Sequence
atgc intronic sequence ATGC exonic sequenceTGCCTTTTGAGGAGGATGACAAAGACACAAGCATATGGTTTCTTGATCACAACTACCACGAGTCGATGTTTCACATGTTCAAGAGAATTAATGgtattgctcgggaaatataatgcttaagagtatatatgtggaaagcctcttttttgactgattttcatatttgctttcag
Basic information
species | Arabidopsis thaliana |
transcript | AT3G11270.1 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G11270.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os04g56646.1 (Oryza sativa), 5'ss of exon 2
TGCCTTTTGAGGAGGATGACAAAGACACAAGCATATGGTTTCTTGATCACAACTACCACGAGTCGATGTTTCACATGTTCAAGAGAATTAATGgtat-tgctcgggaaatataatgcttaa--gagtatatatgtggaaagcctcttttttgactgattttcatatttgctttcag
|||| ||||| ||||||||||| || | || || ||||| || ||||| || |||||||| ||||||||| |||||||||||| || || ||||| | | || | | || || |||| || | | || ||||| | | | | | ||
TGCCGTTTGAAGAGGATGACAAGGATCCGAGGATCTGGTTCCTCGATCATAATTACCACGAATCGATGTTTTCCATGTTCAAGAGGATCAACGgtatgcagtttgcaagtcttccatttgtttgacctgccctgtgtaactgattgtgttgtactgacgagctgttcttcgtgtag
upper sequence: AT3G11270.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G061745_T03 (Zea mays), 5'ss of exon 2
TGCCTTTTGAGGAGGATGACAAAGACACAAGCATATGGTTTCTTGATCACAACTACCACGAGTCGATGTTTCACATGTTCAAGAGAATTAATGgtattgctcgggaaatat-----aatgcttaagagtat-atatgtggaaagcctcttttttgactgattttcatat-ttgctttcag-----
|||| ||||||||||||||||| || | || || ||||| ||||| ||||| ||||||||||| ||||| |||||||||||| ||||||||||| |||| || || ||| | | | | || ||| | || |||| ||||| || || || |
TGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACAATTACCACGAGTCAATGTTCTCCATGTTCAAGAGGATTAATGgtat-gctctatcaaaatcctcaaattttgttgggcctgatccgtgctattgcttcttttgtcctgatgagcacgggctgtttgtggtgcag
upper sequence: AT3G11270.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G368908_T02 (Zea mays), 5'ss of exon 2
TGCCTTTTGAGGAGGATGACAAAGACACAAGCATATGGTTTCTTGATCACAACTACCACGAGTCGATGTTTCACATGTTCAAGAGAATTAATGgtat--tgc-tcgggaaatataatgcttaa-gagtata-tatgtggaaagcctcttttttgactgattttcat-atttgctttcag-----
|||| ||||||||||||||||| || | || || ||||| ||||| ||||| ||||| || |||||||| |||||||||||| ||||| ||||| || || | ||| | | | | | |||| | | | | || ||||| ||| | || || |
TGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACAATTACCATGAATCGATGTTCTCCATGTTCAAGAGGATTAACGgtatgctgtatcaaaattctcggtgcctgttgggcctgctctgtgctatggattctgttgtcctgatgagcatgagctgtttgtggtgcag
upper sequence: AT3G11270.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA18G03360.1 (Glycine max), 5'ss of exon 2
-TGCCTTTTGAGGAGGATGACAAAGACACAAGCATATGGTTTCTTGATCACAACTACCACGAGTCGATGTTTCACATGTTCAAGAGAATTAATGgtattgctcgggaaatataatgcttaagagtatatat------gtggaaagcctcttttttgactgattttcatatttgctttcag------
|||| ||||| || |||||||| || | ||||| ||||||||||| ||||| ||||| || ||||||||| |||||| || ||||| |||||||| | || || | | || |||| | | | ||| |||| | | | ||| | ||| |||| |
GTGCCCTTTGAAGAAGATGACAAGGATCCTAGCATCTGGTTTCTTGACCACAATTACCATGAATCGATGTTTTCCATGTTTAAAAGAATAAATggtatgagtaggaaattttttccttttcttgtatgtctcttttaattgaatatctctgatctaattgaacatgggtttttcttttggtttaca
upper sequence: AT3G11270.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv02s0025g01490.t01 (Vitis vinifera), 5'ss of exon 2
TGCCTTTTGAGGAGGATGACAAAGACACAAGCATATGGTTTCTTGATCACAACTACCACGAGTCGATGTTTCACATGTTCAAGAGAATTAATGgtattgctcg-----ggaaatataatgcttaagagtatatatgtggaaagcctcttttttgactgattttcatatttgctttcag
|||| ||||| || |||||||| ||| |||| ||||| |||||||| |||||||||||||| || |||||| ||||||||||||||| ||||||||| | | | || | | | || | | |||| | | |||| || || ||| ||| ||||||
TGCCCTTTGAAGAAGATGACAAGGACCCAAGTATATGTTTTCTTGACCACAACTACCACGAATCAATGTTTTCCATGTTCAAGAGAATAAATGgtattattggttgtaagtgatgaggtatcttttacaatttttatggacaa--tgttttatgggaatttacaataattg-tttcag
upper sequence: AT3G11270.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv08s0007g01980.t01 (Vitis vinifera), 5'ss of exon 2
TGCCTTTTGAGGAGGATGACAAAGACACAAGCATATGGTTTCTTGATCACAACTACCACGAGTCGATGTTTCACATGTTCAAGAGAATTAATGgtattgctcgggaaatataatgcttaagagtatatatgtggaaagcctcttttttgactgattttcatatttgctttcag
|||| ||||| || |||||||| ||| ||||||||||||||||||| |||||||| || || || |||||| ||||||||||||||| ||||||||| | | || ||| | || | | | | ||| | | | || || || ||||||
TGCCCTTTGAAGAAGATGACAAGGACCCAAGCATATGGTTTCTTGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATGgtattatttttcgtaaatgatgaggtctcgcttacaatttttatgggcgatttcttatgggaatttatgatttgtttcag
upper sequence: AT3G11270.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: PP1S197_115V6.1 (Physcomitrella patens), 5'ss of exon 2
TGCCTTTTGAGGAGGATGACAAAGACACAAGCATATGGTTTCTTGATCACAACTACCACGAGTCGATGTTTCACATGTTCAAGAGAATTAATGgtattgct---------------cgggaaatataatgcttaagagta---tatatgtggaaagcctcttt---tttgactg---attttcatatttgctttcag----------------------------------------------------------------------------------------------
|||| |||||||| |||||||| || | ||||||||||| | || |||||||| || ||| | ||||| ||||||||||||||||||| |||||| | | || | | ||| ||| | ||| ||| || || ||| | | |||| | | ||||
TGCCCTTTGAGGAAGATGACAAGGATGCCAGCATATGGTTCTTGGACCACAACTATCATGAGACTATGTTCGACATGTTCAAGAGAATTAACGgtattcttactacttctttcctccaactgattaacttctttgtagttgtttggatgaagaacgcagctgcaagtttagcggtgtgttttaaccaatattttctaattttgactggtatgtctcgtaacattttgagtatggcagatttgttaaatctgtttgtggtaaaactgactgttgtaagacgtgtttgctcag
upper sequence: AT3G11270.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: EFJ21414 (Selaginella moellendorffii), 5'ss of exon 2
TGCCTTTTGAGGAGGATGACAAAGACACAAGCATATGGTTTCTTGATCACAACTACCACGAGTCGATGTTTCACATGTTCAAGAGAATTAATGgta--ttgctcgggaaatataat-gcttaagagtatatatgtggaaagcctcttttttgactgattttcatatttgctttcag
| || ||||| |||||||||| ||| ||||||| |||||| | ||||||||||| ||||| |||||||| | ||||||||| | || ||||||| || ||| | | | | |||| | || ||||
TACCGTTTGAAGAGGATGACAGGGACCCAAGCATTTGGTTTTTGGATCACAACTATCACGAAGCGATGTTTGATATGTTCAAGCGGATCAATGgtaagttcttcgtgttttttctttgcttggcattacgcttgtgcttgcag---------------------------------
upper sequence: AT3G11270.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: EFJ23777 (Selaginella moellendorffii), 5'ss of exon 2
TGCCTTTTGAGGAGGATGACAAAGACACAAGCATATGGTTTCTTGATCACAACTACCACGAGTCGATGTTTCACATGTTCAAGAGAATTAATGgta--ttgctcgggaaatataat-gcttaagagtatatatgtggaaagcctcttttttgactgattttcatatttgctttcag
| || ||||| |||||||||| ||| ||||||| |||||| | ||||||||||| ||||| |||||||| | ||||||||| | || ||||||| || ||| | | | | |||| | || | ||||
TACCGTTTGAAGAGGATGACAGGGACCCAAGCATTTGGTTTTTGGATCACAACTATCACGAAGCGATGTTTGATATGTTCAAGCGGATCAATGgtaagttcttcgtgttttttctttgcttggcattacgtttgtgcttgcag---------------------------------Mapped 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|19875108|gb|AU235939.1|AU235939EST: TGATCACAACTACCACGAGTCGATGTTTCACATGTTCAAGAGAATTAATG CTAAGGAGCATATTGTGGGTTGGTACAGCACAGGTCCTAAACTTCGAGAGA
genomic: TGATCACAACTACCACGAGTCGATGTTTCACATGTTCAAGAGAATTAATGgtattgctcg ... ttgctttcagCTAAGGAGCATATTGTGGGTTGGTACAGCACAGGTCCTAAACTTCGAGAGA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGCCTTTTGAGGAGGATGACAAAGACACAAGCATATGGTTTCTTGATCACAACTACCACGAGTCGATGTTTCACATGTTCAAGAGAATTAATGgtattgctcgggaaatataatgcttaagagtatatatgtggaaagcctcttttttgactgattttcatatttgctttcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA