Sequence
atgc intronic sequence ATGC exonic sequence...tgtgctgatatgtgaagcaaatgcaagttgtttttcccagtttagatttgctggctctgttttgactgaggattgattgatttttatcctttttttacagGTTAAACCTGCACTTCCTGCTCTTGCCAGTCTTATCCAGTCAAATGATGAAGAAGTCCTGACTGATGCTTGTTGGGCACTTTCATATCTTTCTGATGGTA
Basic information
species | Glycine max |
transcript | GLYMA03G39210.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G39210.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv14s0060g01510.t01 (Vitis vinifera), 3'ss of exon 5
tgtgctgatatgtgaagcaaatgcaagttgtttttcccagtttagatttgc-tggctctgtt--ttgactgaggattgattgatttttatcctttttttacagGTTAAACCTGCACTTCCTGCTCTTGCCAGTCTTATCCAGTCAAATGATGAAGAAGTCCTGACTGATGCTTGTTGGGCACTTTCATATCTTTCTGATGGTA
||| || | | | ||| | | || | | || | | | |||| |||| | | || || | || | || || |||| || ||||| ||||| || |||| ||||||| || |||||||||||||| || | |||||||| ||||||||||| || ||||||||||||||||
tgtaatggtct-tatggcatgccttgttgaatgttgtaggccgtaacctgtattgttatgttatttgattaa--tttttttcctcttgaattttgttgcacagACAAAGCCTGCTCTTCCAGCACTTGAGCGTCTTATTCACTCAAATGATGAAGAGGTGTTAACTGATGCATGTTGGGCACTGTCTTATCTTTCTGATGGTA
upper sequence: GLYMA03G39210.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv00s0183g00210.t01 (Vitis vinifera), 3'ss of exon 4
tgtgctgatatgtgaagcaaatgcaagttgtttttcccagtttagatttgctggctctgttttgactgaggattgattgatttttatccttttttta--cagGTTAAACCTGCACTTCCTGCTCTTGCCAGTCTTATCCAGTCAAATGATGAAGAAGTCCTGACTGATGCTTGTTGGGCACTTTCATATCTTTCTGATGGTA
| | | | | || | ||| ||| | | ||| || | | | | | || || | | | ||| |||| || || ||||| ||||| ||||||| ||||||| || || ||||||||||| || || |||||||| ||||||||||| || || |||||||||||||
tcagttcaaaca-gagattaccttttgttttttattttttctgagagttaacagattt-tatggagtgcaataggggcaagccacaacctccttttgattagACAAAGCCTGCTCTTCCAGCTCTTGGGCGTCTTATTCACTCGAATGATGAAGATGTGCTAACTGATGCGTGTTGGGCACTGTCTTACCTTTCTGATGGTA
upper sequence: GLYMA03G39210.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv00s0183g00040.t01 (Vitis vinifera), 3'ss of exon 1
-----------------------------------------------------------------tgtgctgatatgtgaagcaaatgcaagttgtttttcccagttt-agatttgctggctctgttttgactgaggattgattgatttttatccttttttta--cagGTTAAACCTGCACTTCCTGCTCTTGCCAGTCTTATCCAGTCAAATGATGAAGAAGTCCTGACTGATGCTTGTTGGGCACTTTCATATCTTTCTGATGGTA
| || | | || || | | | | || | | ||| || | | | | | || || | | | ||| |||| || || ||||| ||||| ||||||| ||||||| || || ||||||||||| || || |||||||| ||||||||| | || || |||||||||||||
gttgaagattggacaaaggattataacatctgaacctcgctgaagttaccatagataaatggtccccttctatcagttcaaacagagattaccttctgttttttttctgagagttaacagattt-tatggagtgcaataggggcaagccacaacctccttttgattagACAAAGCCTGCTCTTCCAGCTCTTGGGCGTCTTATTCACTCGAATGATGAAGATGTGCTAACTGATGCATGTTGGGCATTGTCTTACCTTTCTGATGGTAMapped 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|298180071|gb|HO025286.1|HO025286EST: GGACACTATCGAATTTCTGCAGGGGGAAACCACAGCCTGCTTTTGATCAG GTTAAACCTGCACTTCCTGCTCTTGCCAGTCTTATCGAGTCAAATGATGAA
genomic: GGACACTATCGAATTTCTGCAGGGGGAAACCACAGCCTGCTTTTGATCAGgtatgatgtt ... ttttttacagGTTAAACCTGCACTTCCTGCTCTTGCCAGTCTTATCCAGTCAAATGATGAA
EST:
gi|13252252|gb|BG363155.1|BG363155EST: GGACACTATCGAATTTCTGCAGGGGGAAACCACAGCCTGCTTTTGATCAG GTTAAACCTGCACTTCCTGCTCTTGCCAGTCTTATCCAGTCAAATGATGAA
genomic: GGACACTATCGAATTTCTGCAGGGGGAAACCACAGCCTGCTTTTGATCAGgtatgatgtt ... ttttttacagGTTAAACCTGCACTTCCTGCTCTTGCCAGTCTTATCCAGTCAAATGATGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttgctggctctgttttgactgaggattgattgatttttatcctttttttacagGTTAAACCTGCACTTCCTGCTCTTGCCAGTCTTATCCAGTCAAATGATGAAGAAGTCCTGACTGATGCTTGTTGGGCACTTTCATATCTTTCTGATGGTA
tttttatccttttttt CT-rich tract
attgatttttatcctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtgctgatatgtgaagcaaatgcaagttgtttttcccagtttagatttgctggctctgttttgactgaggattgattgatttttatcctttttttacagGTTAAACCTGCACTTCCTGCTCTTGCCAGTCTTATCCAGTCAAATGATGAAGAAGTCCTGACTGATGCTTGTTGGGCACTTTCATATCTTTCTGATGGTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- tgctgat
- - - - - - -gaagcaaa
- - - - - - - - - - -tgcaagt
- - - - - - - - - - - - - - - - -ttcccag
- - - - - - - - - - - - - - - - - - - - - - - - tgctggc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttttg