Sequence
atgc intronic sequence ATGC exonic sequencegtaagtacacacttcaatcttcatggattcatgatttccccctcaaatttctcgggaaaataatgatggattttgacttctttatttttgtttgattaaatctttattagGAGGTTATGATATGGAGGAGAAAGCTGCTCGAGCATATGATCTTGCTGCACTCAAGTACTGGGGTCCCTCTACTCACACCAATTTCTCT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G37750.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G37750.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os03g56050.1 (Oryza sativa), 3'ss of exon 3
gtaagtacacacttcaatcttcatggattcatgatttccccctcaaatttctcgggaaaataatgatggattttgacttctttatttttgtttgattaaatctttattagGAGGTTATGATATGGAGGAGAAAGCTGCTCGAGCATATGATCTTGCTGCACTCAAGTACTGGGGTCCCTCTACTCACACCAATTTCTCT
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------gtgtatcttggtgagtaccagtacacaagtact---tgggatgaattgattagtttttgg-aaacaaagatttgattgtgagattgcaatgtaacctttgctagGTGGGTATGACATGGAGGAGAAGGCTGCCAGGGCGTATGATCTTGCTGCGCTCAAGTACTGGGGCCCTTCCACGCACATCAACTTCCCG
upper sequence: AT4G37750.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA17G17010.1 (Glycine max), 3'ss of exon 4
gtaagtacacacttcaatcttcatggattcatgatttccccctcaaatttctcgggaaaataatgatggattttgact--tctttatttttgtttgattaaatcttta---ttagGAGGTTATGATATGGAGGAGAAAGCTGCTCGAGCATATGATCTTGCTGCACTCAAGTACTGGGGTCCCTCTACTCACACCAATTTCTCT
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-------------cagacagttaaagatagata--tcattaaataaaatgcttatgacgtcaacaaaggaggaaaattgatgtttattcaagtcattccaaacttttgattttagGGGGTTATGATATGGAAGAAAAAGCTGCAAGAGCTTATGATCTAGCTGCACTCAAGTATTGGGGACCCTCCACTCACATAAACTTTCCT
upper sequence: AT4G37750.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA05G22970.1 (Glycine max), 3'ss of exon 6
---------------------------------------------------------gtaagtacacacttcaatct-----tcatggattcatgatttccccctcaaatttctcgggaaaataatgatggattttgact--tctttatttttgtttgattaaatcttta---ttagGAGGTTATGATATGGAGGAGAAAGCTGCTCGAGCATATGATCTTGCTGCACTCAAGTACTGGGGTCCCTCTACTCACACCAATTTCTCT
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gtaaggtttcttaagaccttaatatctttttattttcttttaattcaggttgaaattctcagagcttagattaaccagacagttaaagatagat-atcaattaatataaatgcttatgatgttaacaaaagaggaaaattgatgtttattcaagtcatttcgaacttttgattttagGGGGTTATGATATGGAAGAAAAAGCTGCGAGAGCTTATGATCTAGCGGCACTCAAGTATTGGGGACCCTCCACTCACATAAACTTTCCT
upper sequence: AT4G37750.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA04G05080.1 (Glycine max), 3'ss of exon 4
gtaagtacacacttcaatcttcatggattcatgatttccccctcaaatttctcgggaaaataatgatggattttgacttctttatttttgtttgattaaatctttattagGAGGTTATGATATGGAGGAGAAAGCTGCTCGAGCATATGATCTTGCTGCACTCAAGTACTGGGGTCCCTCTACTCACACCAATTTCTCT
||| | | | | ||| | || || || | |||| ||| | | | | || ||| | || | | | |||||||| || || ||| |||||||||||||||||||||||||| |||| |||||||| || || || ||||||||||| || || || || | || || ||
gtatttgggtaagt-attctcccacactttttgtttgcaatttcaacactcttgctactgt--ttata-attgttacgtggtcaattttgttt--ttgaactaa----agGGGGTTATGATATGGAGGAGAAAGCTGCAAGAGCCTATGATCTCGCGGCCCTTAAGTACTGGGGACCTTCAACGCATATAAACTTTTCG
upper sequence: AT4G37750.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA06G05170.1 (Glycine max), 3'ss of exon 5
-gtaagtacacacttcaatcttcatggattcatgatttccccctcaaatttctcgggaaaataatgatggattttgacttctttatttttgtttgattaaatctttattagGAGGTTATGATATGGAGGAGAAAGCTGCTCGAGCATATGATCTTGCTGCACTCAAGTACTGGGGTCCCTCTACTCACACCAATTTCTCT
|||||| | | || ||||| || || || | | |||| ||| | | | | | ||| | || | | | ||||||||| | || |||||||||||||||||| || |||||||| |||| |||||||| || || || ||||||||||| || || || |||| || || ||
ggtaagtcttctcc-cacacttcaaggtttt-tgttagcattttcaacactcttgctac--tggttcta-attgttacgtggtcaattttgtttg--tgaactaa----agGAGGTTATGATATGGAAGAAAAAGCTGCAAGAGCCTATGATCTCGCGGCTCTTAAGTACTGGGGACCTTCAACGCACATAAACTTTTCG
upper sequence: AT4G37750.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA0041S00200.1 (Glycine max), 3'ss of exon 6
gtaagtacacacttcaatcttcatggattcatgatttcccc-ctca-aatttctcgggaaaataatgatggattttgacttctttatttttgtttgattaaatctttattagGAGGTTATGATATGGAGGAGAAAGCTGCTCGAGCATATGATCTTGCTGCACTCAAGTACTGGGGTCCCTCTACTCACACCAATTTCTCT
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-----tac-tagttcttttccaaagtgtccgcgttttcagtgctcatactttttttactaaatgctaatttgattagtggtgattttttttgtttg--tgaactga----agGTGGTTATGATATGGAAGAGAAAGCTGCAAGGGCTTATGATCTTGCGGCTCTCAAGTATTGGGGACCTTCAACACACATAAACTTCCCG
upper sequence: AT4G37750.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G04910.1 (Glycine max), 3'ss of exon 4
gtaagtacacacttcaatcttcatggattcatgatttccccctcaaatttctcgggaaaataatgatggattttgacttctttatttttgtttgattaaatctttattagGAGGTTATGATATGGAGGAGAAAGCTGCTCGAGCATATGATCTTGCTGCACTCAAGTACTGGGGTCCCTCTACTCACACCAATTTCTCT
||| | | | | |||| | | |||| | | | | | | || || || || | | || || || || | | |||| |||||||||||||| || |||||||| |||| |||||| | || ||||||||||| ||||| ||||| | || | |||||| ||
ttaacttgaagttaaagatatcat----ttaatattttgctcatgatgatggcaaaagaagaaatataaatgctaa------tacaagtgattccaaaattttactatagGGGGTTATGATATGGAAGAAAAAGCTGCAAGAGCTTATGATATGGCCGCACTCAAGTATTGGGGACCCTCCTCCCATATAAATTTCCCT
upper sequence: AT4G37750.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA01G40380.1 (Glycine max), 3'ss of exon 3
--------------------------------------------gtaagtac---acacttcaatcttcatggattcatgatttccccctcaaattt--ctcgggaaaataatgatggattttgact---tctttatttttgtttgattaaa-tctttatta--gGAGGTTATGATATGGAGGAGAAAGCTGCTCGAGCATATGATCTTGCTGCACTCAAGTACTGGGGTCCCTCTACTCACACCAATTTCTCT
|| | | | || | || | | | | | | | | |||| ||| || ||| | || | | | || || | ||| | ||||||| || |||||||||||||| || ||||| || |||| |||||| | || ||||||||||| ||||| ||||| |||| | |||||| |
gtaagattttccaaatccaggattagttttctttttaattttgttcaaattccttgaggatagattaacttgaagttaaaaatatcatttaatattttgctcatgatgatagcaaaagaaaaaaaataaatgcttgcacaagtcatttcaaaatttttattatagGGGGTTATGATATGGAAGAAAAAGCAGCAAGAGCTTATGATATGGCCGCACTCAAGTATTGGGGACCCTCCTCTCATATAAATTTCCCA
upper sequence: AT4G37750.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv18s0001g08610.t01 (Vitis vinifera), 3'ss of exon 4
gtaagtacacacttcaatcttcatggattcatgatttccccctcaaatttctcgggaaaataatgatggattttgacttctttatttttgtttgattaaatctttattagGAGGTTATGATATGGAGGAGAAAGCTGCTCGAGCATATGATCTTGCTGCACTCAAGTACTGGGGTCCCTCTACTCACACCAATTTCTCT
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gtaagcccccttttctttttggtcgaaatgaagaaacc--------atgtat-gagtatattctgttcgtgttta---tatttaattgattctacccatgtcttt--cagGGGGGTATGATATGGAAGAGAAAGCTGCAAGAGCTTACGATCTGGCGGCCCTCAAATACTGGGGACCTTCTACTCATATCAACTTCCCGMapped 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|164101465|gb|ES113874.1|ES113874EST: GAAAAGG-AGACAAGTTTATCTGG GAGGTTATGATATGGAGGAGAAAGCTGC
genomic: GAAAAGGAAGACAAGTTTATCTGG
EST:
gi|164065022|gb|ES122160.1|ES122160EST: GAAAAGGAAGACAAGTTTATCTGG GAGGTTATGATATGGAGGAGAAAGCTG
genomic: GAAAAGGAAGACAAGTTTATCTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaaaataatgatggattttgacttctttatttttgtttgattaaatctttattagGAGGTTATGATATGGAGGAGAAAGCTGCTCGAGCATATGATCTTGCTGCACTCAAGTACTGGGGTCCCTCTACTCACACCAATTTCTCT
tctttatt CT-rich tract
acttctttatttttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtacacacttcaatcttcatggattcatgatttccccctcaaatttctcgggaaaataatgatggattttgacttctttatttttgtttgattaaatctttattagGAGGTTATGATATGGAGGAGAAAGCTGCTCGAGCATATGATCTTGCTGCACTCAAGTACTGGGGTCCCTCTACTCACACCAATTTCTCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC