Sequence
atgc intronic sequence ATGC exonic sequence...gattttttgttatgttgtaaagtatgatttcttgtctgtttctatgttctcccttttttaacctttatactctttcttaaacttagtttttgttgctcagAACTGGCTTTGAGGAGGACAAGAATTTCCATGTTGTTTTAAATTCTGTAATAGCTGGAAGGTATCATGTTACTGAATATTTGGGATCTGCTGCATTTAGC
Basic information
species | Glycine max |
transcript | GLYMA05G33560.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G33560.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g51020.1 (Oryza sativa), 3'ss of exon 2
-------------------------------------------gattttttgttatgttgtaaagtatgatttcttgtctg---tttctatgttctcccttttttaacctttatactctttcttaaacttagtttttgttgct----------cagAACTGGCTTTGAGGAGGACAAGAATTTCCATGTTGTTTTAAATTCTGTAATAGCTGGAAGGTATCATGTTACTGAATATTTGGGATCTGCTGCATTTAGC
| | ||||| | | | || | || || || ||| | | | || |||| | | | | ||| |||| | | | | |||| ||||||||| ||||| || ||||| ||||||||||||||| | || ||||| || |||||| | || ||||| || |||||| |||| || || ||||| ||
gtgctctttttctggtccttaattacttggcatttctttattagttcatttgtattaaaatgatacttggtatcatgcttggtgtttgcgtttgttaatttgtttatctctaacgatattttttaactccattatatcctgctgacaatataacagAACTGGTTTTGAAGAAGACAAAAATTTCCATGTTGTTCTCAACTCTGTCATTGCTGGACGTTACCATGTCACAGAATATCTGGGTTCAGCAGCATTCAGT
upper sequence: GLYMA05G33560.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G181002_T01 (Zea mays), 3'ss of exon 2
----------------------------------------------------------------------gattttttgttatg-ttgtaaagtatgatttcttgtctg-tttctatgttctcccttttttaacctttatactctttcttaaacttagtttttgttgct---cagAACTGGCTTTGAGGAGGACAAGAATTTCCATGTTGTTTTAAATTCTGTAATAGCTGGAAGGTATCATGTTACTGAATATTTGGGATCTGCTGCATTTAGC
|| | | || | |||| || || || ||| | | ||| | || || |||| | || | |||| | ||||||||||||||| || ||||| ||||||||||||||| | |||||||| || ||||| | |||||||| | || |||||||| || ||||| || |||
gtattttctttaaatgattgttccatctgttaatcttgttaaagcataaaaaaatgatatggtaatttccagttatctattgtccttgtgtgcctgtgttcacagtgtggcacctacgccgtatttttaaaagatattttatatcttctaacacc-gtctcctgttaattaacagAACTGGCTTTGAAGAAGACAAAAATTTCCATGTTGTTCTCAATTCTGTCATTGCTGGGCGTTATCATGTATCAGAGTATTTGGGGTCAGCTGCTTTCAGC
upper sequence: GLYMA05G33560.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G015073_T01 (Zea mays), 3'ss of exon 2
--------------------------------------------------------------gattttttgttat--gttgtaaa-gtatgatt-tcttgtctgtttc-tatgttctcccttttttaacctttatactctttcttaaacttagtttttgttgct---cagAACTGGCTTTGAGGAGGACAAGAATTTCCATGTTGTTTTAAATTCTGTAATAGCTGGAAGGTATCATGTTACTGAATATTTGGGATCTGCTGCATTTAGC
|||||| ||||| |||| || || | | || | || | | | || |||| ||| | | | | | | ||| ||| | | || | ||||||||||||||| || ||||| || |||||||||||| | |||||||| || ||||| | |||||||| | || |||||||| || |||||||| |||
gtaatgcatttaaatgtttgtcccatattttaatcttactaaagcataaaaaatgatgtggtgattttcagttatctattgtccttgtgtgcctgtgttcacagtgtggcacttaaacctttttataaagtattttgtgtattctaacattatctcctattaattatcagAACTGGCTTTGAAGAAGACAAAAACTTCCATGTTGTTCTCAATTCTGTCATTGCTGGGCGTTATCATGTATCAGAGTATTTGGGTTCAGCTGCATTCAGC
upper sequence: GLYMA05G33560.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G17750.1 (Arabidopsis thaliana), 3'ss of exon 3
-----------------------------------------gattttttgt---tatgttgtaaagtatgatt-tcttgtctgtttctatgttctcccttttttaacctttatactc-tttcttaaacttagtttttgttgctcagAACTGGCTTTGAGGAGGACAAGAATTTCCATGTTGTTTTAAATTCTGTAATAGCTGGAAGGTATCATGTTACTGAATATTTGGGATCTGCTGCATTTAGC
||| ||| || || |||| || | | | |||||| | | | | | | || | |||||| | || || |||||| ||| ||||| ||||||||||| ||||| |||||||| ||||| |||||||| || ||||| | || ||||| ||||| || | ||||| || || ||||||
gtctgttcccttacaatatcgtggtttattatgtattaaatgatgtttcgtacacattttgtttagaagggggatgaagtctgtcccgaatcttgtgaaccctcaggaaatttatttgtttcttctatttgtcttctgttgcccagGACTGGTTTTGAGGAGGATAAGAACTTCCATGTGGTTTTGAATTCTGTCATTGCTGGTCGTTACCATGTCACTGAGCATCTTGGATCAGCAGCTTTTAGC
upper sequence: GLYMA05G33560.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv01s0011g01590.t01 (Vitis vinifera), 3'ss of exon 8
gattttttgttatgttgtaaagtatgatttcttgtctgtttctatg--ttctcccttttttaacctttatactctttcttaaacttagtttttgttgctcagAACTGGCTTTGAGGAGGACAAGAATTTCCATGTTGTTTTAAATTCTGTAATAGCTGGAAGGTATCATGTTACTGAATATTTGGGATCTGCTGCATTTAGC
| | | ||| || | | | | || | | | | | | || |||| | |||| | || || |||||| | ||||||||| |||||||||||||| || |||||||||||||||||||| || |||||||| | ||||||||||| || ||| | || || |||||||| |||
--gccagtttcaagttcacaacttttccaccagttttgccattgggaactttgcttgttctaacaggaagtttcttatctcaatttctgttttgtggtgcagAACTGGGTTTGAGGAGGACAAAAACTTCCATGTTGTTTTAAATTCAGTCATAGCTGGGCGCTATCATGTTACCGAGTATCTTGGGTCAGCTGCATTCAGCMapped 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|192295803|gb|FG992614.1|FG992614EST: GAGGAGGAATTTGAAACCTTCAATCTAAAGATTGTTCACAGAAAAAACAG AACTGGCTTTGAGGAGGACAAGAATTTCCATGTTGTTTTAAATTCTGTAAT
genomic: GAGGAGGAATTTGAAACCTTCAATCTAAAGATTGTTCACAGAAAAAACAGgcatgttttt ... tgttgctcagAACTGGCTTTGAGGAGGACAAGAATTTCCATGTTGTTTTAAATTCTGTAAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttctcccttttttaacctttatactctttcttaaacttagtttttgttgctcagAACTGGCTTTGAGGAGGACAAGAATTTCCATGTTGTTTTAAATTCTGTAATAGCTGGAAGGTATCATGTTACTGAATATTTGGGATCTGCTGCATTTAGC
ttttaac putative branch site (score: 2)
tttttgtt putative PPT
ttttttaacctttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gattttttgttatgttgtaaagtatgatttcttgtctgtttctatgttctcccttttttaacctttatactctttcttaaacttagtttttgttgctcagAACTGGCTTTGAGGAGGACAAGAATTTCCATGTTGTTTTAAATTCTGTAATAGCTGGAAGGTATCATGTTACTGAATATTTGGGATCTGCTGCATTTAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - -tgttatg
- - - - - - - - - - - - - - - - -gtctgtt