Sequence
atgc intronic sequence ATGC exonic sequenceTCCCGAAGAATGTGCTTGGGCTTATGGAATGAATATCTTTGATCTACGGACTTGGAGGAAGACAAATATCAGAGAAACGTATCATTCTTGGCTTAAAGAGgtaaagtatcagagaagcctgtaatgttttgagttttagattcgaaattggcaaattattgatcatgcttactggttttgctttgatgtgcag
Basic information
species | Arabidopsis thaliana |
transcript | AT3G01040.2 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G01040.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G113506_T01 (Zea mays), 5'ss of exon 5
TCCCGAAGAATGTGCTTGGGCTTATGGAATGAATATCTTTGATCTACGGACTTGGAGGAAGACAAATATCAGAGAAACGTATCATTCTTGGCTTAAAGAGgtaaagtat----cagagaagcctgtaatgttttgagttttagattcgaaattggcaaattattgatcatgctt---actggttttgctttgatgtgcag-
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CCCAGATGAATGTGCTTGGGCATATGGTATGAATATATTTGATCTGGCAGCTTGGAGGAAGACAAATATCAGGGATACATATCATTTCTGGTTGAAGGAGgtaatgcatttcaccaacaaggatatacatttcccagtcttac-tctatgttccatagttcgttgactatgttttgaactgaaatctttctggtattttgg
upper sequence: AT3G01040.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G113506_T02 (Zea mays), 5'ss of exon 5
TCCCGAAGAATGTGCTTGGGCTTATGGAATGAATATCTTTGATCTACGGACTTGGAGGAAGACAAATATCAGAGAAACGTATCATTCTTGGCTTAAAGAGgtaaagtat----cagagaagcctgtaatgttttgagttttagattcgaaattggcaaattattgatcatgctt---actggttttgctttgatgtgcag--------
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CCCAGATGAATGTGCTTGGGCATATGGTATGAATATATTTGATCTGGCAGCTTGGAGGAAGACAAATATCAGGGATACATATCATTTCTGGTTGAAGGAGgtaatgcatttcaccaacaaggatatacatttcccagtcttac-tctatgttccatagttcgttgactatgttttgaactgaaatctttctggtattttggcatgcag
upper sequence: AT3G01040.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G107854_T01 (Zea mays), 5'ss of exon 5
TCCCGAAGAATGTGCTTGGGCTTATGGAATGAATATCTTTGATCTACGGACTTGGAGGAAGACAAATATCAGAGAAACGTATCATTCTTGGCTTAAAGAGgtaaagtatcagagaagcctgtaatgttttgagttttagattcgaaattg-gcaaattattgatcatgctt----actggttttgctttgatgtgcag--
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CCCAGATGAATGTGCTTGGGCATATGGTATGAATATATTTGATCTGGCAGTTTGGAGGAAGACAAACATCAGGGATACATACCATTTCTGGTTGAAGGAGgtaatgcattttacacccacatatccatttcccagtcttactcgatgttccattgttcgttgactatgtttgtgaactgaaatcgttctggtatttttgc
upper sequence: AT3G01040.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA18G49960.1 (Glycine max), 5'ss of exon 5
TCCCGAAGAATGTGCTTGGGCTTATGGAATGAATATCTTTGATCTACGGACTTGGAGGAAGACAAATATCAGAGAAACGTATCATTCTTGGCTTAAAGAGgtaaagtat-cagaga---agcctgtaatgttttgagtttt---agattcgaaattggcaaattattgatcatgcttactggttttgctttgatgtgcag
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CCCTGATGAGTGTGCTTGGGCTTATGGAATGAATATCTTTGATCTGCATGCATGGAGAAGAACTAATATAAGAGAGATATATCATTCTTGGCTGAAAGAGgtaaagtccacatatactcagactaatataattgcagtttttcaaaattttaaattattattttgattttcatacaaaatccacacattattataaatta
upper sequence: AT3G01040.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA08G26480.1 (Glycine max), 5'ss of exon 5
