Sequence
atgc intronic sequence ATGC exonic sequence...gcctgctgttgtttatcaagcaactaagcttttgccctgtaaaagatcaatagtcttttttttctgctaattatcttcttttttttcctgctaattgcagGGAGCAGTAAATTTTGCTTTAATGATGTCCCAAATGGAAGGAGGTTGTCCAGTTGACTACAACACTATCACTGATCTTTTCCTTCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G11130.1 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 14
------------gcctgctgttgtttatcaagc--aactaagct--tttgccctgtaaaagatcaatagtcttttttttctgctaattatcttcttttttttcctgctaattgcagGGAGCAGTAAATTTTGCTTTAATGATGTCCCAAATGGAAGGAGGTTGTCCAGTTGACTACAACACTATCACTGATCTTTTCCTTCAG
||| || | | | || || || |||| |||| | || | | ||| ||||||| | || | | | || || |||||||| || || ||||| | |||||||| |||||||| || || ||||||||||| ||||| ||||| |||||||| |||||||||
gtaatgtattggttaagctattttgggctagggtgaaatactctgctttgttctgtgggttgttgatt-tttatttgcaaaattaattatttactgtatatctcttttac---cagGGAGCTGTCAACTTTGCGCTCATGATGTCACAAATGGAGGGGGGCTGTCCAGTTGATTACAATACTATAACTGATCTCTTCCTTCAG
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 14
------------gcctgctgttgtttatcaagcaactaagcttttgccctgtaaaa-gatcaatagtcttttttttctgctaattatcttcttttttttcctgctaattgcagGGAGCAGTAAATTTTGCTTTAATGATGTCCCAAATGGAAGGAGGTTGTCCAGTTGACTACAACACTATCACTGATCTTTTCCTTCAG
||| || | | | | || || ||| ||| | | | |||| ||| | |||| | | | | | || | |||||||| || || ||||| | |||||||| |||||||| || || ||||||||||| ||||| ||||| |||||||| |||||||||
gtaatttattggttaagctattttgtgctagggtga-aatattctgctttgttctgtgggttgttgatttttatttgcaaaatttattatttactgtatatctcttttaccagGGAGCTGTCAACTTTGCGCTCATGATGTCACAAATGGAGGGGGGCTGTCCAGTTGATTACAATACTATAACTGATCTCTTCCTTCAG
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 12
--gcctgctgttgtttatcaagc---aactaagcttttgccctgtaaaagatcaata---gtcttttttttctgctaattatcttcttttttttc---ctgctaattg--cagGGAGCAGTAAATTTTGCTTTAATGATGTCCCAAATGGAAGGAGGTTGTCCAGTTGACTACAACACTATCACTGATCTTTTCCTTCAG
|| | | || | ||| | || | | | | | | | || || | |||| ||| || | | ||| || || || ||| |||||||| || || ||||| || |||||||| |||||||| |||||||||||||| ||||||||||||||||||||||| |||||||||
gtaattggttattttaagcaaacttgggcttaatgtgaggtattcatttgtttggtacatgtttcttttatctcagaaatccttgcttcattgtcaatttgtatcttgaccagGGAGCTGTCAACTTTGCATTGATGATGTCACAAATGGAGGGAGGTTGTCCAGTAGACTACAACACTATCACTGATCTCTTCCTTCAG
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 14
----------------------------------------------------------------------------------------------gcctgctgttgttt--atcaagcaactaagcttttgccctgta-aaagatcaatagtcttttttttctgctaattatcttcttttttttcctgctaattgcagGGAGCAGTAAATTTTGCTTTAATGATGTCCCAAATGGAAGGAGGTTGTCCAGTTGACTACAACACTATCACTGATCTTTTCCTTCAG
| ||| | || ||||| | | | | | | || |||||| | | | | ||| |||||| | || |||| || || |||||||| ||||||||||| |||||||| |||||||| |||||||| |||||||| || |||||||| || ||||||
gtatgagagaatcctctgtagttcatattaactatttctttgtatttctcccattgtctgccacactgttggataattgattatcaaattatatattttctgacatggaaattctataactatttcatctcaatttgcagaaattaatagttgtaaaaactaattcaacaactttcttttttcattttggtttctagGGTGCTGTTAATTTTGCATTAATGATGTCGCAAATGGAGGGAGGTTGCCCAGTTGATTACAACACCATAACTGATCTGTTTCTTCAG
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 14
gcctgctg-ttgtttatcaagcaactaagcttttgccctgtaaaagatcaatagtcttttttttctgct-aattatcttcttttttttcctgctaattgcagGGAGCAGTAAATTTTGCTTTAATGATGTCCCAAATGGAAGGAGGTTGTCCAGTTGACTACAACACTATCACTGATCTTTTCCTTCAG
| || || | || | | | | | | | | | || |||||| | | | || | |||||||| | || | || |||| || || |||||||| ||||||||||| |||||||| |||||||| |||||||| |||||||| || |||||||| || ||||||
acatggaaattctataactatttttttttcatctcaatttgcagaaattaatagttgtataaactaattcaagaactttctttttcattttggt--ttctagGGTGCTGTTAATTTTGCATTAATGATGTCGCAAATGGAGGGAGGTTGCCCAGTTGATTACAACACCATAACTGATCTGTTTCTTCAG
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 14
---------------------------------------------------------------------------gcctgc-----tgttgtttatcaagcaactaagc---ttttgccctgtaaaagatcaata-gtcttttttttctgctaattatcttcttttttttcctgctaattgcagGGAGCAGTAAATTTTGCTTTAATGATGTCCCAAATGGAAGGAGGTTGTCCAGTTGACTACAACACTATCACTGATCTTTTCCTTCAG
| |||| |||| | | | | |||| ||||| | ||| | | || || || | |||||| | | | |||| | || | |||||||| || || |||||||| ||||||||||| |||||||| |||||| | |||||||| |||||||| || |||||||| || ||||||
gtgtgagagaaacctctgcagttcatacaatttttttatttgaacctgaaccatttctttgtagctccccttattgtctgcgtccttgttatatctgtggtaactgtttttgttttgaacagtatatgtacattaagttgacaatgtctgctgacagttaccattttcattttgat--ttgcagGGCGCTGTTAATTTTGCATTAATGATGTCTCAAATGGAGGGAGGTAGCCCAGTTGATTACAACACAATAACTGATCTCTTTCTTCAG
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 14
------------------------------------------------gcctg---ctgttgtttatcaagcaactaagcttttgcc-ctgtaaaagatcaatagtcttttttttctgctaattatcttcttttttttcctgctaattgcagGGAGCAGTAAATTTTGCTTTAATGATGTCCCAAATGGAAGGAGGTTGTCCAGTTGACTACAACACTATCACTGATCTTTTCCTTCAG
|||| | || ||| | | || | | || | | | | ||| | | | | | | ||| | ||| | | || |||| | |||||||| || || |||||||| ||||||||||| |||||||| |||||| | |||||||| |||||||| || |||||||| || ||||||
gtgtgagagaaacctctgcagtttatattatataatttttttagttgaacctgaaccatttctttgtagctccccttattctctgtctccttgttatatctgttgacaatgtctgctgacagttaccattttcattttgat-----ttgcagGGCGCTGTTAATTTTGCATTAATGATGTCTCAAATGGAGGGAGGTAGCCCAGTTGATTACAACACAATAACTGATCTCTTTCTTCAG
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 14
--------------gcctgctgtt-gtttatcaagcaactaagcttttgccctgtaaaagatcaatagtcttttttttctgctaattatcttctt---------ttttttcctgctaattgcagGGAGCAGTAAATTTTGCTTTAATGATGTCCCAAATGGAAGGAGGTTGTCCAGTTGACTACAACACTATCACTGATCTTTTCCTTCAG
|| |||| | || | || | ||| | ||| ||||| ||| || | || ||| | ||| | ||||||||||| ||||||||||| |||||||||| |||||||| ||||||||||| |||| | || || || |||||||| || ||||||
gtatgcaagcctttttctagtgtttgcagattttccttttatgaaattgttccagaaaggatcagcttaaatttcaaattggataaaattttcctgagtggaggcatttatttttgggttgcagGGAGCTGTAAATTTTGCGCTAATGATGTCTCAAATGGAGGGAGGTTGTCCCATTGATTTTAATACGATAACTGATCTCTTTCTTCAG
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 14
gcctgctgttgtttatcaagcaactaagcttttgccctgtaaaagatcaatagtcttttttttctgctaattatcttcttttttttcctgctaattgcagGGAGCAGTAAATTTTGCTTTAATGATGTCCCAAATGGAAGGAGGTTGTCCAGTTGACTACAACACTATCACTGATCTTTTCCTTCAG
||||| | || | | || || | ||| | || | || | |||| || |||||||||||| | |||||| | ||||||||||| || |||||| | ||||||||| ||| || |||||||| || |||
-----------------------------------------------gtatagt-tcgttgtcttactcatggttttcccgtattga-tcctctgtccagGCGGCCGTAAATTTTGCTCTCATGATGGCTCAAATGGAAGGCGGATGTCCAATGGACTACAACGTTATTACCGATCTTTTTCTGCAG
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: EFJ13237 (Selaginella moellendorffii), 3'ss of exon 14
gcctgctgttgtttatcaagcaactaagcttttgccctgtaaaagatcaatagtcttttttttctgctaattatcttcttttttttcctgctaattgcagGGAGCAGTAAATTTTGCTTTAATGATGTCCCAAATGGAAGGAGGTTGTCCAGTTGACTACAACACTATCACTGATCTTTTCCTTCAG
||||| | || | | || || | ||| | || | || |||||| || |||||||||||| | |||||| | ||||||||||| || |||||| | ||||||||| ||| || |||||||| || |||
-----------------------------------------------gtatagt-tcgttgtcttactcatggttttcccgtattga-tcctctgtgcagGCGGCCGTAAATTTTGCTCTCATGATGGCTCAAATGGAAGGCGGATGTCCAATGGACTACAACGTTATTACCGATCTTTTTCTGCAGMapped 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|164184287|gb|ES118110.1|ES118110EST: CACCTGATTACATGTTTCTTCTGCAAACGATACTCCGTACGGATCCTCAG GGAGCAGTAAATTTTGCTTTAATGA
genomic: CACCTGATTACATGTTTCTTCTGCAAACGATACTCCGTACGGATCCTCAGgttagtttgc ... ctaattgcagGGAGCAGTAAATTTTGCTTTAATGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcaatagtcttttttttctgctaattatcttcttttttttcctgctaattgcagGGAGCAGTAAATTTTGCTTTAATGATGTCCCAAATGGAAGGAGGTTGTCCAGTTGACTACAACACTATCACTGATCTTTTCCTTCAG
tgctaat putative branch site (score: 2)
tcttttttttctgcta CT-rich tract
taattatcttcttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcctgctgttgtttatcaagcaactaagcttttgccctgtaaaagatcaatagtcttttttttctgctaattatcttcttttttttcctgctaattgcagGGAGCAGTAAATTTTGCTTTAATGATGTCCCAAATGGAAGGAGGTTGTCCAGTTGACTACAACACTATCACTGATCTTTTCCTTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- ctgctgt
- - - - - - - - caagcaa
- - - - - - - - - - - - - -gcttttg
- - - - - - - - - - - - - - - - - - - gtaaaag