Sequence
atgc intronic sequence ATGC exonic sequence...agttgtttcagataagttaacggtttgagtttagaaggccttaagcttggtggttatgtttctggactgcagcaatttaactgacatctcttctcatcagATTCTTGTGGAGGAAAAATGCTACTTTTGCTATTTCTAGACATTACAAACGATTTGATGTCTTAGTGGAAGCCGAAGCAAATAAAGCTGCTGGTAAATAT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G28240.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G28240.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os05g45490.1 (Oryza sativa), 3'ss of exon 6
agttgtttcagataagttaacggtttgagtttagaaggccttaagcttg-gtggttatgtttctggactgcagcaatttaactgacatctcttctcatcagATTCTTGTGGAGGAAAAATGCTACTTTTGCTATTTCTAGACATTACAAACGATTTGATGTCTTAGTGGAAGCCGAAGCAAATAAAGCTGCTGGTAAATAT
||| | | | || || ||| | || ||| || | ||| || | | | | ||| || || || || ||||||||||| ||||||||||||||||| ||| | || |||||||| |||||||| || | ||||| ||||| |||||||||||||| || |||
tagaatttggaacttaccagcttttcattattttaagatcgcaatattgcaatatttgactactgtgttgagtctgactgtgtcatatcatggct-attagGTTTTTGTGGAGGAAGAATGCTACTTTTGCTATCTCTCGGCACTACAAACGCTTTGATGTATTTGAAGAAGCAGAAGCTAATAAAGCTGCTGGCAAGTAT
upper sequence: AT1G28240.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os01g19870.1 (Oryza sativa), 3'ss of exon 6
---agttgtttcagataagttaacggtttg-agtttagaaggccttaagcttggtggttatgtttctggactgcagcaatttaactgacatctcttctcatcagATTCTTGTGGAGGAAAAATGCTACTTTTGCTATTTCTAGACATTACAAACGATTTGATGTCTTAGTGGAAGCCGAAGCAAATAAAGCTGCTGGTAAATAT
| | | | | | | | | | || | |||| || | | ||| | | ||| | ||| | | | | ||| ||||||||||||||| || |||| || || |||||||| || ||||||| ||| ||||||||||| | |||||| || || || || | || ||| || |||
tccatctaatgtataaagacctaagttgcataaattgtcaaagtttaatctgagcaatggcatttattgtctgttc---tctaatagcactgttatgtca-cagATTCTTGTGGAGAAAGAATGTTAGCTTCGCTATTTCCAGGCATTACAGACGCTTTGATGTCTTTGAGGAAGCAGAGGCCAACAAGGTTGGTGGAAAGTAT
upper sequence: AT1G28240.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G421791_T01 (Zea mays), 3'ss of exon 6
-agttgtttcagataagttaacggt-ttgagtttagaaggccttaagcttggtggttatgtttctggactgcagcaatttaactgacatctcttctcatcagATTCTTGTGGAGGAAAAATGCTACTTTTGCTATTTCTAGACATTACAAACGATTTGATGTCTTAGTGGAAGCCGAAGCAAATAAAGCTGCTGGTAAATAT
| | ||| | | | |||| || | || | || | | | | | ||| ||| | |||||| | | | |||| | || || ||| |||||||||| ||| | |||||||| || ||| | ||||||||||| |||||||| || | ||||| ||||| || ||||||||||| || |||
gtatcttatcatttcaat--acggcatttatttgacggttccatgaaaattggactgctgtaactgataaggagcaatctgatttcttactctgcatattagGTTCCTGTGGAGGAAGAATACCACTTTTGCAATCTCTCGGCATTACAAACGCTTTGATGTGTTCGAAGAAGCAGAAGCTAACAAAGCTGCTGGAAAGTAT
upper sequence: AT1G28240.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G044866_T01 (Zea mays), 3'ss of exon 6
-agttgtttcagataagttaacggtttgagtttagaaggccttaagcttggtggttatgtttctggactgcagcaatttaactgacatctcttctcatcagATTCTTGTGGAGGAAAAATGCTACTTTTGCTATTTCTAGACATTACAAACGATTTGATGTCTTAGTGGAAGCCGAAGCAAATAAAGCTGCTGGTAAATAT
| ||| ||| ||| | || | || | | | | | | ||| || || ||| | | | |||| | | || ||| | |||||||| ||| | |||||||| || ||| | ||||||||||| |||||||| || | ||||| ||||| || ||||||||||| || ||
gtatcccatcattgtagtacgacattt-atttgactgatccatgaaagttgggctgctgtaagtgataatgagtaatctgatttctcactctacctgttagGTTCCTTTGGAGGAAGAATACCACTTTTGCAATCTCTCGGCATTACAAACGCTTTGATGTGTTTGAAGAAGCAGAAGCGAACAAAGCTGCTGGAAAGTAC
upper sequence: AT1G28240.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA13G31260.1 (Glycine max), 3'ss of exon 6
---agttgtttcagataagttaacggtttgagtttagaaggccttaagcttggtggttatgtttctggactgcagcaatttaactgacatctcttctcatcagATTCTTGTGGAGGAAAAATGCTACTTTTGCTATTTCTAGACATTACAAACGATTTGATGTCTTAGTGGAAGCCGAAGCAAATAAAGCTGCTGGTAAATAT
| | | || | | || |||| | | | | || | | || | | | | ||| |||| || || | | || || ||||||||||| ||||| |||||||| || |||| |||||| | ||| |||||||| || || || ||||||||||||||||||||||| || |||
acacataatcatacctatgctgac--tttgtactaggtttatgtgagattttcttgatagaatacatgtgt-tggcacattaattgttctcatccttatttagGTTTTTGTGGAGGAAGAATGCAACTTTTGCAATATCTAAACATTATAGACGCTTTGATGTATTTGTTGAGGCCGAAGCAAATAAAGCTGCTGGAAAGTAT
upper sequence: AT1G28240.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA15G08090.1 (Glycine max), 3'ss of exon 6
---agttgtttcagataagttaacggtttgagtttagaaggccttaagcttggtggttatgtttctggactgcagcaatttaactgacatctcttctcatcagATTCTTGTGGAGGAAAAATGCTACTTTTGCTATTTCTAGACATTACAAACGATTTGATGTCTTAGTGGAAGCCGAAGCAAATAAAGCTGCTGGTAAATAT
| | | || | || |||| | | || || | | || | | | | | ||| |||| || || | | || || ||||||||||| ||||| |||||||| || |||| |||||| | ||| |||||||| || || || ||||||||||||||||||||||| || |||
acacataatcatacctatgccgac--tttgtactaggtttatgttggattttcttgatagaatacatgttt-cggcacattaattgctctcatccttatttagGTTTTTGTGGAGGAAGAATGCAACTTTTGCAATATCTAAACATTATAGACGCTTTGATGTATTTGTTGAGGCCGAAGCAAATAAAGCTGCTGGAAAGTAT
upper sequence: AT1G28240.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA07G18630.1 (Glycine max), 3'ss of exon 5
---agttgtttcagataagttaacggtttgagtttagaaggccttaagcttggtggttatgtttctggactgcagcaatttaactgacatctcttctcatcagATTCTTGTGGAGGAAAAATGCTACTTTTGCTATTTCTAGACATTACAAACGATTTGATGTCTTAGTGGAAGCCGAAGCAAATAAAGCTGCTGGTAAATAT
| | | || | | || |||| | | |||| || | | || | | | | ||| |||| || || | | ||| | ||||||||||| ||||| | |||||| || |||| |||||| | | | |||||||| || || || ||||||||||||||||||||||| ||
tcacataatcatacctatggtgac--tttgtactaggtttatgttaaattttcttgatagaatacatgtgt-tggcacattaattgttgtcatccttatttagACTTTTGTGGAGGAAGAATGCAATTTTTGCAATATCTAAACATTATAGATGCTTTGATGTATTTGTTGAGGCCGAAGCAAATAAAGCTGCTGGAAA----
upper sequence: AT1G28240.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA07G31680.1 (Glycine max), 3'ss of exon 6
agttgtttcagataagttaacggtttgagtttagaaggccttaagcttggtggttatgtttctggactgca-------gcaatttaactgacatctcttctcatcagATTCTTGTGGAGGAAAAATGCTACTTTTGCTATTTCTAGACATTACAAACGATTTGATGTCTTAGTGGAAGCCGAAGCAAATAAAGCTGCTGGTAAATAT
| ||||| | | | | | ||| ||| | || | ||| | |||||| || | | || || | |||| | || | | | || || |||||||| || |||||||||||||| || || | |||||| | ||| |||||||| || | || || || ||||||||||||||||| || |||
---tatttcatacatgatttt--tctgactttttacaagctatattttgct--ttatgtatccataatacatgttttgacacctaaactcccttcacacttgtttagGTTTTTGTGGAGAAAGAATGCTACTTTTGCCATATCAAAACATTATAGACGCTTTGATGTATTCATTGAGGCTGAGGCAAATAAAGCTGCTGGAAAGTAT
upper sequence: AT1G28240.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA13G24770.1 (Glycine max), 3'ss of exon 6
--agttgtttcagataagttaacggtttgagtttagaaggccttaagcttggtggttatgtttctggactgcagcaatttaactgacatctcttctcatcagATTCTTGTGGAGGAAAAATGCTACTTTTGCTATTTCTAGACATTACAAACGATTTGATGTCTTAGTGGAAGCCGAAGCAAATAAAGCTGCTGGTAAATAT
| | |||| || ||| | | | ||| | | || | | || | | | | || | |||| | || | | || || |||||||| || |||||||||||||| || || | |||||| | ||| |||||||| || | || || || ||||||||||||||||| || |||
tatgctctttctgactttttacaagctatatttttgctttgcctatccataa-acccataatacatgttt-tgacacctaaactcccttcacacttatctagGTTTTTGTGGAGAAAGAATGCTACTTTTGCAATATCAAAACATTATAGACGCTTTGATGTATTCATTGAGGCTGAGGCAAATAAAGCTGCTGGAAAGTAT
upper sequence: AT1G28240.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv00s0265g00120.t01 (Vitis vinifera), 3'ss of exon 6
------agttgtttcagataagttaacggtttgagtttagaaggccttaagcttggtggttatgtttctggactgcagcaatttaactgacat----ctcttctcatcagATTCTTGTGGAGGAAAAATGCTACTTTTGCTATTTCTAGACATTACAAACGATTTGATGTCTTAGTGGAAGCCGAAGCAAATAAAGCTGCTGGTAAATAT
| |||| | | | | | || | | ||| ||||| ||| | | ||| |||||| ||| | ||| | | | || |||| |||| ||| |||||||||||||||| | |||||| || ||||||||||| | ||| |||||||| || || ||||| || |||||||||||||||| || |||
gcttgcatttgtat-ggttgaataaaagctatgattttag-----ctt----ctagatgttctgtttcatgacaattgatgtttgggtaccttaatcctattcttttcagGTTCCTGTGGAGGAAAAATGCCAGTTTTGCAATCTCTAGACATTATAGACGCTTTGATGTGTTTGTAGAAGCTGAGGCAAATAAAGCTGCTGCGAAGTATMapped 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|124932673|gb|EL009909.1|EL009909EST: TATCAAATTCTTGAAAG ATTCTTGTGGAGGAAAAATGCTACTTTTGCTATTTCTAGACATTACAAACG
genomic: TATCAAATTCTTGAAAGgtgaggccta ... ttctcatcagATTCTTGTGGAGGAAAAATGCTACTTTTGCTATTTCTAGACATTACAAACG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttggtggttatgtttctggactgcagcaatttaactgacatctcttctcatcagATTCTTGTGGAGGAAAAATGCTACTTTTGCTATTTCTAGACATTACAAACGATTTGATGTCTTAGTGGAAGCCGAAGCAAATAAAGCTGCTGGTAAATAT
aactgac putative branch site (score: 2)
catctcttctcatc CT-rich tract
aatttaact TA-rich tract
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agttgtttcagataagttaacggtttgagtttagaaggccttaagcttggtggttatgtttctggactgcagcaatttaactgacatctcttctcatcagATTCTTGTGGAGGAAAAATGCTACTTTTGCTATTTCTAGACATTACAAACGATTTGATGTCTTAGTGGAAGCCGAAGCAAATAAAGCTGCTGGTAAATAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - -ggtttga