TCCCGAAGAATGTGCTTGGGCTTATGGAATGAATATCTTTGATCTACGGACTTGGAGGAAGACAAATATCAGAGAAACGTATCATTCTTGGCTTAAAGAGgtaaagtatcagagaagcctgtaatgttttgagttttagattcgaaattggcaaattattgatc--atgcttactggttttgctttgatgtgcag-------
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CCCTGATGAGTGTGCATGGGCTTATGGAATGAATATCTTTGATCTGCATGCATGGAGAAGAACTAATATAAGAGAGATATATCATTCTTGGCTGAAAGAGgtaagtc--cacatatactcgtactaacataatttcagtttttcaaaattttaaattattcttttgattttcaatagtttgaagttcatacaaaatccacat
upper sequence: AT3G01040.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA19G03460.1 (Glycine max), 5'ss of exon 5
TCCCGAAGAATGTGCTTGGGCTTATGGAATGAATATCTTTGATCTACGGACTTGGAGGAAGACAAATATCAGAGAAACGTATCATTCTTGGCTTAAAGAGgtaaagtatcagagaagcctgtaatgttttgagttttagattcgaaat--tggcaaattattgatcatgc-ttactggttttgctttgatgtgcag------
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TCCTGATGAGTGTGCTTGGGCTTATGGGATGAATTTATTTGATCTGCGTACGTGGAGAACAACAAACATAAGAGAGACATATCATACCTGGCTGAAAGAGgtaaagt--catatatactcaaactaatacaatccattaatttgaatttctagcaaattctgaattttaaattaatgctgtcgtactgattcaaatatctac
upper sequence: AT3G01040.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA13G05950.1 (Glycine max), 5'ss of exon 5
TCCCGAAGAATGTGCTTGGGCTTATGGAATGAATATCTTTGATCTACGGACTTGGAGGAAGACAAATATCAGAGAAACGTATCATTCTTGGCTTAAAGAGgtaaagtatcagagaagcctgtaatgttttgagttttagattcgaaatt--ggcaaattattgatcatgc-ttactggttttgctttgatgtgcag-------
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TCCTGATGAGTGTGCTTGGGCTTATGGGATGAATGTATTTGATCTGCGTGCATGGAGAACAACAAACATAAGAGAGACATATCATACCTGGCTGAAAGAGgtaaagtcatatata---ctcaaataatacaatccataaatttaaacttctagcaaattctgaattttaaactattgatgtggtactgattcaaatgtttacc
upper sequence: AT3G01040.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv14s0108g01520.t01 (Vitis vinifera), 5'ss of exon 5
TCCCGAAGAATGTGCTTGGGCTTATGGAATGAATATCTTTGATCTACGGACTTGGAGGAAGACAAATATCAGAGAAACGTATCATTCTTGGCTTAAAGAGgtaaagtatcagagaagcctgtaatgttttgagttttagattcgaaattggcaaattattgatca-tgcttactggttttgctttgatgtgcag------
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TCCTGATGAATGTGCATGGGCTTATGGGATGAACATCTTTGATCTAAGTGCATGGAGGAAGACCAATATAAGAGAAACTTACCATTCCTGGCTGAAGGAGgtaagaactaagcactacatttgttttacacacttatgtgatagttttccttagtttcttcattgcttcaaactgcagtgagcttcaagttcaataggtaMapped 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|116476603|gb|EG519195.1|EG519195EST: CTTGGAGGAAGACAAATATCAGAGAAACGTATCATTCTTGGCTTAAAGAG AATCTGAAGTCGAATCTAACAATGTGGAAACTTGGAACATTGCCTCCTGCT
genomic: CTTGGAGGAAGACAAATATCAGAGAAACGTATCATTCTTGGCTTAAAGAGgtaaagtatc ... tgatgtgcagAATCTGAAGTCGAATCTAACAATGTGGAAACTTGGAACATTGCCTCCTGCT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TCCCGAAGAATGTGCTTGGGCTTATGGAATGAATATCTTTGATCTACGGACTTGGAGGAAGACAAATATCAGAGAAACGTATCATTCTTGGCTTAAAGAGgtaaagtatcagagaagcctgtaatgttttgagttttagattcgaaattggcaaattattgatcatgcttactggttttgctttgatgtgcag
- - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA