Sequence
atgc intronic sequence ATGC exonic sequencegtaagttacagcactaagcttcttttactatgagaggtcaaacttttcataacagactgttctttcttacatggtctgcgtggttactatgtgcagGCGGAACATCAAATCATCGGTCTCCTCATTGATCGATGCGCTGATCCGGACAAACGAACACAGAAATTCGCTTGTTTTGCT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G50240.2 |
intron # | 19 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G50240.2 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GLYMA20G16860.1 (Glycine max), 3'ss of exon 20
gtaagttacagcactaagcttcttttactatgagaggtcaaacttttcataacagactgttctt---tcttacatggtct---gcgtggttactatgtgcagGCGGAACATCAAATCATCGGTCTCCTCATTGATCGATGCGCTGATCCGGACAAACGAACACAGAAATTCGCTTGTTTTGCT
|| | || ||| |||| | || || | | ||||||| | || || ||| || || | ||||| ||||||||| | ||| |||| ||||| |||| ||||||| ||||||||||||| |||||| ||||||||||||
--tttctagatgacagagcacacattacattaaggtttctgatactctgctttctgctgttctcctattttgaattctcttatttacaattgggatttccagGCAAGACATCAAATTGTTGGTATCCTTATTGAAAGATGTTCTGATCCAGACAAACGAACACGGAAATTTGCTTGTTTTGCT
upper sequence: AT1G50240.2 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GLYMA10G22860.1 (Glycine max), 3'ss of exon 18
-gtaagttacagcactaagcttcttttactatgagaggtcaaacttttcataacagactgttctt-tcttacatggtct---gcgtggttactatgtgcagGCGGAACATCAAATCATCGGTCTCCTCATTGATCGATGCGCTGATCCGGACAAACGAACACAGAAATTCGCTTGTTTTGCT
| | ||| || ||| | | | | | | || | ||| | | | | || | | || || ||| || || | ||||| ||||||||| | ||| |||| ||||| |||| ||||||| ||||||||||||| |||||| ||||||||||||
tttctgatact-cagtaaaaatgtgaaaaaacaataagtgatactctgctttctgcttttctcctattttgaattctcttatttacaattgggatttccagGCAAGACATCAAATTGTTGGTATCCTTATTGAAAGATGTTCTGATCCAGACAAACGAACACGGAAATTTGCTTGTTTTGCT
upper sequence: AT1G50240.2 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: Vv16s0039g02400.t01 (Vitis vinifera), 3'ss of exon 19
----gtaagttacagcactaagcttcttttactatgagaggtcaaacttttcataacagact-gttctttcttacatggtctgcgtggttactatgtgcagGCGGAACATCAAATCATCGGTCTCCTCATTGATCGATGCGCTGATCCGGACAAACGAACACAGAAATTCGCTTGTTTTGCT
| ||| | | | | | || | |||| | | ||| || ||| || | | || | | | | | | | | ||||| ||||| |||||| |||| || |||||||| || |||||||| |||||| ||||| ||||||||||||||||||
ataggcaaggattaataattatgtaattattctattaattaaataccttggaatggtgaacttattgtgtgttttcttatatttttatctgat-tctccagGCTAGGCATCATATCATCAGTCTTCTAATTGATCGGTGTGCTGATCCAGACAAAAGAACAAGGAAATTCGCTTGTTTTGCAMapped 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|116426498|gb|EG469090.1|EG469090EST: GTGCTCTTGGCAATATGTGCAGACACAATGGATATTTCTACAGCGCTCTT GCGGAACATCAAATCATCGGTCTCCTCATTGATCGATGCGCTGATCCGGAC
genomic: GTGCTCTTGGCAATATGTGCAGACACAATGGATATTTCTACAGCGCTCTTgtaagttaca ... ctatgtgcagGCGGAACATCAAATCATCGGTCTCCTCATTGATCGATGCGCTGATCCGGAC
EST:
gi|164145082|gb|EL996069.1|EL996069EST: GACACAATGGATATTTCTACAGCGCTCTT GCGGAACATCAAATCATCGGTCTCCTCATTGATCGATGCGCTGATCCGGAC
genomic: GACACAATGGATATTTCTACAGCGCTCTTgtaagttaca ... ctatgtgcagGCGGAACATCAAATCATCGGTCTCCTCATTGATCGATGCGCTGATCCGGAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acttttcataacagactgttctttcttacatggtctgcgtggttactatgtgcagGCGGAACATCAAATCATCGGTCTCCTCATTGATCGATGCGCTGATCCGGACAAACGAACACAGAAATTCGCTTGTTTTGCT
ttcttac putative branch site (score: 2)
tttctta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttacagcactaagcttcttttactatgagaggtcaaacttttcataacagactgttctttcttacatggtctgcgtggttactatgtgcagGCGGAACATCAAATCATCGGTCTCCTCATTGATCGATGCGCTGATCCGGACAAACGAACACAGAAATTCGCTTGTTTTGCT
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