Sequence
atgc intronic sequence ATGC exonic sequencegttagctgcttatatccggctgatcgctggatataatttgacttttaactcttctcgtttgtttcgttggtgattgagtttgaaaagTTGTGTTGTGCCGTTGTTACAGAAATGGCGAAATCGAAGAATCACACGGCGCACAATCAGTCTGCCAAGGCGCATAAGAACGGAATCAAGAAGCCAAGGA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G06680.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G06680.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os01g19840.1 (Oryza sativa), 3'ss of exon 1
------gttagctgctt-atatccggctgatcgctggatataa-tttgacttttaactcttctcgtttgtttcgttggtgattgagtttgaaaagTTGTGTTGTGCCGTTG-------TTACAGAAATGGCGAAATCGAAGAATCACACGGCGCACAATCAGTCTGCCAAGGCGCATAAGAACGGAATCAAGAAGCCAAGGA------------
| | || || ||| | || | ||| | ||||| || | ||||| ||| || | || | ||| ||| |||| | | ||| || ||||| || |||||||| |||||||||||||| ||||| ||||||||| |||||||| ||||||||||| | |
gtaaccgacgattcctccatttccatcgcctcattcgatgtctctttgatttatcgatcttcgt-tttcttcccctgattcctgatttttttcgtttgttcgtcgtctttgaagGATTCGGGGGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTACAAGGCGCACAAGAACGGGATCAAGAAGCCCAAGCGCCACCGCCAGA
upper sequence: AT3G06680.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G009894_T01 (Zea mays), 3'ss of exon 1
gttagctgcttata-tccggctgatcgctggatataatttgacttttaactcttctcgtttgtttcgttggtgattgagtttgaaaag-
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gtaactctccggcactccgctcgatctgttcctactagatgtgttgttcgtcttcaccgtcaatccacctcccccttactctgagtcgccttttgtttgcagGGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTACAAGGCGCACAAGAACGGCATCAAGAAGCCCAAGCGCCACCGGCAG
upper sequence: AT3G06680.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G147791_T01 (Zea mays), 3'ss of exon 1
gttagctgcttatatccggct-gatcgctggata--taatttgacttttaactcttctcgtttgtttcgttggtgattgagtttgaa--aagTTGTGTTGTGCCGTTGTT--ACAGAAATGGCGAAATCGAAGAATCACACGGCGCACAATCAGTCTGCCAAGGCGCATAAGAACGGAATCAAGAAGCCAAGGA-----------
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gtaattctcaggcaccccgctcgatctcatcctaatcggtgtgattttcgtcttcac-cgtcaacccacccctccacttactctgattcgcactttgttg-gcagGCATCCGGAAGAAATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTTCAAGGCGCACAAGAACGGCATTAAGAAACCCAAGCGCCACCGCCAG
upper sequence: AT3G06680.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G147791_T02 (Zea mays), 3'ss of exon 1
gttagctgcttatatccggctgatcgctggatataatttgacttttaactcttctcgtttgtttcgttggtgattgagtttgaaaagTTGTGTTGTGCCGTTGTTACAGAAATGGCGAAATCGAAGAATCACACGGCGCACAATCAGTCTGCCAAGGCGCATAAGAACGGAATCAAGAAGCCAAGGA-----------
| | |||| | || || | | | | | | | || | |||| | | | | ||||||||| || |||||||| |||||||||||||| ||||| ||||||||| |||||||| || ||||| || | |
------------------------------gtgtgattttcgtcttcaccgtcaac--ccacccctccacttactctgattcgcactttgttggcagGCATCCGGA-AGAAATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTTCAAGGCGCACAAGAACGGCATTAAGAAACCCAAGCGCCACCGCCAG
upper sequence: AT3G06680.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G147791_T03 (Zea mays), 3'ss of exon 1
gttagctgctt-atatccggctgatcgctggatataatttgacttttaactcttctcgtttgtttcgttggtgattgagtttgaaaagTTGTGTTGTGCCGTTGTTACAGAAATGGCGAAATCGAAGAATCACACGGCGCACAATCAGTCTGCCAAGGCGCATAAGAACGGAATCAAGAAGCCAAGGA-----------
| | ||| || || || |||| || | |||| | || || | | | | | | | || | |||| | | | | ||||||||| || |||||||| |||||||||||||| ||||| ||||||||| |||||||| || ||||| || | |
gcaccccgctcgatctcatcctaatcggtg----tgattttcgtcttcaccgtcaac--ccacccctccacttactctgattcgcactttgttggcagGCATCCGGA-AGAAATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTTCAAGGCGCACAAGAACGGCATTAAGAAACCCAAGCGCCACCGCCAGMapped 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|19874731|gb|AU235562.1|AU235562EST: ATGTCACCTATCTTTCCTCTCGCGTCTCTCCCCTTTACTCAG TTGTGTTGTGCCGTTGTTACAGAAATGGCGAAATCGAANAATCACACGGCG
genomic: ATGTCACCTATCTTTCCTCTCGCGTCTCTCCCCTTTACTCAGgttagctgct ... gtttgaaaagTTGTGTTGTGCCGTTGTTACAGAAATGGCGAAATCGAAGAATCACACGGCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataatttgacttttaactcttctcgtttgtttcgttggtgattgagtttgaaaagTTGTGTTGTGCCGTTGTTACAGAAATGGCGAAATCGAAGAATCACACGGCGCACAATCAGTCTGCCAAGGCGCATAAGAACGGAATCAAGAAGCCAAGGA
ttttaac putative branch site (score: 2)
acttttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagctgcttatatccggctgatcgctggatataatttgacttttaactcttctcgtttgtttcgttggtgattgagtttgaaaagTTGTGTTGTGCCGTTGTTACAGAAATGGCGAAATCGAAGAATCACACGGCGCACAATCAGTCTGCCAAGGCGCATAAGAACGGAATCAAGAAGCCAAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC