Sequence
atgc intronic sequence ATGC exonic sequenceAGCTTATGGGAAAGAAGGAAACTTTTCTTTTCCGAATGTTCCACCTATGGCAGACTTGTTATATGAGGTGGAAGTTATTGGGTTTGATGAAACAAAGGAGgtaagttatttcctataccatcatcttgtttccttaccaagacgactccacatccaagctttatcccaacctccttgcttacctctctgacttagatgatgtattgaacag
Basic information
species | Arabidopsis thaliana |
transcript | AT3G21640.1 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G21640.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os12g05090.1 (Oryza sativa), 5'ss of exon 4
AGCTTATGGGAAAGAAGGAAACTTTTCTTTTCCGAATGTTCCACCTATGGCAGACTTGTTATATGAGGTGGAAGTTATTGGGTTTGATGAAACAAAGGAGgtaagtta----tttcctataccatc----atcttg--tttccttaccaagacgactccacatccaagctttatcccaacctccttgcttacctctctgacttagatgatgtattgaacag
| |||||||||||||||| |||||| || || ||||| || || ||||||||| | ||||||| || ||| |||||||||||||||| || |||||| | || | | || || | || ||| ||| ||| || | | | | ||| || | || || | | | | | |||
TGGCTATGGGAAAGAAGGAAGCTTTTCATTCCCAAATGTCCCTCCAATGGCAGACCTTGTATATGAAGTTGAACTTATTGGGTTTGATGATGTCAAAGAGgtaggataaatatccctcttatcacccttgattttgattttttttaaaaaaatatttgtgaaccaaaggttcctaggaagcttacagataa--tgtaaaactacag---------------
upper sequence: AT3G21640.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os11g05090.1 (Oryza sativa), 5'ss of exon 4
AGCTTATGGGAAAGAAGGAAACTTTTCTTTTCCGAATGTTCCACCTATGGCAGACTTGTTATATGAGGTGGAAGTTATTGGGTTTGATGAAACAAAGGAGgtaagttatttcctataccatcatcttgtttccttaccaagacgactcc----acatccaagctttatcccaacctccttgcttacctctctgacttagatgatgtattgaacag----------------------------------------------
|| |||||||||||||| | |||||| || || ||||| || || |||||||| | |||||||| || ||| |||||||||||||||| || |||||| | | | | | ||||| | | | | | | | || | | ||| | || ||| | | | | || | ||| || | |
AGGCTATGGGAAAGAAGGGAGCTTTTCATTCCCAAATGTCCCTCCAATGGCAGATCTTTTATATGAAGTTGAACTTATTGGGTTTGATGATGTCAAAGAGgtagggaaacatccttcttaccatctccacccaacataatgcttatccttattatttctgatagtaatctgagacta-ttgttggttggtttcattttatttatggttttcaaggtgatttggatgttctaaggaaccttacaaattgtgtacaactgcag
upper sequence: AT3G21640.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA12G01080.1 (Glycine max), 5'ss of exon 4
AGCTTATGGGAAAGAAGGAAACTTTTCTTTTCCGAATGTTCCACCTATGGCAGACTTGTTATATGAGGTGGAAGTTATTGGGTTTGATGAAACAAAGGAGgtaagttatttcctataccatcatc--ttgtttccttaccaagacgactccacatccaagctttatcccaacctccttgcttacctctctgacttagatgatgtattgaacag
|| ||||| | ||||||| ||| |||||||| ||||||||||| | |||||| || | ||||| || || | ||||| |||||||||||||| || ||||||| || | || ||| ||| ||| | | | || || |
AGGATATGGAGAGGAAGGAAGCTTCTCTTTTCCAAATGTTCCACCCAAGGCAGATTTAGTTTATGAAGTTGAGCTCATTGGCTTTGATGAAACAAAAGAAgtaagttgccat-taaattatggatggctgtggacttggttagatgcttatagcacctgatttcacag---------------------------------------------
upper sequence: AT3G21640.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv13s0064g00580.t01 (Vitis vinifera), 5'ss of exon 5
AGCTTATGGGAAAGAAGGAAACTTTTCTTTTCCGAATGTTCCACCTATGGCAGACTTGTTATATGAGGTGGAAGTTATTGGGTTTGATGAAACAAAGGAGgtaagttatttcctataccatcatctt--gtttccttaccaagacgactccacatccaagctttatccca----acctccttgcttacctctctg-----acttagatg--atgtattgaacag
| |||||||||||||||| |||||||| ||||||||||| ||||||||||| | || ||||| || || ||||||| ||||||||||| || |||||||||| | |||| | || || ||||| ||| | | | | || ||| || | | ||| || | || | || || | | | | || ||||
GGGCTATGGGAAAGAAGGAAGTTTTTCTTTCCCGAATGTTCCGCCTATGGCAGATATTTTGTATGAAGTTGAGCTTATTGGCTTTGATGAAACTAAAGAGgtaagtt-tctccttcatgattttccaaagtttctttattg---ctgtttcctgcctaaacttcattgtatgcgagctcattatagaattcaatatatgaacctacaagcaacgcatgttacag
upper sequence: AT3G21640.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: EFJ37527 (Selaginella moellendorffii), 5'ss of exon 3
AGCTTATGGGAAAGAAGGAAACTTTTCTTTTCCGAATGTTCCACCTATGGCAGACTTGTTATATGAGGTGGAAGTTATTGGGTTTGATGAAACAAAGGAGgtaagttatttcctataccatcatcttgtttccttaccaagacgactccacatccaagctttatcccaacctccttgcttacctctctgacttagatgatgtattgaacag
| ||||| |||||||| |||||||| ||||| || |||||||||||||| || | | || || ||||| | || || || || | || ||||||| | ||| | | | || | || || | | | | | ||| || | |
TGGGTATGGAAAAGAAGGGAACTTTTCGTTTCCAAACGTTCCACCTATGGCTGATCTTGTGTACGAAGTGGAGCTCATCGGATTCGAGAATGCACGCGAGgtaaagttgctcccg-atcgtgattcggattggttttttaattttgttttctttc---ttttgtctccag-----------------------------------------
upper sequence: AT3G21640.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: EFJ34019 (Selaginella moellendorffii), 5'ss of exon 3
AGCTTATGGGAAAGAAGGAAACTTTTCTTTTCCGAATGTTCCACCTATGGCAGACTTGTTATATGAGGTGGAAGTTATTGGGTTTGATGAAACAAAGGAGgtaagttatttcctataccatcatcttgtttccttaccaagacgactccacatccaagctttatcccaacctccttgcttacctctctgacttagatgatgtattgaacag
| ||||| |||||||| |||||||| ||||| ||||||||||| ||||| || | | || || ||||| | || || || || | || ||||||| | ||| | | | || | || || | | | | | ||| || | |
TGGGTATGGAAAAGAAGGGAACTTTTCGTTTCCAAATGTTCCACCAATGGCTGATCTTGTGTACGAAGTGGAGCTCATCGGATTCGAGAATGCACGCGAGgtaaagttgctcccg-atcgtgattcggattggttttttaattttgttttctttc---ttttgtctccag-----------------------------------------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|163982217|gb|EL977558.1|EL977558EST: TGATGAAACAAAGGAG GG-AAAGCTCGCAGTGATATGACTGTAGAGGAAAGGATTGGTGCAGCAGAC
genomic: TGATGAAACAAAGGAGgtaagttatt ... tattgaacagGGAAAAGCTCGCAGTGATATGACTGTAGAGGAAAGGATTGGTGCAGCAGAC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AGCTTATGGGAAAGAAGGAAACTTTTCTTTTCCGAATGTTCCACCTATGGCAGACTTGTTATATGAGGTGGAAGTTATTGGGTTTGATGAAACAAAGGAGgtaagttatttcctataccatcatcttgtttccttaccaagacgactccacatccaagctttatcccaacctccttgcttacctctctgacttagatgatgtattgaacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG