Sequence
atgc intronic sequence ATGC exonic sequencegtttgcaaaatgataccctctttttattacttacttctgttgatcttcgcctttgtgactaacttactcttctaccggacagGATTTTGCTTACCTCAACCTCGGAGGTATATGGAGATCCTCTCATTCATCCCCAGCCTGAGAGCTATTGGGGAAATGTCAACCCAATTG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G46440.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA13G40960.1 (Glycine max), 3'ss of exon 7
gtttgcaaaatgataccctctttttattacttacttctgttgatcttcgcctttgtgactaacttactct--tctaccggacagGATTTTGCTTACCTCAACCTCGGAGGTATATGGAGATCCTCTCATTCATCCCCAGCCTGAGAGCTATTGGGGAAATGTCAACCCAATTG
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--------gttgggatattttcttaaacaataatctcaactgctgccattagttggtcttaattagttctaattttattgacagGATTTTGCTTACATCAACTTCAGAGGTATATGGGGATCCTCTTGTGCATCCCCAACCTGAAAGTTATTGGGGCAATGTTAACCCTATTG
upper sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA12G06990.1 (Glycine max), 3'ss of exon 6
-------------gtttgcaaaatgataccctc--tttttattacttact----tctgttgatcttcgcctttgtga-ctaacttactcttctaccggacagGATTTTGCTTACCTCAACCTCGGAGGTATATGGAGATCCTCTCATTCATCCCCAGCCTGAGAGCTATTGGGGAAATGTCAACCCAATTG
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gttggtaaattgtctttggaaaatgataatttcagcttctatcatcagttggtctttattctttttcttcttgttagtcttagttcttattttattgg-cagGATTTTACTCACATCAACATCTGAGGTATATGGGGATCCTCTTGTGCATCCCCAACCTGAAAGCTATTGGGGCAATGTGAACCCTATTG
upper sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA15G04500.2 (Glycine max), 3'ss of exon 7
gtttgcaaaatgataccctctttt-tattacttacttctgttgatcttcgcctttgtgactaacttactcttctaccggacagGATTTTGCTTACCTCAACCTCGGAGGTATATGGAGATCCTCTCATTCATCCCCAGCCTGAGAGCTATTGGGGAAATGTCAACCCAATTG
|||| |||| | || || | ||| || || | | | | | | || || || || ||||||| ||||||| ||||| || ||||||||||| |||||||| | |||||||| ||||| || |||||||| ||||| ||||| ||||
------gttgggatattttcttaaacaataatttcaactgctgccattagttggtcttaattagtttgaattttattgg-cagGATTCTGCTTACATCAACTTCAGAGGTATATGGGGATCCTCTTGTGCATCCCCAACCTGAAAGTTATTGGGGCAATGTTAACCCTATTG
upper sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G15020.1 (Glycine max), 3'ss of exon 6
-------------gtttgcaaaatgataccctc--tttttatta----cttacttctgttgatcttcgcctttgt---gactaacttactcttctaccggacagGATTTTGCTTACCTCAACCTCGGAGGTATATGGAGATCCTCTCATTCATCCCCAGCCTGAGAGCTATTGGGGAAATGTCAACCCAATTG
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gttggaaaattgtctttggaaaatgataatttcagcttctatcatcatttggtctttattctttttctttttagtagagtcttagttcttattttattgg-cagGATTTTACTCACATCAACATCTGAGGTATATGGGGATCCTCTTGTGCATCCCCAACCTGAAGGCTATTGGGGCAATGTGAACCCTATTG
upper sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 6
--------gtttgcaaaatgataccctctttttattacttacttctgttgatcttcgcctttgtgactaacttactcttctaccggacagGATTTTGCTTACCTCAACCTCGGAGGTATATGGAGATCCTCTCATTCATCCCCAGCCTGAGAGCTATTGGGGAAATGTCAACCCAATTG
||| | |||| | | || | ||| || ||| | || | | | || || | || | ||||||||||||||||| || || || || |||||||| || ||||| | ||||| || || || ||||||||||| ||||| ||||| ||||
gttatctctttttctaaatacaaaagtgg----atgatctacatc-attgccatccgtgtatcttac-aagtagtaattttgattgacagGATTTTGCTTACATCTACTTCAGAAGTATATGGGGACCCTCTTGTGCATCCACAACCAGAAAGCTATTGGGGCAATGTAAACCCCATTG
upper sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 6
gtttgcaaaatgataccctctttttattactt--acttctgttgatcttcgcctttgtgactaacttactcttctaccggacagGATTTTGCTTACCTCAACCTCGGAGGTATATGGAGATCCTCTCATTCATCCCCAGCCTGAGAGCTATTGGGGAAATGTCAACCCAATTG
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gtttgggatttga---cttcattttattcctttaaccaggatcataaatttctcaatttattaaattatgttaatgtttaacagGATATTGCTTACATCAACTTCAGAAGTATATGGAGATCCTCTTGAGCATCCCCAAACTGAGAGCTATTGGGGAAATGTTAACCCAATAGMapped 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|47831999|gb|CK121683.1|CK121683EST: GTGATTGGCACACTGAACATGCTAGGTCTCGCCAAGCGTGTTGGAGCAAG GATTTTGCTTACCTCAACCTCGGAGGTATATGGAGATCCTCTCATTCATCC
genomic: GTGATTGGCACACTGAACATGCTAGGTCTCGCCAAGCGTGTTGGAGCAAGgtttgcaaaa ... taccggacagGATTTTGCTTACCTCAACCTCGGAGGTATATGGAGATCCTCTCATTCATCC
EST:
gi|19876171|gb|AU237002.1|AU237002EST: GTGATTGGCACACTGAACATGCTANGTCTCGCCAAGCGTGTTGGANCAAG GATTTTGCTTACCTCAACC
genomic: GTGATTGGCACACTGAACATGCTAGGTCTCGCCAAGCGTGTTGGAGCAAGgtttgcaaaa ... taccggacagGATTTTGCTTACCTCAACC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacttacttctgttgatcttcgcctttgtgactaacttactcttctaccggacagGATTTTGCTTACCTCAACCTCGGAGGTATATGGAGATCCTCTCATTCATCCCCAGCCTGAGAGCTATTGGGGAAATGTCAACCCAATTG
cttactcttctacc CT-rich tract
taactta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgcaaaatgataccctctttttattacttacttctgttgatcttcgcctttgtgactaacttactcttctaccggacagGATTTTGCTTACCTCAACCTCGGAGGTATATGGAGATCCTCTCATTCATCCCCAGCCTGAGAGCTATTGGGGAAATGTCAACCCAATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT