Sequence
atgc intronic sequence ATGC exonic sequenceCTCCTTTGCTGGTGAACTTCTTCAAAACGCTGAGGAGCTTATCAGGATGGGACTTCATCCGAGTGAGATCATTAGTGGATATACTAAAGCTGTCAGCAAGgttggtgaatacctgaattactgttttgtgcttttcaatttgtttgtcttgagtatttgacgaatgctattggattttgattatgcag
Basic information
species | Arabidopsis thaliana |
transcript | AT3G03960.1 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G03960.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os03g59020.1 (Oryza sativa), 5'ss of exon 2
CTCCTTTGCTGGTGAACTTCTTCAAAACGCTGAGGAGCTTATCAGGATGGGACTTCATCCGAGTGAGATCATTAGTGGATATACTAAAGCTGTCAGCAAGgttggtgaatacctgaatta---ctgttttgtgcttttcaat--------ttgtttg-tcttgagtatttgacgaatgctattggattttgattatgcag
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ATCTTTTGCTGGTGAACTGCTTGAGAAGGCCGAGGAGCTTATCAGGATGGGGTTGCATCCAAGTGAGATCATCATTGGCTACACCAAGGCCATTAATAAGgttacttaccctcccgattgagctggccttatattgattaaaaaaacctgttgcctgatggcaggctagttattcatgcatttgcatctgcaatgcgcag
upper sequence: AT3G03960.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G381744_T01 (Zea mays), 5'ss of exon 2
CTCCTTTGCTGGTGAACTTCTTCAAAACGCTGAGGAGCTTATCAGGATGGGACTTCATCCGAGTGAGATCATTAGTGGATATACTAAAGCTGTCAGCAAGgttggtgaatacctgaattactgttttgtgcttttcaatttgtttgtcttg-agtatt-tgacgaatgctattggattttgat----tatgcag
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ATCGTTTGCTGGTGAACTGCTTGAGAAGGCTGAGGAGCTCATCAGGATGGGCTTGCATCCGAGTGAGATCATCATTGGCTACACCAAAGCCATCAACAAGgt-gacacccctccccccgactcctgtaggcttctgtacaacattgacatgcagtctgatagcaggtcctttgtgctttgtatttggtatgcag
upper sequence: AT3G03960.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G083095_T02 (Zea mays), 5'ss of exon 2
CTCCTTTGCTGGTGAACTTCTTCAAAACGCTGAGGAGCTTATCAGGATGGGACTTCATCCGAGTGAGATCATTAGTGGATATACTAAAGCTGTCAGCAAGgttggtgaatacctgaattactgttttgtgcttttcaatttgtttgtcttg-agtatttgacgaatgctattggattttgattatgcag------------------------------
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ATCGTTTGCCGGTGAACTGCTTGAGAAGGCTGAGGAGCTCATCAGGATGGGCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAGgtgacttgccccctgactctggcttttgtaatattgaaacgtgcagtctgatagcaggctctttgtgcttttgtctttgg--tatgcagacaattgagatcttggaggatcttgttgag
upper sequence: AT3G03960.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G083095_T03 (Zea mays), 5'ss of exon 2
CTCCTTTGCTGGTGAACTTCTTCAAAACGCTGAGGAGCTTATCAGGATGGGACTTCATCCGAGTGAGATCATTAGTGGATATACTAAAGCTGTCAGCAAGgttggtgaatacctgaattactgttttgtgcttttcaatttgtttgtcttg-agtatttgacgaatgctattggattttgattatgcag
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ATCGTTTGCCGGTGAACTGCTTGAGAAGGCTGAGGAGCTCATCAGGATGGGCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAGgtgacttgccccctgactctggcttttgtaatattgaaacgtgcagtctgatagcaggctctttgtgcttttgtctttgg--tatgcag
upper sequence: AT3G03960.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA16G26920.1 (Glycine max), 5'ss of exon 2
CTCCTTTGCTGGTGAACTTCTTCAAAACGCTGAGGAGCTTATCAGGATGGGACTTCATCCGAGTGAGATCATTAGTGGATATACTAAAGCTGTCAGCAAGgtt--ggtgaatacctgaattactgttttgtgcttttcaatttgtttgtcttgagtatttgacgaatgctattggattttgattatgcag
|| |||||||| ||||| || || |||||||| |||||||||||||| | |||||||| |||||||| |||||||| |||||||| ||| ||||||| | ||| ||| | | | | ||| | | ||| ||| | ||| | || | |||| ||||| || ||
TTCATTTGCTGGGGAACTCCTGCAGGGTGCTGAGGAACTTATCAGGATGGGTTTGCATCCGAGCGAGATCATCAGTGGATACACTAAAGCGATCAACAAGgttttgatgagagccttagtcattcatttttaaatgtcatattgctgctctc---tcttcttctaatg-tattgttttgtgtcag-----
upper sequence: AT3G03960.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA02G07910.1 (Glycine max), 5'ss of exon 2
CTCCTTTGCTGGTGAACTTCTTCAAAACGCTGAGGAGCTTATCAGGATGGGACTTCATCCGAGTGAGATCATTAGTGGATATACTAAAGCTGTCAGCAAGgttggtgaatacctgaattactgttttgtgcttttcaatttgtttgtcttgagtatttgacgaatgctattggattttgattatgcag---
|| |||||||| || || || || || ||||| |||||||||||||| | |||||||| |||||||| |||||||| |||||||| ||| ||||||| | | | || | | || | | ||| |||| | | | | | || | || ||
TTCATTTGCTGGGGAGCTCCTGCAGGGTGCCGAGGAACTTATCAGGATGGGTTTGCATCCGAGCGAGATCATCAGTGGATACACTAAAGCAATCAACAAGgttttttcagtttttgatgaaagccttagtgatctgtctttaaatgtcatattgctgctctctctccctctaatttcttgttttgtttcag
upper sequence: AT3G03960.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv08s0007g07460.t01 (Vitis vinifera), 5'ss of exon 2
CTCCTTTGCTGGTGAACTTCTTCAAAACGCTGAGGAGCTTATCAGGATGGGACTTCATCCGAGTGAGATCATTAGTGGATATACTAAAGCTGTCAGCAAGgttggtgaatacctga-attactgttttgtgcttttcaatttgtttgtcttga-gtatttgacga-atgctatt--ggattttgattatgcag-------
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TTCTTTTGCTGGAGAGCTCCTCCAAAATGCTGAGGAGCTTATCAGGATGGGGCTGCACCCGAGTGAGATCATCAGTGGATACTCAAAAGCCATTAATAAGgtttctccatgcttgctaatgctttgttttaacaactagtcttctcccctggatgaatttctagacatgctattctgactctctctctctctgtcttcagMapped 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|125208059|gb|EL223013.1|EL223013EST: CTGTCAGCAAG GCTGTTGAAATACTGGAACAACTGGTTGAGACTGGTTCTGAGACCATGGAT
genomic: CTGTCAGCAAGgttggtgaat ... gattatgcagGCTGTTGAAATACTGGAACAACTGGTTGAGACTGGTTCTGAGACCATGGAT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CTCCTTTGCTGGTGAACTTCTTCAAAACGCTGAGGAGCTTATCAGGATGGGACTTCATCCGAGTGAGATCATTAGTGGATATACTAAAGCTGTCAGCAAGgttggtgaatacctgaattactgttttgtgcttttcaatttgtttgtcttgagtatttgacgaatgctattggattttgattatgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG