| ||||||| ||||||||||| || ||||| || ||||| || || ||||| || ||||| || ||||| ||||||||||| |||||| || || || | || | | | | |||| || | |||| | || | | |||| | | || | | |||| |
TCCTCAGTGCTACATTCACAACCAAAATCTACAGTTGGTACCCCTGCATATATTGCTCCAGAAGTTTTGCTTAAGAAGGAATATGATGGCAAGgtatgttataacttctatcacttg-gaattcatctaact-tcatactttgataatttaacattaagatgttctttatttagcttatgtgtttgtatagatta-----
upper sequence: AT4G33950.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv03s0063g01080.t01 (Vitis vinifera), 5'ss of exon 6
TCATCAGTGTTACATTCGCAACCAAAATCAACTGTTGGAACTCCTGCTTACATCGCTCCTGAGGTTTTACTAAAGAAAGAATATGATGGAAAGgtactccattttcatagttccc------aaactagtatgataaccatatcttatagaaagaacaatctttgtatttt---tatcctctgattatagataggggaaacat
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TCCTCAGTGCTGCATTCACAACCAAAATCGACTGTTGGAACCCCTGCATACATTGCTCCTGAAGTCTTACTTAAGAAAGAATATGACGGGAAGgtaaattaatgtcctaattacctgagttaaatttatatggtgtacagattctgtggaaatgacagttttagcatataaggtagtcctattttgtcaatct---------Mapped 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|164175149|gb|EL997597.1|EL997597EST: ACATCGCTCCTGAGGTTTTACTAAAGAAAGAATATGATGGAAAG GTTGCAGATGTTTG
genomic: ACATCGCTCCTGAGGTTTTACTAAAGAAAGAATATGATGGAAAGgtactccatt ... tttttttcagGTTGCAGATGTTTG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TCATCAGTGTTACATTCGCAACCAAAATCAACTGTTGGAACTCCTGCTTACATCGCTCCTGAGGTTTTACTAAAGAAAGAATATGATGGAAAGgtactccattttcatagttcccaaactagtatgataaccatatcttatagaaagaacaatctttgtatttttatcctctgattatagataggggaaacat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA