Sequence
atgc intronic sequence ATGC exonic sequenceATTCCTGTTTAGCGCTTGGGCTTGTGCAGCAGTTGGTCGAACTGCACAGGAGGTTGTCAACGAAGTAAGAAGACAGTTCATTGAGAGGCCTGGCATAATGgtaaatgtaattccgctggagtccgttcccttttatttttatttttttcatcgggtgtctttttgaactttatgtcacag
Basic information
species | Arabidopsis thaliana |
transcript | AT1G16780.1 |
intron # | 13 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G16780.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: LOC_Os02g33490.1 (Oryza sativa), 5'ss of exon 12
ATTCCTGTTTAGCGCTTGGGCTTGTGCAGCAGTTGGTCGAACTGCACAGGAGGTTGTCAACGAAGTAAGAAGACAGTTCATTGAGAGGCCTGGCATAATGgtaaatgtaattccgctggagtccgttcccttttatttttatttttttca---tcgggtgtctttttgaactttatgtcacag--
|||||||||||| || ||||||||| | || ||||| |||||||||| || ||||| ||||| || || |||||||| ||||||||||||||||| ||||| | | | | | | | ||| || || |||| | | | | | || || | |||| |
ATTCCTGTTTAGTGCATGGGCTTGTTCTGCTGTTGGCAGAACTGCACAAGAAGTTGTTAACGAGGTCAGGAGACAGTTTATTGAGAGGCCTGGCATTATGgtgagtaca--tgcatataattaagtttgtcatttttcttatgcctataaaagttaatgctaacttctaatataatgttatgcag
upper sequence: AT1G16780.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GRMZM2G075900_T01 (Zea mays), 5'ss of exon 12
ATTCCTGTTTAGCGCTTGGGCTTGTGCAGCAGTTGGTCGAACTGCACAGGAGGTTGTCAACGAAGTAAGAAGACAGTTCATTGAGAGGCCTGGCATAATGgtaaatgta--attccgctggagtccgttcccttttatttttatttttttcatcgggtgtctttttg-aactttatgtcacag
|||||||||||| || ||||||||| |||||||||| |||||||||||| ||||| || || || || ||||| || || ||||||||||| || ||||| | || | ||| | || ||| | ||| |||||| || | | | || ||| ||| ||| |||
ATTCCTGTTTAGTGCATGGGCTTGTTCAGCAGTTGGCAAAACTGCACAGGAAGTTGTTAATGAGGTCAGGAGACAATTTATCGAGAGGCCTGGTATTATGgtgagtgcatgattaccatgaagttc-ttcagttttatgcttggaaa----agctgatgctaacttgtaacaatatcatccag
upper sequence: AT1G16780.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GRMZM2G069410_T01 (Zea mays), 5'ss of exon 4
ATTCCTGTTTAGCGCTTGGGCTTGTGCAGCAGTTGGTCGAACTGCACAGGAGGTTGTCAACGAAGTAAGAAGACAGTTCATTGAGAGGCCTGGCATAATGgtaaatgta--attccgctggagtccgttcccttttatttttatttttttcatcgggtgtctttttg-aactttatgtcacag
||||||||| || || |||||||| |||||||||| |||||||||||| ||||| || || || || ||||| || |||||||||||||| || ||||| | | | ||| | || ||| | | | | ||| | || | | | || || ||| ||| |||
ATTCCTGTTCAGTGCATGGGCTTGCTCAGCAGTTGGCAAAACTGCACAGGAAGTTGTTAAAGAGGTCAGGAGACAATTTATTGAGAGGCCTGGTATCATGgtgagtacatgattaccatgaagttc--ttcagtccttttatgcttggaaaagcagatgctaacatgtaacaatatcatccag
upper sequence: AT1G16780.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GLYMA07G00350.1 (Glycine max), 5'ss of exon 12
ATTCCTGTTTAGCGCTTGGGCTTGTGCAGCAGTTGGTCGAACTGCACAGGAGGTTGTCAACGAAGTAAGAAGACAGTTCATTGAGAGGCCTGGCATAATGgtaaatgtaattccgc--tggagtccgttcccttttatttttatttttttcatcgggtgtctttttgaactttatgtcacag----
||| | ||||| |||||||| ||||| || ||||| |||||||||| || ||||| |||||||| ||||| |||||||||||||||||||| |||||||| | | | | | | | | | | | ||| |||| | | | ||||| |||||| |
ATTTGTTTTTAGTGCTTGGGCCTGTGCTGCTGTTGGCAGAACTGCACAAGAAGTTGTTAACGAAGTGAGAAGGCAGTTCATTGAGAGGCCTGGTATAATGgtgagtttgggtttgtaaagtaatattatgtatgccagtttaggttttgatcttctctctttttttcccttttatgcttttgacag
upper sequence: AT1G16780.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GLYMA08G24120.1 (Glycine max), 5'ss of exon 11
ATTCCTGTTTAGCGCTTGGGCTTGTGCAGCAGTTGGTCGAACTGCACAGGAGGTTGTCAACGAAGTAAGAAGACAGTTCATTGAGAGGCCTGGCATAATGgtaaatgtaattccgctggagtccgttcccttttatttttatttttttcatcgggtgtctttttgaactttatgtcacag----
||| | ||||| |||||||| ||| | || ||||| |||||||||| || ||||| |||||||| ||||| |||||||||||||||||||| |||||||| | | | | | || | | | || |||| || | ||||| ||||| |
ATTTGTTTTTAGTGCTTGGGCCTGTTCTGCTGTTGGCAGAACTGCACAAGAAGTTGTTAACGAAGTGAGAAGGCAGTTCATTGAGAGGCCTGGTATAATGgtgagtttgggtttgtaaagtaatattatgtatgacagtttcgattttgatgaccgctttttttcctgtttatacttttgacag
upper sequence: AT1G16780.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GLYMA08G24120.2 (Glycine max), 5'ss of exon 12
--------ATTCCTGTTTAGCGCTTGGGCTTGTGCAGCAGTTGGTCGAACTGCACAGGAGGTTGTCAACGAAGTAAGAAGACAGTTCATTGAGAGGCCTGGCATAATGgtaaatgtaattccgctggagtccgttcccttttatttttatttttttcatcgggtgtctttttgaactttatgtcacag----
||| | ||||| |||||||| ||| | || ||||| |||||||||| || ||||| |||||||| ||||| |||||||||||||||||||| |||||||| | | | | | || | | | || |||| || | ||||| ||||| |
ATGCTTATATTTGTTTTTAGTGCTTGGGCCTGTTCTGCTGTTGGCAGAACTGCACAAGAAGTTGTTAACGAAGTGAGAAGGCAGTTCATTGAGAGGCCTGgtataatggtgagtttgggtttgtaaagtaatattatgtatgacagtttcgattttgatgaccgctttttttcctgtttatacttttgacag
upper sequence: AT1G16780.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: Vv09s0054g00700.t01 (Vitis vinifera), 5'ss of exon 12
ATTCCTGTTTAGCGCTTGGGCTTGTGCAGCAGTTGGTCGAACTGCACAGGAGGTTGTCAACGAAGTAAGAAGACAGTTCATTGAGAGGCCTGGCATAATGgtaaatgtaattccgctggagtccgttcccttttat------------ttttatttttt--tcatcgggtg---tctttttgaactttatgtcacag
||||| ||||| || ||||| ||| | |||||||| || ||||| || ||||||||||| ||||||||||||||||| ||||||||||| || || ||||| | | | |||| || ||||| ||||| ||||| | | || | |||| | | | || ||||
TTTCCTATTTAGTGCATGGGCATGTTCTGCAGTTGGCCGGACTGCTCAAGAGGTTGTCAATGAAGTAAGAAGACAGTTTATTGAGAGGCCAGGTATCATGgtgagtatgattctctatagcatttttatggtttatcatgaatgtaggttttaatttttaattgatgcatgaaattgttttaacatgtttgctacagMapped 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|164126329|gb|ES197996.1|ES197996EST: TTGAGAGGCCTGGCATAATG GACTACAAGGAGAAGCCAGATTATGGTCGATGTGTCGCCATTGTCGCATCT
genomic: TTGAGAGGCCTGGCATAATGgtaaatgtaa ... tatgtcacagGACTACAAGGAGAAGCCAGATTATGGTCGATGTGTCGCCATTGTCGCATCT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ATTCCTGTTTAGCGCTTGGGCTTGTGCAGCAGTTGGTCGAACTGCACAGGAGGTTGTCAACGAAGTAAGAAGACAGTTCATTGAGAGGCCTGGCATAATGgtaaatgtaattccgctggagtccgttcccttttatttttatttttttcatcgggtgtctttttgaactttatgtcacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG