Sequence
atgc intronic sequence ATGC exonic sequenceGCGTGGGCGAAGTGGCCGGCAAGGGGATCCTGGAAGTTCCCGATTCTTCCTTAGTCTTGAAGATAACATATTCCGCATTTTTGGTGGAGATCGGATTCAGgtgacatttgtatctacaatttattgattcttctggaaaataatcgtctaaacatagttgccgtataactcttag
Basic information
species | Arabidopsis thaliana |
transcript | AT4G01800.2 |
intron # | 15 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G01800.1 (Arabidopsis thaliana), 5'ss of exon 15
lower sequence: LOC_Os01g21820.1 (Oryza sativa), 5'ss of exon 14
GCGTGGGCGAAGTGGCCGGCAAGGGGATCCTGGAAGTTCCCGATTCTTCCTTAGTCTTGAAGATAACATATTCCGCATTTTTGGTGGAGATCGGATTCAGgtgacatttgtatctacaattt--attgattcttctggaaaataatcgtctaaacatagttgccgtataactcttag-----------------------
||||| ||||||||| |||||||||||||||| || || || ||||| ||||||||||| ||||| |||||||| |||||||| || || |||| ||||| || | | | |||| ||| ||| | | || | || || | ||| || |
CCGTGGTCGAAGTGGCAGGCAAGGGGATCCTGGGAGCTCTCGGTTCTTTCTTAGTCTTGAGGATAATATATTCCGAATTTTTGGAGGTGACAGGATACAGgtttgtgttatcttccctatttccatttcctctctctggatgacattgcaacaatatcaatattgtagggctgcaaatgtacatcattgcatccaaagta
upper sequence: AT4G01800.1 (Arabidopsis thaliana), 5'ss of exon 15
lower sequence: GLYMA10G27810.1 (Glycine max), 5'ss of exon 16
GCGTGGGCGAAGTGGCCGGCAAGGGGATCCTGGAAGTTCCCGATTCTTCCTTAGTCTTGAAGATAACATATTCCGCATTTTTGGTGGAGATCGGATTCAGgtgacatttgtatctacaat-ttattgattcttctggaaaat--aatcgtctaaacatagttgccgt-ataactcttag
|||||| ||||||||| | ||||| ||||| ||||| ||||| || ||| | |||||||||||||||||||| || ||||||||||||||||| |||||||| | || || | | || || | | ||||| | | | | | ||| | ||| | | | |||
GCGTGGTCGAAGTGGCAGACAAGGAGATCCAGGAAGCTCCCGCTTTTTCTTAAGTCTTGAAGATAACATATTTCGTATTTTTGGTGGAGATCGAATTCAGgtaa----tgcatttgttgtgttgctgctacacttggaattttgattggccagaacttggttaatattgtgatgtgtag
upper sequence: AT4G01800.1 (Arabidopsis thaliana), 5'ss of exon 15
lower sequence: GLYMA02G01060.1 (Glycine max), 5'ss of exon 16
GCGTGGGCGAAGTGGCCGGCAAGGGGATCCTGGAAGTTCCCGATTCTTCCTTAGTCTTGAAGATAACATATTCCGCATTTTTGGTGGAGATCGGATTCAGgtgacatttgtatctacaat-ttattgattcttctggaaaataatcgtctaaa-catagttgccgt-ataactcttag
|||||| ||||||||| | ||||| ||||| ||||| || || || ||| | |||||||||||||||||||| || ||||||||||||||||| |||||||| | || || || | || || | | ||||| | || | | ||| | ||||| | | | |||
GCGTGGTCGAAGTGGCAGACAAGGAGATCCGGGAAGCTCACGCTTTTTCTTAAGTCTTGAAGATAACATATTTCGTATTTTTGGTGGAGATCGAATTCAGgtaa----tgcatttattgtgttgctgctacacttggaatttgattgcccaaaacttagttaatattgtgatatgtag
upper sequence: AT4G01800.1 (Arabidopsis thaliana), 5'ss of exon 15
lower sequence: Vv07s0005g02610.t01 (Vitis vinifera), 5'ss of exon 16
GCGTGGGCGAAGTGGCCGGCAAGGGGATCCTGGAAGTTCCCGATTCTTCCTTAGTCTTGAAGATAACATATTCCGCATTTTTGGTGGAGATCGGATTCAGgt--gacatttgtatctacaatttattgattcttctggaaaataatcgtctaaacatagttgccgtataactcttag------
|||||| ||||||||||| ||||||||||| ||||||||||| |||||||||||||||||||||||||| || || |||||||| ||||| | |||||||| | | || | || | | |||| | | | || || | || | || | ||
GCGTGGTCGAAGTGGCCGCCAAGGGGATCCAGGAAGTTCCCGTTTCTTCCTTAGTCTTGAAGATAACATCTTTCGAATTTTTGGGGGAGACAGAATTCAGgtttagcctatggttttaaagtctattcgccactacagtttaggatttgcttgttaaagggttctcatttttgctaattgtagMapped 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|163994316|gb|ES019300.1|ES019300EST: ATTTTTGGTGGAGATCGGATTCAG GGTATGATGAGGGCATTTAGGGTGGAAGATTTACCGATCGAATCCAAGATG
genomic: ATTTTTGGTGGAGATCGGATTCAGgtgacatttg ... taactcttagGGTATGATGAGGGCATTCAGGGTGGAAGATTTACCGATCGAATCCAAGATG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GCGTGGGCGAAGTGGCCGGCAAGGGGATCCTGGAAGTTCCCGATTCTTCCTTAGTCTTGAAGATAACATATTCCGCATTTTTGGTGGAGATCGGATTCAGgtgacatttgtatctacaatttattgattcttctggaaaataatcgtctaaacatagttgccgtataactcttag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC