Sequence
atgc intronic sequence ATGC exonic sequence...catggtttattcatggaagacttttactacatgatgccttagtttccaatctttgctataattatttcatttattcttttcttgtgtgtgtgcactctagACATTTGATGCTGTTGACGGGAAGCAAGCTAGACGAACAAATTCCTCAAGCCCATTGGGGGAGCTCTTTGATCATG
Basic information
species | Glycine max |
transcript | GLYMA02G14210.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G14210.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G13560.2 (Arabidopsis thaliana), 3'ss of exon 4
-----catggtt-tattcatggaagacttttactacatgatgccttagtttccaatctttgctataattatttcatttattcttttcttgtgtgtgtgcactctagACATTTGATGCTGTTGACGGGAAGCAAGCTAGACGAACAAATTCCTCAAGCCCATTGGGGGAGCTCTTTGATCATG
| | | | || | || | ||| ||| || | | | | | | | || | ||| ||||| | | | | || | |||||||||||||| ||||| ||||||||||| ||| | ||||||||||| ||||| | || |||||||| |||||||
gtttgcgtctctctttttcttcaaaagtttaactttctgttatatgtgctggtgaaggtgttttgaagtcttt--tttatcttacaccttt-tgagcttttattagACATTTGATGCGGTTGATGGGAAGCAAGCAAGAAGGACAAATTCCTCTAGCCCCCTAGGAGAGCTCTTCGATCATG
upper sequence: GLYMA02G14210.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G25585.3 (Arabidopsis thaliana), 3'ss of exon 4
-----catggtttattcatggaagacttttactacatgatgccttagtttccaatctttgctataattatttcatttattcttttcttgtgtgtgtgcactctagACATTTGATGCTGTTGACGGGAAGCAAGCTAGACGAACAAATTCCTCAAGCCCATTGGGGGAGCTCTTTGATCATG------------------------
| | ||| | || | || | | || | | || || || | || | | | ||| || | |||| | ||| | |||||||||||||||| ||||| ||||||||||| || |||||||||| || |||||| | || ||||| ||||| ||||
gtctgcttcttttttctatatcaacctaatttcatctgcttgttaagggtc--atgtaatctgtcttcctgacata-gttggtgcattgt-cgagtgaattctagACATTTGATGCGGTTGATGGGAAGCAAGCACGAAGAACAAATTCATCTAGCCCACTAGGAGAGCTTTTTGACCATGGTTGCGATGCACTTGGCTGTGCGT
upper sequence: GLYMA02G14210.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv01s0010g00950.t01 (Vitis vinifera), 3'ss of exon 5
catggtttattcatggaagacttttactacatgatgccttagtttccaatctttgctataatta-tttcattt---attcttttcttgtgtgtgtgcactctagACATTTGATGCTGTTGACGGGAAGCAAGCTAGACGAACAAATTCCTCAAGCCCATTGGGGGAGCTCTTTGATCATG
| ||| || ||| | || || || | |||| |||||||| ||||||| | |||| || | || | |||| |||||||||||||| ||||||||||| || || ||||||||||| || |||||||| || || ||||| ||||
--tttgctatgattgagtagtgtttcatttattatattttggcaat--gccttttctataatttctttcattcttggtattttttttccctaaaaacatgccagACTTTTGATGCTGTTGATGGGAAGCAAGCAAGGCGGACAAATTCCTCTAGTCCATTGGGAGAACTTTTTGACCATG
upper sequence: GLYMA02G14210.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S269_30V6.1 (Physcomitrella patens), 3'ss of exon 5
catggtttatt-catggaagacttttactacatgatgccttagtttccaatctttgctataattatttcatttattcttttcttgtgtgtgtgcactctagACATTTGATGCTGTTGACGGGAAGCAAGCTAGACGAACAAATTCCTCAAGCCCATTGGGGGAGCTCTTTGATCATG
|| | | || || ||| | ||| | | | | || || ||| || | || | | | | | |||| |||||||||||||| ||||| |||||||| || |||||||| || || || | || || || |||||||| |
-ataactagtggcagctgcgatatttctcaattgacggatatggatgcagcgttaattatccacccttaagatacggctctaaacccaatcttcttcacagACCTTTGATGCTGTTGATGGGAAACAAGCTAGGCGGACAAATTCGTCGAGTCCTCTTGGAGAACTTTTTGATCACGMapped 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|192327207|gb|FK018089.1|FK018089EST: CTCCAAGATGGGTTCATTTTGCTCATGGACTACTTCTGTTTTTATACCAG ACATTTGATGCTGTTGACGGGAAGCAAGCTAGACGAACAAATTCCTCAAGC
genomic: CTCCAAGATGGGTTCATTTTGCTCATGGACTACTTCTGTTTTTATACCAGgtatgattaa ... tgcactctagACATTTGATGCTGTTGACGGGAAGCAAGCTAGACGAACAAATTCCTCAAGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccaatctttgctataattatttcatttattcttttcttgtgtgtgtgcactctagACATTTGATGCTGTTGACGGGAAGCAAGCTAGACGAACAAATTCCTCAAGCCCATTGGGGGAGCTCTTTGATCATG
tttgctataattattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catggtttattcatggaagacttttactacatgatgccttagtttccaatctttgctataattatttcatttattcttttcttgtgtgtgtgcactctagACATTTGATGCTGTTGACGGGAAGCAAGCTAGACGAACAAATTCCTCAAGCCCATTGGGGGAGCTCTTTGATCATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - -catggaa
- - - - - - - - - - - - - - - -tgatgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgctata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgtgtg