Sequence
atgc intronic sequence ATGC exonic sequencegtttgttgctataactttttcccaccttatatttaatgtgtcatgtgttatttcattacaccagcttcattcattgaacttgcttcacatgcagcaaaacattggcttgcagtgtgttaatattctccttttgcagGCTGCCCATGATGCTTTTGTTGAAACTAGTGGAGCACTTAACACTATTGCGGCTTCTTTGATGAAGATTGCTAATGATATACGGTTGTTAGGAAG
Basic information
species | Glycine max |
transcript | GLYMA10G02040.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G02040.2 (Glycine max), 3'ss of exon 9
lower sequence: AT5G50950.3 (Arabidopsis thaliana), 3'ss of exon 8
gtttgttgcta--taactttttcccacctta-tatttaatgtgtcatgtgttatttcattacaccagcttc--attcattgaacttgcttcacatgcagcaaaacat-tggcttgcagtgtgttaatattctccttttgcagGCTGCCCATGATGCTTTTGTTGAAACTAGTGGAGCACTTAACACTATTGCGGCTTCTTTGATGAAGATTGCTAATGATATACGGTTGTTAGGAAG
||| | ||| ||||||| | | | | | | || | || ||| || ||| | ||| | ||| || |||||| | | || || | ||| |||| | |||| ||||||| || ||||||| ||||||||| |||||| | |||||||| || || | || |||||||||||||| ||||||||||| || | |||||
gttagcctctaaataactttcatcatcatcaatgtccaa---atttagtcttagcgtcttccactgggttctaaatcaaacaagatgcttctgaatggttgatgtatatgaaataagttgttgagttattacgcctttgtagGCTGCACACGATGCTTGTGTTGAAACAAGTGGATCTCTTAACACAATCGCCACATCATTGATGAAGATTGCCAATGATATACGTTTTCTTGGAAG
upper sequence: GLYMA10G02040.2 (Glycine max), 3'ss of exon 9
lower sequence: AT2G47510.1 (Arabidopsis thaliana), 3'ss of exon 10
gtttgttgctataactttttcccaccttatatttaatgtgtcatgtgttatttcattacaccagcttcattcattgaacttgcttcaca---tgcagcaaaacattggcttgcagtgtgttaatattct-ccttttgcagGCTGCCCATGATGCTTTTGTTGAAACTAGTGGAGCACTTAACACTATTGCGGCTTCTTTGATGAAGATTGCTAATGATATACGGTTGTTAGGAAG
|| | | | | | |||| || | | | |||| | |||| | | | || ||| || | |||| || | || | |||||| | |||| |||||||| || ||||||| ||||||||| ||||| |||||||||| || || | || |||||||||| || ||||||||||| || | |||||
----------gtagcctccaaactacctctatt--atttattgacacgaaacccattc--ctagctctgcctctggtgccaactagacaagatgttcctaaacggtgaaatcagttgctaaattattctgctttttccagGCTGCACACGATGCTTGTGTTGAAACCAGTGGGTCACTTAACACAATCGCCACATCGCTGATGAAGATCGCCAATGATATACGTTTTCTTGGAAG
upper sequence: GLYMA10G02040.2 (Glycine max), 3'ss of exon 9
lower sequence: Vv07s0005g00880.t01 (Vitis vinifera), 3'ss of exon 10
gtttgttgctataactttttcccaccttatatttaatgtgtcatgtgttatttcattacaccagcttcattcattgaacttgcttcacatgcagcaaaacattggcttgcagtgtgttaatattctccttttg---cagGCTGCCCATGATGCTTTTGTTGAAACTAGTGGAGCACTTAACACTATTGCGGCTTCTTTGATGAAGATTGCTAATGATATACGGTTGTTAGGAAG
|| | || || | | ||| || | | |||| | |||| | | | ||||| ||| ||||| | | | ||| || | ||||| |||||||| |||||||| ||||||||||||||||| || |||||||| |||| |||| ||||||||||||||||||||||||| || ||||||||
--------------------------------ttgttaggtagtgaaggaatatattccatttattgc-ctcat--atcttgtaaaatttactacaaaatatt---ttgcattct-taaatgtttttcttttctgccagGCTGCACATGATGCATTTGTTGAAACTAGTGGTTCAGTTAACACTGTTGCTACTTCCCTGATGAAGATTGCTAATGATATACGCTTATTAGGAAGMapped 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|207780421|gb|GD750774.1|GD750774EST: AGGAAACAAATCTGCCTTTTGTTACGGCAGAAAATAAGTTTGAGGCCTTG GCTGCCCATGATGCTTTTGTTGAAACTAGTGGAGCACTTAACACTATTGCG
genomic: AGGAAACAAATCTGCCTTTTGTTACGGCAGAAAATAAGTTTGAGGCCTTGgtttgttgct ... ccttttgcagGCTGCCCATGATGCTTTTGTTGAAACTAGTGGAGCACTTAACACTATTGCG
EST:
gi|254343540|gb|GR857296.1|GR857296EST: AGGAAACAAATCTGCCTTTTGTTACGGCAGAAAATAAGTTTGAGGCCTTG GCTGCCCATGATGCTTTTGTTGAAACTAGTGGAGCACTTAACACTATTGCG
genomic: AGGAAACAAATCTGCCTTTTGTTACGGCAGAAAATAAGTTTGAGGCCTTGgtttgttgct ... ccttttgcagGCTGCCCATGATGCTTTTGTTGAAACTAGTGGAGCACTTAACACTATTGCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcttcacatgcagcaaaacattggcttgcagtgtgttaatattctccttttgcagGCTGCCCATGATGCTTTTGTTGAAACTAGTGGAGCACTTAACACTATTGCGGCTTCTTTGATGAAGATTGCTAATGATATACGGTTGTTAGGAAG
tgttaat putative branch site (score: 3)
tattctccttttgc CT-rich tract
tgttaatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgttgctataactttttcccaccttatatttaatgtgtcatgtgttatttcattacaccagcttcattcattgaacttgcttcacatgcagcaaaacattggcttgcagtgtgttaatattctccttttgcagGCTGCCCATGATGCTTTTGTTGAAACTAGTGGAGCACTTAACACTATTGCGGCTTCTTTGATGAAGATTGCTAATGATATACGGTTGTTAGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA