Sequence
atgc intronic sequence ATGC exonic sequenceGTATGTGAAGAATTTGATGGCACTTGCTGGTCTTACTGTTAGAGAAGATGCTGTTGGTAACATATTTGGCAAATGgtttggttctcgctctctgttgctaattgtttcgttaagaagataggtttgattatgttatccatgtgaggtgtgttgttttgacttctctaacttag
Basic information
species | Arabidopsis thaliana |
transcript | AT5G43600.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G43600.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G130034_T02 (Zea mays), 5'ss of exon 3
GTATGTGAAGAATTTGATGGCACTTGCTGGTCTTACTGTTAGAGAAGATGCTGTTGGTAACATATTTGGCAAATGgt---ttggttctcgct-----------ctctgtt----gctaattgtttcg---ttaagaag-----ataggtttgattat--gttatccatgtgag-gtgtgttgttttgacttctctaacttag------------------------------------------------
|||| | || | ||| | ||| ||| |||| ||||||||||||||||||||||||||||| |||| ||||| | || ||||| | | | ||| || | ||| |||| | | ||| | | || | ||| || | | | |||| || ||| || |
GTATATAAAAGGGATAATGAATCAACTTGGCCTTGTTGTTCGAGAAGATGCTGTTGGTAACATATTTGGCCGCTGgtgagttggtcttgactgcccttggattctctgctcttggttcatttctttggatttaggaagcatacaaggattttgctgtaaattgtgcatctggctgaaaagtctcttgattttgttaaatttgctgtgtgctggaattctcatgcccattgaacattgcaaccttctacag
upper sequence: AT5G43600.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA20G34790.1 (Glycine max), 5'ss of exon 3
GTATGTGAAGAATTTGATGGCACTTGCTGGTCTTACTGTTAGAGAAGATGCTGTTGGTAACATATTTGGCAAATGgtttggttc---tcgctctctgttgctaattgtttcgttaagaagataggtttgattatgt-tatccatgtgaggtgtgtt-gttttgacttctctaacttag
|||||| || | ||||| |||||||||||| |||| ||||| ||||||||||||||||||||||| |||| | || | | | | | || || |||| | ||| | || | | || || | | | || | | ||||| ||
GTATGTAAAAACCCAGATGGAACTTGCTGGTCTATCTGTGAGAGAGGATGCTGTTGGTAACATATTTGGTCGTTGgtgagtgtctgcttgttttgttccgcaaaaactttccaaatgaaatctcatccaataacttctaacctcaatatttatatttataattgtctctctgtct---
upper sequence: AT5G43600.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA10G32850.2 (Glycine max), 5'ss of exon 2
-------------------------GTATGTGAAGAATTTGATGGCACTTGCTGGTCTTACTGTTAGAGAAGATGCTGTTGGTAACATATTTGGCAAATGgtttg-gttctcgctctctgttgct-aattgtttcgttaagaagataggtttgattatgttatccatgtgaggtgtgttgttttgact-tctctaacttag
|||||| || | ||||| ||||||||| || |||| ||||| ||||||||||||||||||||||| |||| | || | | |||| || | | | || | ||| | | || || | | | | | || | | | ||||| ||
CTCCTTCCTTGTCTTGCGTCTGTAGGTATGTAAAAACCCAGATGGAACTTGCTGGCCTATCTGTGAGAGAGGATGCTGTTGGTAACATATTTGGTCGTTGgtgagtgtctgcttgttttgttcctcgaaagaattccaaatgaaatatcatccaataacttctaacctcaatatttatatttataattgtctctgtctct-
upper sequence: AT5G43600.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA10G32850.1 (Glycine max), 5'ss of exon 3
GTATGTGAAGAATTTGATGGCACTTGCTGGTCTTACTGTTAGAGAAGATGCTGTTGGTAACATATTTGGCAAATGgtttg-gttctcgctctctgttgct-aattgtttcgttaagaagataggtttgattatgttatccatgtgaggtgtgttgttttgact-tctctaacttag
|||||| || | ||||| ||||||||| || |||| ||||| ||||||||||||||||||||||| |||| | || | | |||| || | | | || | ||| | | || || | | | | | || | | | ||||| ||
GTATGTAAAAACCCAGATGGAACTTGCTGGCCTATCTGTGAGAGAGGATGCTGTTGGTAACATATTTGGTCGTTGgtgagtgtctgcttgttttgttcctcgaaagaattccaaatgaaatatcatccaataacttctaacctcaatatttatatttataattgtctctgtctct-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|124948426|gb|EL024174.1|EL024174EST: GCTGGTCTTACTGTTAGAGCAGATGCTGTTGGTAACATATTTGGCAAATG GGATGGTTTAGAGCCAAATCTGCCTG
genomic: GCTGGTCTTACTGTTAGAGAAGATGCTGTTGGTAACATATTTGGCAAATGgtttggttct ... tctaacttagGGATGGTTTAGAGCCAAATCTGCCTG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTATGTGAAGAATTTGATGGCACTTGCTGGTCTTACTGTTAGAGAAGATGCTGTTGGTAACATATTTGGCAAATGgtttggttctcgctctctgttgctaattgtttcgttaagaagataggtttgattatgttatccatgtgaggtgtgttgttttgacttctctaacttag
- - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - GCTGTT