Sequence
atgc intronic sequence ATGC exonic sequenceAACGACATAAAGAGTATTGCCTCTGAGATGGAAGGGAAAACTGAGGAAGAGGTTGAACGATATGCTCAAGTTTTCCAAGTGCGATATAAAGAGCTGAATGgttagtaactttagattgttaagtaaagttaatgagtgtttgcagtgcgacaaagttggatatttatcctaagtaagctctgcctcttgttttcctttgtaaaaattgtag
Basic information
species | Arabidopsis thaliana |
transcript | AT5G18620.1 |
intron # | 21 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G18620.1 (Arabidopsis thaliana), 5'ss of exon 21
lower sequence: LOC_Os01g27040.1 (Oryza sativa), 5'ss of exon 21
AACGACATAAAGAGTATTGCCTCTGAGATGGAAGGGAAAACTGAGGAAGAGGTTGAACGATATGCTCAAGTTTTCCAAGTGCGATATAAAGAGCTGAATGgttagtaa---ctttagattgttaagtaaagttaatgagtgtttg--cagtgcgacaaagttggatatttatcctaagt---aagctctgcctcttgttttcctttgtaaaaattgtag------------------------------
|| || || | |||||||||| |||| ||||| ||||| || ||||| || ||| ||||||||||| |||||||| | | | |||| || || |||| |||| || || || | | || | ||||| | | || ||| | || || | | | | | | | || | || || | || ||| | |
AATGATATTAGGAGTATTGCCGCTGAAATGGAGGGGAAGACAGAGGAGGAAGTTCAACGATATGCTAAAGTTTTCAAGGAGAGATACAAGGAACTGAGTGgtaagcaagtgtttcaattgagtatacatgattaataaattgttaattagtacataaatcttcaccaaacagctaatttcttatgtggtgaatggtgagttgagaactgaagattattggctgatcattattattgactgtccaaccag
upper sequence: AT5G18620.1 (Arabidopsis thaliana), 5'ss of exon 21
lower sequence: GLYMA13G28720.1 (Glycine max), 5'ss of exon 21
AACGACATAAAGAGTATTGCCTCTGAGATGGAAGGGAAAACTGAGGAAGAGGTTGAACGATATGCTCAAGTTTTCCAAGTGCGATATAAAGAGCTGAATGgttagtaactttagattgttaagtaaagttaatgagtgtttgcagtgcgacaaagttggatatttatcctaagtaagctctgc-ctcttgttttcc--tttgtaaaaattgtag
|| || ||||| ||||||| |||||||||||||| ||||||||||| || |||||| ||||||| | || ||| ||| |||| || || | |||||| | ||| | | | || || | | | |||| |||| | ||| ||| ||| || || | | | || | ||| | |||||| | |
AATGATATAAAAGGTATTGCTTCTGAGATGGAAGGAAAAACTGAGGAGGAAGTTGAAAGATATGCAAAGGTCTTCAAAGAAAGATACAAGGAATTAAATGgt-----atgttacagttacagccaatgtgacta--tatttg-agtgtgg--aagcaaaatacttagccaaatccaaatgagtgttcatatttgctagtttgtagtactc----
upper sequence: AT5G18620.1 (Arabidopsis thaliana), 5'ss of exon 21
lower sequence: GLYMA15G10370.1 (Glycine max), 5'ss of exon 21
AACGACATAAAGAGTATTGCCTCTGAGATGGAAGGGAAAACTGAGGAAGAGGTTGAACGATATGCTCAAGTTTTCCAAGTGCGATATAAAGAGCTGAATGgttagtaactttagattgttaagtaaagttaatgagtgtttgcagtgcgacaaagttggatatttat-cctaagtaagctctgcctcttgttttcctttgtaaaaattgtag
|| || ||| | |||||||| |||||||||||||| ||||| ||||| || |||||| ||||||| | || || ||| |||| || || | |||||| | ||| | | | || || ||| | | | || || |||| |||||| | | | | | ||| || || ||
AATGATATACAAAGTATTGCTTCTGAGATGGAAGGAAAAACCGAGGAGGAAGTTGAAAGATATGCAAAGGTCTTTAAAGAAAGATACAAGGAATTAAATGgt-----atgttacagttacagttacagccaat-----tcttctatg-gattttgttgattatttaagtgtggaagaaaaatacttagccaaatccaaatgaatgtttata-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|163993867|gb|ES200109.1|ES200109EST: GATATGCTCAAGTTTTCCAAGTGCGATATAAAGAGCTGAATG ATTACGACAGAATCATCAAGAATATTGAGAGAGGGGAAGCAAGAATCTCTA
genomic: GATATGCTCAAGTTTTCCAAGTGCGATATAAAGAGCTGAATGgttagtaact ... aaaattgtagATTACGACAGAATCATCAAGAATATTGAGAGAGGGGAAGCAAGAATCTCTA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AACGACATAAAGAGTATTGCCTCTGAGATGGAAGGGAAAACTGAGGAAGAGGTTGAACGATATGCTCAAGTTTTCCAAGTGCGATATAAAGAGCTGAATGgttagtaactttagattgttaagtaaagttaatgagtgtttgcagtgcgacaaagttggatatttatcctaagtaagctctgcctcttgttttcctttgtaaaaattgtag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA