Sequence
atgc intronic sequence ATGC exonic sequenceCGATGGAGTCACGAATGGATCAGTACGAGCTTATGGAACAGATCGGGAGAGGAGCGTTTGGTGCTGCTATTTTAGTTCATCATAAAGCTGAGAGAAAGAAgtaaaattggtttctccatttataaactcttttctttgaagatccttaggtttttgatttttgtgtattggtgtgtatttttag
Basic information
species | Arabidopsis thaliana |
transcript | AT3G44200.1 |
intron # | 1 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G44200.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GRMZM2G074262_T01 (Zea mays), 5'ss of exon 2
CGATGGAGTCACGAATGGATCAGTACGAGCTTATGGAACAGATCGGGAGAGGAGCGTTTGGTGCTGCTATTTTAGTTCATCATAAAGCTGAGAGAAAGAAgtaaaattggtttctccatttataaactcttttctttgaagatccttaggtttttgatttttg-tgtattggtgtgtatttttag
| ||||||||||| ||||||||||||||| || |||| ||||| || | || || ||||||||||| || | || | || || | |||| ||||||||| || || | || | |||| | | ||| | ||||| | | | ||
CCATGGAGTCACGGATGGATCAGTACGAGGTTTTGGAGCAGATTGGTCGCGGCGCCTTTGGTGCTGCCATCCTCGTCAACCACAAGACAGAGAAAAAGAAgtacggttcaatttagttactgagcctgtttccccgtgaatttgcctagccgacagtcttttgctttgctactgcag--------
upper sequence: AT3G44200.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA11G18340.1 (Glycine max), 5'ss of exon 1
CGATGGAGTCACGAATGGATCAGTACGAGCTTATGGAACAGATCGGGAGAGGAGCGTTTGGTGCTGCTATTTTAGTTCATCATAAAGCTGAGAGAAAGAAgtaaaattggtttctccatttataaactcttttctttgaagatccttaggtttttgatttttgtgtattggtgtgtatttttag-----------------------------------------
|||||||| || ||||||||||| ||| | ||||| |||||||| |||||||| ||||| ||||||||| | ||||| || || ||||||| |||||||||| | || | | ||| || || || | | || || | || | |||||| ||| |||
--ATGGAGTCTCGGATGGATCAGTATGAGATCATGGAGCAGATCGGTAGAGGAGCATTTGGAGCTGCTATTCTTGTTCACCACAAGGCTGAGAAAAAGAAgtaa---tagtcaccactttttgaatttcattgatggggttatgtttgtttgttcataagaaattcgttggtgggtaggtttgtaagtttgatgatgactgaagctttgttttactggattgcag
upper sequence: AT3G44200.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA12G09910.1 (Glycine max), 5'ss of exon 1
CGATGGAGTCACGAATGGATCAGTACGAGCTTATGGAACAGATCGGGAGAGGAGCGTTTGGTGCTGCTATTTTAGTTCATCATAAAGCTGAGAGAAAGAAgtaaaattggtttctccatttataaactcttttctttgaagatccttaggtttttgatttttgtgta-----ttggtgtgtatttttag--------------------------------------
|||||||| || ||||||||||| ||| | ||||| |||||||| ||||||| ||||| || |||||| | ||||| || || ||||||| ||||||||| | | || ||| || |||| |||| | || | ||||| || || | | ||| || ||| |||
--ATGGAGTCTCGGATGGATCAGTATGAGATCATGGAGCAGATCGGTCGAGGAGCATTTGGAGCGGCTATTCTTGTTCACCACAAGGCTGAGAAGAAGAAgtaatagtcaccactt--tttgta------tttcattgatggggctacgtttttttgttcatgagaaattcgttgatgggtaggtttgtaagtttgatgactgaagctttgttttattgggttgcag
upper sequence: AT3G44200.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: Vv06s0009g00690.t01 (Vitis vinifera), 5'ss of exon 1
CGATGGAGTCACGAATGGATCAGTACGAGCTTATGGAACAGATCGGGAGAGGAGCGTTTGGTGCTGCTATTTTAGTTCATCATAAAGCTGAGAGAAAGAAgtaaaattg-gtttctccatttataaactcttt---tctttgaagatccttaggtt-------tttgatttttgtgtattggtgtgt----atttttag
|||||||| |||||||||||||||||| | ||||| |||||||| | |||||||| || ||||| ||| | || |||| ||| | |||| |||||||| || | || | || | ||| | | |||| || || | |||| |||| | || | | ||| ||||| ||
TCATGGAGTCTCGAATGGATCAGTACGAGATCATGGAGCAGATCGGACGCGGAGCGTTCGGGGCTGCCATTCTTGTGAATCACAAATCGGAGAAGAAGAAgtatttttatgatttttttttggcgcaatctatgaatttttggtgagttttgtaatgagatggtttggttttggagtgatcgagtggttcgattttcag
upper sequence: AT3G44200.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: EFJ20709 (Selaginella moellendorffii), 5'ss of exon 1
CGATGGAGTCACGAATGGATCAGTACGAGCTTATGGAACAGATCGGGAGAGGAGCGTTTGGTGCTGCTATTTTAGTTCATCATAAAGCTGAGAGAAAGAAgtaaaattggtttctccatttataaactcttttctttgaagatccttaggtttttgatttttgtgtattggtgtgtatttttag
||||||||||||||| ||||||| ||| | |||||||| || |||||| |||| || | || |||| ||| |||| ||||||| | | | ||| || ||||||| | | | | || | | | || |
--------------ATGGATCAGTACGAGATTATGGAGCAGGTTGGGAGAGGGGCATTTGGTTCTGCGATACTCGTCAATCACAAAATCGAGAAGAAGAAgtga----gtgctgagaattggctaagatttttcttcttggctgatgaagtgtgttctcttgcag-------------------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|124728988|gb|EH820390.1|EH820390EST: GGAGCGTTTGGTGCTGCTATTTTAGTTCATCATAAAGCTGAGAGAAAGAA GTATGTTTTGA
genomic: GGAGCGTTTGGTGCTGCTATTTTAGTTCATCATAAAGCTGAGAGAAAGAAgtaaaattgg ... gtatttttagGTATGTTTTGA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CGATGGAGTCACGAATGGATCAGTACGAGCTTATGGAACAGATCGGGAGAGGAGCGTTTGGTGCTGCTATTTTAGTTCATCATAAAGCTGAGAGAAAGAAgtaaaattggtttctccatttataaactcttttctttgaagatccttaggtttttgatttttgtgtattggtgtgtatttttag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA