Sequence
atgc intronic sequence ATGC exonic sequenceAGCAGCATGTTCATCTGCTGATGGAAGGCAACTTCTGGAGTCATCTAAAACAGCTTTAGACAAAGGAAAGCTTGAAGATGCAGTTACATATGGAACGAAGgtccatgtctactcctcagctatttcttcatattacttgttttttatacagcgtcatgattttgttttgttgttttgtctctttctttttttcctccattag
Basic information
species | Arabidopsis thaliana |
transcript | AT1G01320.1 |
intron # | 17 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G01320.1 (Arabidopsis thaliana), 5'ss of exon 17
lower sequence: LOC_Os07g23990.1 (Oryza sativa), 5'ss of exon 15
AGCAGCATGTTCATCTGCTGATGGAAGGCAACTTCTGGAGTCATCTAAAACAGCTTTAGACAAAGGAAAGCTTGAAGATGCAGTTACATATGGAACGAAGgtccatgtctactcctcagctatttcttcatattacttgttttttatacagcgtcatgattttgttttgttgttttgtctctttctttttttcctccattag
|| ||||| ||||||||||||||||||||||| ||||| || |||||||| || | ||||| ||||| ||||||||||| || | ||||| || ||||| || || | | | || | || ||||| | | | || |||| | | || | |
AGTTGCATGCTCATCTGCTGATGGAAGGCAACTGCTGGAATCCTCTAAAACTGCCCTTGACAAGGGAAAACTTGAAGATGCTGTCAATTATGGGACCAAGgt--atcctctttcacaaaacagtctatctttttgaacatttttgg-atgccatt-tgttttttaatcactattccaatggatgaatgcag-----------
upper sequence: AT1G01320.1 (Arabidopsis thaliana), 5'ss of exon 17
lower sequence: GLYMA16G02770.1 (Glycine max), 5'ss of exon 17
AGCAGCATGTTCATCTGCTGATGGAAGGCAACTTCTGGAGTCATCTAAAACAGCTTTAGACAAAGGAAAGCTTGAAGATGCAGTTACATATGGAACGAAGg--tccatgtcta---ctcctcagct--atttcttcatatt----acttgttttttatacagcgtcatgattttgttttgttgtt-ttgtctctttctttttttcctccattag------
||||||||| |||||||| ||||||||||| || || |||||||| ||||| ||||||||||| ||||||||||| ||||||||||| ||||| || |||| || | ||| | | | | | | |||||| | | || | ||||| |||| | ||| ||| || | || | | | | | | | || |
AGCAGCATGCTCATCTGCAGATGGAAGGCAGCTCCTAGAGTCATCCAAAACTGCTTTAGACAAGGGAAAGCTTGAGGATGCAGTTACCTATGGCACAAAGgtatctacgtccagaaccctttgtttggaaatcttcaaagtgtcgacaaggtttttcaacagtctacacctttcatttcagaattgtcgtttgatatctgctataattcgttggtgacag
upper sequence: AT1G01320.1 (Arabidopsis thaliana), 5'ss of exon 17
lower sequence: GLYMA07G06160.1 (Glycine max), 5'ss of exon 17
AGCAGCATGTTCATCTGCTGATGGAAGGCAACTTCTGGAGTCATCTAAAACAGCTTTAGACAAAGGAAAGCTTGAAGATGCAGTTACATATGGAACGAAGgt--ccatgtctac--tcctcagct---atttcttcatatt----acttgttttttatacagcgtcatgattttgttttgttgtt-ttgtctctttctttttttcctccattag------
|| || |||||||| ||||| ||||||||||| ||||||||||| ||||||||||| ||||| || ||||| | | || | ||| | | | |||||| ||| || | ||||| |||| |||| ||| || |||| | | | | | | | || |
-------------------------------CTCCTAGAGTCATCCAAAACTGCTTTAGACAAGGGAAAGCTTGAGGATGCAGTTACCTATGGCACAAAGgtatctacatccagaaccctttgtttggaaatcttcaaattgtggacaaggtttttcaacagtcaacacatttcatttcagaattgttgtgtgatatctgctataattcgttggtgacag
upper sequence: AT1G01320.1 (Arabidopsis thaliana), 5'ss of exon 17
lower sequence: Vv15s0046g00740.t01 (Vitis vinifera), 5'ss of exon 17
AGCAGCATGTTCATCTGCTGATGGAAGGCAACTTCTGGAGTCATCTAAAACAGCTTTAGACAAAGGAAAGCTTGAAGATGCAGTTACATATGGAACGAAGgtccatg---------tctactcctcagctatttcttcatattacttgtttttta--tacagcgtcatgattttgttttgttgttttgtctctttctttttttcct-ccattag--------------------
||||||||| |||||||| |||||| | |||||||| || ||||| ||||||||| |||| || ||||| |||||||||||||| | ||||| || ||||| || || | | | |||||| || | | | | | |||| | || || |||| || | | || | | || || || |
AGCAGCATGCTCATCTGCAGATGGACGACAACTTCTAGAATCATCAAAAACAGCTCTAGATAAGGGAAAACTTGAAGATGCAGTCAGCTATGGGACAAAGgtatttgatttaaaagtccatcggtttgtcatttctatatgtaaactaccaatcgggtgcagcagaaaaatctttctttgcctgttcattggtaaattaatatgctaccttttgtatttttgtggtttttgcag
upper sequence: AT1G01320.1 (Arabidopsis thaliana), 5'ss of exon 17
lower sequence: Vv00s0388g00080.t01 (Vitis vinifera), 5'ss of exon 2
AGCAGCATGTTCATCTGCTGATGGAAGGCAACTTCTGGAGTCATCTAAAACAGCTTTAGACAAAGGAAAGCTTGAAGATGCAGTTACATATGGAACGAAGgtccatg---------tctactcctcagctatttcttcatattacttgtttttta--tacagcgtcatgattttgttttgttgttttgtctctttctttttttcct-ccattag--------------------
||||||||| |||||||| |||||| | |||||||| || ||||| |||||| || |||| || ||||| |||||||||||||| | ||||| || ||||| || || | | | |||||| || | | | | | ||| | || || |||| || | | || | | || | || |
AGCAGCATGCTCATCTGCAGATGGACGACAACTTCTAGAATCATCAAAAACAACTATAGATAAGGGAAAACTTGAAGATGCAGTCAGCTATGGGACAAAGgtatttgatttaaaagtccatcggtttgtcatttctatatgtaaactaccaatcgggtgcagtagaaaaatctttctttgcatgttcattggtaaattaatatgctatcttttgtatttttgtggtttttgcagMapped 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|124986469|gb|EL058989.1|EL058989EST: ATGGAACGAAG GCTCTTGCTAAACTCGTAGCAGTTTGCGGTCCCTATCACAGAATGACAGCC
genomic: ATGGAACGAAGgtccatgtct ... cctccattagGCTCTTGCTAAACTCGTAGCAGTTTGCGGTCCCTATCACAGAATGACAGCC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AGCAGCATGTTCATCTGCTGATGGAAGGCAACTTCTGGAGTCATCTAAAACAGCTTTAGACAAAGGAAAGCTTGAAGATGCAGTTACATATGGAACGAAGgtccatgtctactcctcagctatttcttcatattacttgttttttatacagcgtcatgattttgttttgttgttttgtctctttctttttttcctccattag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG