Sequence
atgc intronic sequence ATGC exonic sequencegtaagattagtcttcaacttttaagttacaccttcttctttcattcccaatttcccattatgagaagcttaacatttgttttcctgtatctacatcttttcttacctagATATGGAATCTTGGCTCTCCGGATCCAAATTTTACTTTGGATGCACATCTCAAAGGGGTAAACTGTGTAGACTACTTTACTGGTGGGGATAAACCATACC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G79990.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 6
gtaagattagtcttcaacttttaagttacaccttcttctttcattcccaatttcccattatgagaagcttaacatttgttttcctgtatctacatcttttcttacctagATATGGAATCTTGGCTCTCCGGATCCAAATTTTACTTTGGATGCACATCTCAAAGGGGTAAACTGTGTAGACTACTTTACTGGTGGGGATAAACCATACC
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------------------------gtagaattatgttctt--gttcctggttgtttcctatgatataat--gcattaatgcacctgt-----tgtcttctcttttc-agATTTGGAATCTTGGCTCTCCTGATCCTAATTTTACTTTGGATGCTCATCAGAAAGGAGTGAATTGTGTTGATTATTTTACAGGTGGTGACAAACCATATC
upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 6
gtaagattagtcttcaacttttaagttacaccttcttctttcattcccaatttcccattatgagaagctt--aacatttgttttcctgtatc--tacatcttttcttacct------agATATGGAATCTTGGCTCTCCGGATCCAAATTTTACTTTGGATGCACATCTCAAAGGGGTAAACTGTGTAGACTACTTTACTGGTGGGGATAAACCATACC
|| |||| | | | | | || || | || | | || || || | | | || | | || || | || || || | | || |||| ||||||||||||||||| || || ||||||||||||||||| |||| ||||| || || ||||| || || ||||| ||||| || |||||||| |
gtgtaattatgttcttgttcctggat---gtttcttttttaaaaaaaaaaaaaagtaaaaagaaaaactatgatcctatgatataatgcattgatgcaactgttatcatctcttttcagATTTGGAATCTTGGCTCTCCTGACCCTAATTTTACTTTGGATGCTCATCAGAAAGGAGTGAATTGTGTTGATTATTTTACAGGTGGTGACAAACCATATC
upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 6
gta-agattagtcttcaacttttaagttacaccttcttctttcattcccaatttcccattatgagaagcttaacatttgttttcctgtatctacatcttttcttacc-tagATATGGAATCTTGGCTCTCCGGATCCAAATTTTACTTTGGATGCACATCTCAAAGGGGTAAACTGTGTAGACTACTTTACTGGTGGGGATAAACCATACC
||| | | || ||| || |||| | | |||| || |||||| || || || | ||||| | | | | | |||| ||||||||||||||||| || || |||||||| |||||||| |||| ||||| || || ||||| || |||||||| ||||| || ||||| ||||
gtatatacatgtgttcttctcgctagttgtgtcctgaattttctttgtttatttccatacatctatgataaaaatttaaaagtaatgtattaatgttatcttcaattgcagATTTGGAATCTTGGCTCTCCTGACCCCAATTTTACGTTGGATGCCCATCAAAAAGGAGTGAATTGTGTTGATTACTTTACAGGTGGTGACAAACCTTACC
upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 6
------gtaagattagtcttcaacttttaagttacaccttcttctttcattcccaatttcccattatgagaagcttaacatttgttttcctgtatctacatcttttcttacctagATATGGAATCTTGGCTCTCCGGATCCAAATTTTACTTTGGATGCACATCTCAAAGGGGTAAACTGTGTAGACTACTTTACTGGTGGGGATAAACCATACC
| | | | | | || | | || ||||| || ||| |||| || || || | || | || | | | | | | |||||||||| | |||| ||||||||||||||||| || || |||||||| |||||||| |||| ||||| || || ||||| || |||||||| ||||| || || || || |
gtatacatgtgttcttcttgctagttgtgtcctgcattttctttgtttatttccaaacacctatgataaaaa-ttaaaaagtaatgtattaatgtt---atcttttcttgc--agATTTGGAATCTTGGCTCTCCTGACCCCAATTTTACATTGGATGCGCATCAAAAAGGAGTGAATTGTGTTGATTACTTTACAGGTGGTGACAAGCCTTATC
upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 6
gtaagattag--tcttcaacttttaagttac-accttcttctttcattcccaatttcccattatgagaagcttaacatttgttttcctgtatctac-atcttttcttacctagATATGGAATCTTGGCTCTCCGGATCCAAATTTTACTTTGGATGCACATCTCAAAGGGGTAAACTGTGTAGACTACTTTACTGGTGGGGATAAACCATACC
||| ||| | | ||| | || || | || | | ||| || ||||||| | | || | || | | | | || || | || | | ||| | |||||||||||||||||||||| || || |||||||| ||||||| |||| ||||||||||| ||||| || |||||||| || || ||||||||||| |
gtatgatctggattttctgttggcaacttgttaactgcattttt--ttaccaattttgcttcatca--agtatgagtgtgctatttatgctctgatgatatctccttttccagATATGGAATCTTGGCTCTCCAGACCCTAATTTTACACTGGATGCCCATCAGAAAGGGGTAAATTGTGTTGATTACTTTACAGGCGGTGATAAACCATATC
upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 6
gtaagattagtcttcaacttttaagttacaccttcttctttcattcccaatttcccattatgagaagcttaacatttgttttcctgtatctacatcttttcttacctagATATGGAATCTTGGCTCTCCGGATCCAAATTTTACTTTGGATGCACATCTCAAAGGGGTAAACTGTGTAGACTACTTTACTGGTGGGGATAAACCATACC
|| ||| || | ||| | ||| || || | |||| | || | || | || | ||| | | | || | |||| |||||||| ||||| || || ||||||||||||||||||| || | ||||||||||||||||| || ||||| |||||||| || || ||||||
-------tatactttaagtcgct-gttttggcggctttttcaatacagtttttctcctttacttataaaaaaaaaaagtcctaatgttgatctggcgtc-ctgttccagATTTGGAATCTCGGCTCCCCTGACCCAAATTTTACTTTGGATGACCACATGAAAGGGGTAAACTGTGTTGATTACTTCACTGGTGGTGACAAGCCATACTMapped 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|164181299|gb|ES085031.1|ES085031EST: CCAAAGACACCAATACTTTTGCTAGTGCATCCCTTGACCGTACCATAAAA ATATGGAATCTTGGCTCTCCGGATCCAAATTTTACTTTG
genomic: CCAAAGACACCAATACTTTTGCTAGTGCATCCCTTGACCGTACCATAAAAgtaagattag ... tcttacctagATATGGAATCTTGGCTCTCCGGATCCAAATTTTACTTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccattatgagaagcttaacatttgttttcctgtatctacatcttttcttacctagATATGGAATCTTGGCTCTCCGGATCCAAATTTTACTTTGGATGCACATCTCAAAGGGGTAAACTGTGTAGACTACTTTACTGGTGGGGATAAACCATACC
ttcttac putative branch site (score: 2)
tctacatcttttctt CT-rich tract
ttaacatttgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagattagtcttcaacttttaagttacaccttcttctttcattcccaatttcccattatgagaagcttaacatttgttttcctgtatctacatcttttcttacctagATATGGAATCTTGGCTCTCCGGATCCAAATTTTACTTTGGATGCACATCTCAAAGGGGTAAACTGTGTAGACTACTTTACTGGTGGGGATAAACCATACC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG