Sequence
atgc intronic sequence ATGC exonic sequencegtaagcagcaatatttaaagaattttattacatgcatacttgccatatccatttgattcaaccttgctttgttactgccactacttaaaatttgttaattcagttttctgatttcctttcagACCTTGTTAATGTGTTTGAGGTGTTTCTTCCTCAACTTCTTCTGTACCCCAATGCATCAGATCCATTAAATGGTGATGCTGCTGCCTTGATGATTCGAGA
Basic information
species | Glycine max |
transcript | GLYMA08G01940.4 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G01940.3 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os10g31000.1 (Oryza sativa), 3'ss of exon 4
gtaagcagcaatatttaaagaattttattacatgcatacttgccatatccatttgattcaaccttgctttgttactgccactacttaaaatttgttaattcagttttctgatttcctttcagACCTTGTTAATGTGTTTGAGGTGTTTCTTCCTCAACTTCTTCTGTACCCCAATGCATCAGATCCATTAAATGGTGATGCTGCTGCCTTGATGATTCGAGA
| || || | | |||| ||| | | | ||| || || ||| ||| | | | | || ||| || | |||| || ||||||||||| || || || ||||| |||||||| ||||||| ||| | || || ||||||||||| || |||||||| ||||||| || ||
---------------------gtgagataactctcgtccttgtcattattagtacgggtacttgctgtttattctagcttcta--taaccctgggttgaatatttccatgaatttttggcagATCTAGTTAATGTGTTCGAAGTCTTCCTTCCACAACTTCTATTGTACCCAAATCCTTCTGACCCATTAAATGGAGAGGCTGCTGCACTGATGATGCGTGA
upper sequence: GLYMA08G01940.3 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G150867_T02 (Zea mays), 3'ss of exon 4
-------------gtaagcagcaatatttaaa--gaattttattacatgcatact-tgccatatccatttgattcaaccttgctttgttactgccactacttaaaatttgttaattcagttttctg---atttcctttcagACCTTGTTAATGTGTTTGAGGTGTTTCTTCCTCAACTTCTTCTGTACCCCAATGCATCAGATCCATTAAATGGTGATGCTGCTGCCTTGATGATTCGAGA
| || |||| | || | | ||| | || |||| |||| | || || ||| | | || | || | || ||||| | | || | || |||| |||||||||||||| ||||| || ||||| |||||||| | || || ||| | || |||||||||||||| ||||| ||||| |||||||| || ||
gtaagattgatctttgcatttcattattaggatcgacaaccagttcattctctctgtgccttatctgtacagttaaagcttcatgttttgta--ctctgttataacagggttaacttgaacctgtgtgtgatattttgcagATCTTGTTAATGTGTTCGAGGTCTTCCTTCCACAACTTCTGTTATATCCTAATCCTTCTGATCCATTAAATGGAGATGCAGCTGCGTTGATGATGCGTGA
upper sequence: GLYMA08G01940.3 (Glycine max), 3'ss of exon 4
lower sequence: AC149818.2_FGT006 (Zea mays), 3'ss of exon 4
gtaagcagcaatatttaaagaattttattacatgcatacttgccatatccatttgattcaaccttgctttgttactgccactacttaaaatttgttaa-ttcagttttctg---atttcctttcagACCTTGTTAATGTGTTTGAGGTGTTTCTTCCTCAACTTCTTCTGTACCCCAATGCATCAGATCCATTAAATGGTGATGCTGCTGCCTTGATGATTCGAGA
||||| | || |||| | |||||| | | | ||| |||| | | | | | |||| | || | || ||||| || | || | || |||| ||||| |||||||| ||||| || ||||| |||||||| | || || ||| | || |||||||||||||| ||||| ||||| |||||||| || ||
gtaag-attgatctttacatctcattattaggatc-tccgcgccttatctgtatacaattagcgctccatgttttgtactctgttataacagggttaactttgaacctatgtgtgatattttgcagATCTTGTCAATGTGTTCGAGGTCTTCCTTCCACAACTTCTGTTATATCCTAATCCTTCTGATCCATTAAATGGAGATGCAGCTGCGTTGATGATGCGTGA
upper sequence: GLYMA08G01940.3 (Glycine max), 3'ss of exon 4
lower sequence: AT5G41340.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaagcagcaatatttaaagaattttattacatgcatacttgccatatccatttgattcaaccttgctttgttactgccactacttaaaatttgttaattcagttttctgatttcctttcagACCTTGTTAATGTGTTTGAGGTGTTTCTTCCTCAACTTCTTCTGTACCCCAATGCATCAGATCCATTAAATGGTGATGCTGCTGCCTTGATGATTCGAGA
||||| || |||| || | |||||| || ||| ||| | |||| | || ||| | |||| ||| | || ||| | || ||||||||||||| |||||||||||| ||||||||||| ||||||||||| || || ||||||||||||| ||||| || |||||||| || ||||| || ||
gtaag-ggcgatatcaaatgtggtttattt--tgaatatttg------------ggatcaaa------tgattgctgttgtgatttaac-tttatgtttttggttctt---ctttttttcagACCTTGTGAATGTGTTTGAGACATTTCTTCCTCAGCTTCTTCTGTATCCAAACCCATCAGATCCATTGAATGGAGAAGCTGCTGCGTTAATGATGCGTGA
upper sequence: GLYMA08G01940.3 (Glycine max), 3'ss of exon 4
lower sequence: AT1G63800.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaagcagcaatatttaaagaattttattacatgcatacttgccatatccatttgattcaaccttgctttgttactgccactacttaaaatt-tgttaattcagttttctgatttcct-ttcagACCTTGTTAATGTGTTTGAGGTGTTTCTTCCTCAACTTCTTCTGTACCCCAATGCATCAGATCCATTAAATGGTGATGCTGCTGCCTTGATGATTCGAGA
|| |||| | | || || ||| | | ||| ||| | || || || |||||||| | ||| || | ||||||||| || |||||||| ||| |||||||| |||||||||||||| || ||| | ||||||||||| |||||||| || ||||| |||||||| || ||
---------------------------gtatgatcataacaaatggaacaat---atacaagatagtttta--actcctgttagtttttgttatgttaattatgatttggatttagttattcagACCTGGTGAATGTGTTCGAGACATTTCTTCCGCAACTTCTTCTGTATCCGAATCCGTCAGATCCATTGAATGGTGAAGCAGCTGCATTGATGATGCGTGAMapped 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|192294461|gb|FG987390.1|FG987390EST: TGGTTCTGTTTGCTTAGATGTTATTAGCCAGACTTGGAGTCCAATGTTTG ACCTTGTTAATGTGTTTGAGGTGTTTCTTCCTCAACTTCTTCTGTACCCCA
genomic: TGGTTCTGTTTGCTTAGATGTTATTAGCCAGACTTGGAGTCCAATGTTTGgtaagcagca ... ttcctttcagACCTTGTTAATGTGTTTGAGGTGTTTCTTCCTCAACTTCTTCTGTACCCCA
EST:
gi|298163300|gb|HO012033.1|HO012033EST: TGGTTCTGTTTGCTTAGATGTTATTAGCCAGACTTGGAGTCCAATGTTTG ACCTTGTTAATGTGTTTGAGGTGTTTCTTCCTCAACTTCTTCTGTACCCCA
genomic: TGGTTCTGTTTGCTTAGATGTTATTAGCCAGACTTGGAGTCCAATGTTTGgtaagcagca ... ttcctttcagACCTTGTTAATGTGTTTGAGGTGTTTCTTCCTCAACTTCTTCTGTACCCCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgttactgccactacttaaaatttgttaattcagttttctgatttcctttcagACCTTGTTAATGTGTTTGAGGTGTTTCTTCCTCAACTTCTTCTGTACCCCAATGCATCAGATCCATTAAATGGTGATGCTGCTGCCTTGATGATTCGAGA
ttctgat putative branch site (score: 3)
ttttctgatttccttt CT-rich tract
ttaaaatttgttaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcagcaatatttaaagaattttattacatgcatacttgccatatccatttgattcaaccttgctttgttactgccactacttaaaatttgttaattcagttttctgatttcctttcagACCTTGTTAATGTGTTTGAGGTGTTTCTTCCTCAACTTCTTCTGTACCCCAATGCATCAGATCCATTAAATGGTGATGCTGCTGCCTTGATGATTCGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC