Sequence
atgc intronic sequence ATGC exonic sequencegtaagctttgtagttttatgtcaaatgagagtgtagattgttttctgggagagttacaccacaacaatgatggacatcttttcctactttctgatgtagGCATAAAGGAGCAGTTGCAATTCGCCAGCCTTATATCCGAGTTGTTGGACTGGAAGACACAAATGAGGCCAGTTCCCGTGGCCCTGCCAACTTCACTCCT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G07690.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G07690.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G11220.1 (Glycine max), 3'ss of exon 5
gtaagctttgtagttttatgtcaaatgagagtgtagattgttttctgggagagttacaccacaacaatgatggacatcttttcctactttctg-atgtagGCATAAAGGAGCAGTTGCAATTCGCCAGCCTTATATCCGAGTTGTTGGACTGGAAGACACAAATGAGGCCAGTTCCCGTGGCCCTGCCAACTTCACTCCT
|| || || | | | | | | | | | | | |||| | | |||| | | || | || | ||| || | |||||||||||||||||| | ||||||||||| | ||||| ||| | ||||| ||||||||| ||| ||| || || || || || || |
gtgagattcatcaccattt-ttatttttgtatatttaattttttttcattcccccatctgtagttaatgtctggcttcaaatatattttgttatatgcagTAACAAAGGAGCAGTTGCAATTAGACAGCCTTATATTAGGGTTGTAGGAATAGAAGAAACAAATGAGACCAATTCTCGGGGTCCAGCTGCATTTACACAA
upper sequence: AT2G07690.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA13G22420.1 (Glycine max), 3'ss of exon 5
gtaagctttgtagttttatgtcaaatgagagtgtagattgttttctgggagagttacaccacaacaatgatggacatcttttcctactttctg----atgtagGCATAAAGGAGCAGTTGCAATTCGCCAGCCTTATATCCGAGTTGTTGGACTGGAAGACACAAATGAGGCCAGTTCCCGTGGCCCTGCCAACTTCACTCCT
|| || || | | ||| || || | |||| | | | | ||||| ||| || || || ||| || || |||||||||||||||||| | ||||||||||| | ||||| ||| | ||||| ||||||||| ||| || || || || || || || |
gtgagattcatcacca---atttaatttttgtatatttaatttttttttcattctcccatctgtaattgatgtctggcttcaaatatattgtgttatatgcagCCACAAAGGAGCAGTTGCAATTAGACAGCCTTATATTAGGGTTGTAGGAATAGAAGAAACAAATGAGACCAACTCTCGCGGTCCAGCAGCATTTACACAA
upper sequence: AT2G07690.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv11s0149g00130.t01 (Vitis vinifera), 3'ss of exon 5
-------------------------------gtaagctttgtagttttatgtcaaatgagagtgtagattgttttctgggagagttacaccacaacaatgatggac-atcttttcctactttctgatgtagGCATAAAGGAGCAGTTGCAATTCGCCAGCCTTATATCCGAGTTGTTGGACTGGAAGACACAAATGAGGCCAGTTCCCGTGGCCCTGCCAACTTCACTCCT
| ||||| ||| || | | | | | | ||||||| ||| | | ||| | || | |||| ||| || |||||||| ||||||||| || | |||||||||||| ||||||| ||| | ||||| | |||||||||| ||||| || || || ||| || |
gtaaggatcatttgacactgagataagcataacacaatttgtgatttaatcttcact---aattttgattgttggaattacatgtttatttatgggtcagttggtttgttgattgattggttcttatgcagCCATAAAGGGGCAGTTGCAGTTAGACAGCCTTATATCAGAGTTGTAGGAATAGAAGAAGCTAATGAGGCCAACTCCCGAGGTCCAGCTGCCTTTACATCAMapped 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|116420153|gb|EG462745.1|EG462745EST: ACAGTAATGGGTATCTACAGCATTTTCCAAGCTTCGTCATCATCTAACTC GCATAAACGAGCAGT
genomic: ACAGTAATGGGTATCTACAGCATTTTCCAAGCTTCGTCATCATCTAACTCgtaagctttg ... tctgatgtagGCATAAAGGAGCAGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgggagagttacaccacaacaatgatggacatcttttcctactttctgatgtagGCATAAAGGAGCAGTTGCAATTCGCCAGCCTTATATCCGAGTTGTTGGACTGGAAGACACAAATGAGGCCAGTTCCCGTGGCCCTGCCAACTTCACTCCT
ttctgat putative branch site (score: 3)
catcttttcctacttt CT-rich tract
atctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagctttgtagttttatgtcaaatgagagtgtagattgttttctgggagagttacaccacaacaatgatggacatcttttcctactttctgatgtagGCATAAAGGAGCAGTTGCAATTCGCCAGCCTTATATCCGAGTTGTTGGACTGGAAGACACAAATGAGGCCAGTTCCCGTGGCCCTGCCAACTTCACTCCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA