Sequence
atgc intronic sequence ATGC exonic sequence...tcactccattgaaccacccaatgatcatgttgctctgttcatttcttcaatgctagctcctgagtcctattatataatgcaattaaattttatctaacagGAGGTGGATCCATGCGAAGATTTGACTGATGATGATATTCGCACAGCCATACAGAATGCAACTGGACCTAAATCAGCACTGTTTGTTCCTGAA
Basic information
species | Glycine max |
transcript | GLYMA08G07160.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G07160.1 (Glycine max), 3'ss of exon 9
lower sequence: AT2G14120.3 (Arabidopsis thaliana), 3'ss of exon 10
tcactccattgaaccacccaatgatcatgttgctctgttcatttcttcaatgctagctcctgagtcctattatat-aatgcaattaaattttatctaacagGAGGTGGATCCATGCGAAGATTTGACTGATGATGATATTCGCACAGCCATACAGAATGCAACTGGACCTAAATCAGCACTGTTTGTTCCTGAA
| || || | | || || | | | ||| | | | ||| | | || | | | ||||| ||| | ||||||| |||||||| ||||| || || | |||||||||||| || || ||||| ||||||||||| || | ||| ||| | |||||||| ||
-tgttgtatagagatctttacctac--tgatgttgtcagtgctacttgataggggtttaatgattttaaactcattagtttctctcaatttgctctga-aggagGTTGATCCATGTGAAGACTTAACAGCTGATGATATTCGGACTGCAATACAAAATGCAACTGGTCCCAGATCTGCATTATTTGTTCCAGAT
upper sequence: GLYMA08G07160.1 (Glycine max), 3'ss of exon 9
lower sequence: AT2G14120.2 (Arabidopsis thaliana), 3'ss of exon 9
tcactccattgaaccacccaatgatcatgttgctctgttcatttct--tcaatgctagctcctgagtccta--ttatataatgcaattaaattttatctaacagGAGGTGGATCCATGCGAAGATTTGACTGATGATGATATTCGCACAGCCATACAGAATGCAACTGGACCTAAATCAGCACTGTTTGTTCCTGAA
||| ||| | | | | || | | ||| | || | || | | | || | || | | ||||| ||| | ||||||| |||||||| ||||| || || | |||||||||||| || || ||||| ||||||||||| || | ||| ||| | |||||||| ||
---ctctgttgtatagagatctttacctactgatgttgtcagtgctacttgataggggtttaatgattttaaactcattagtttctctcaatttgctctga-agGAGGTTGATCCATGTGAAGACTTAACAGCTGATGATATTCGGACTGCAATACAAAATGCAACTGGTCCCAGATCTGCATTATTTGTTCCAGAT
upper sequence: GLYMA08G07160.1 (Glycine max), 3'ss of exon 9
lower sequence: AT4G33650.1 (Arabidopsis thaliana), 3'ss of exon 9
-tcactccattgaaccacccaatgatcatgttgctctgttcatttcttcaatgctagctcctgagtcctatt-atataatgcaattaaattttatctaacagGAGGTGGATCCATGCGAAGATTTGACTGATGATGATATTCGCACAGCCATACAGAATGCAACTGGACCTAAATCAGCACTGTTTGTTCCTGAA
|| | | | |||| | | | |||| | || | | || | | | | || ||| | | | ||| ||| |||||||| ||||||||||| || ||||| |||||||||||||| || || || |||||||||||||| || | ||| ||| | |||||||| ||
gacattatccaaatggaaataatg-tagtatatttctgacgttgagctcgtggatctctgtaaatttagactgattgaattccttcacattgcctctt-cagGAGGTTGATCCATGCGAGGACTTGACAGATGATGATATTCGGACTGCAATTCAGAATGCAACTGGTCCAAGATCTGCATTATTTGTTCCAGAT
upper sequence: GLYMA08G07160.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv03s0038g00970.t01 (Vitis vinifera), 3'ss of exon 10
-----tcactccattgaaccacccaatgatcatgttgctctgttcatttcttcaatgctagctcctgagtcctattatataatgcaattaaattttatctaacagGAGGTGGATCCATGCGAAGATTTGACTGATGATGATATTCGCACAGCCATACAGAATGCAACTGGACCTAAATCAGCACTGTTTGTTCCTGAA
|| || || | || | | || | | || | |||| ||| ||| || | | | | | ||| | | | | | ||||||||||||||||| || ||||||||||||||||| ||||| || || || ||||||||||| || |||| ||| ||| | ||||| || |||
atggagaacctcac--aattttttattggtaaatctgatgt-ttgctaatttcagagct-gctatgagctcatcaagtctgaggagatttgaatatctgtg-cagGAGGTGGATCCATGTGAGGATTTGACTGATGATGACATTCGAACTGCAATTCAGAATGCAACCGGCCCTAGATCTGCATTATTTGTGCCAGAA
upper sequence: GLYMA08G07160.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S221_85V6.1 (Physcomitrella patens), 3'ss of exon 11
-----tcactccattgaacca---cccaatgatcatgttgctctgttcatttcttcaatgctagctcctgagtcctattatataatgcaattaaattttatctaacagGAGGTGGATCCATGCGAAGATTTGACTGATGATGATATTCGCACAGCCATACAGAATGCAACTGGACCTAAATCAGCACTGTTTGTTCCTGAA
| | | | | | || | ||| | ||| | | | | | | | || || | || | |||||| | | ||||||| |||||| ||| ||||||||||||||||| || || ||||| |||||||| ||||| ||||| ||| | ||| || || || ||
tgttgtttcccggcttaggtagtttttcttgttattgtagaactgatgaaatatacgttcacgttgcttgggttttttttttgaatgca--------cggcattatagGAGGTAGATCCAAACGACGATTTGACTGATGATGACATACGGACAGCTATACAGAACGCAACAGGACCCAAAAATGTACTTTTCGTACCGGAGMapped 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|7924507|gb|AW830533.1|AW830533EST: GTGCAAGAATTCATTACATTTTTCAATCCATCTTTGTGAAGAGCTTAGAG GAGGTGGATCCATGCGAAGATTTGACTGATGATGATATTCGCACAGCCATA
genomic: GTGCAAGAATTCATTACATTTTTCAATCCATCTTTGTGAAGAGCTTAGAGgcatacactt ... tatctaacagGAGGTGGATCCATGCGAAGATTTGACTGATGATGATATTCGCACAGCCATA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcaatgctagctcctgagtcctattatataatgcaattaaattttatctaacagGAGGTGGATCCATGCGAAGATTTGACTGATGATGATATTCGCACAGCCATACAGAATGCAACTGGACCTAAATCAGCACTGTTTGTTCCTGAA
ttttatct CT-rich tract
tattatataatgcaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcactccattgaaccacccaatgatcatgttgctctgttcatttcttcaatgctagctcctgagtcctattatataatgcaattaaattttatctaacagGAGGTGGATCCATGCGAAGATTTGACTGATGATGATATTCGCACAGCCATACAGAATGCAACTGGACCTAAATCAGCACTGTTTGTTCCTGAA
-cactcca
- - - - - - - cacccaa
- - - - - - - - - - - - - -tgttgct
- - - - - - - - - - - - - - - - - - - - - - - - aatgcta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ctcctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgcaa