Sequence
atgc intronic sequence ATGC exonic sequence...tgagttatccccccgcccccctctcccaattcatacaatagctatcttttatactttaaactttcaaagtttaattatttgtgaatattatgtggtacagCAAAGTCATGGATGTCTTCATCAAGGCTGCTGAATATATGGAAATTCCAGTTCGTAGGACTGATGATGAACCTCTTCAGAAGCTTTTTATGTTGGTAAGG
Basic information
species | Glycine max |
transcript | GLYMA15G20400.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G20400.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os04g24180.1 (Oryza sativa), 3'ss of exon 6
-tgagttatccc---cccgcccccctctcccaattcatacaatagctatcttttatactttaaactttcaa--agtttaattatttgtgaatattatgtggtacagCAAAGTCATGGATGTCTTCATCAAGGCTGCTGAATATATGGAAATTCCAGTTCGTAGGACTGATGATGAACCTCTTCAGAAGCTTTTTATGTTGGTAAGG
| || ||| | | | | || ||| || || | | || | | | | || || |||| | | | || | |||||||||||||||||||||||| |||||||| || |||||||| || ||||| || | | ||| |||||||| | ||||| | ||| | || |||
ccaaattgtcctgagcatcctttctgttatcagttctagatatgaaaatgcctcgtttttgacatatctgatccgtggaactattggc------tgtatgttgcagCAAAGTCATGGATGTCTTCATTAAGGCTGCAGAGTATATGGAGATGCCAGTCCGGCGCAGTGACGATGAACCCTTGCAGAAATTATTTGTAGCTGTTAGG
upper sequence: GLYMA15G20400.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G167868_T01 (Zea mays), 3'ss of exon 5
-tgagttatccccccgcccccctctcccaattcatacaatagctatctt--ttatactttaaactttcaaagtttaattatttgtgaatattatgtggtacagCAAAGTCATGGATGTCTTCATCAAGGCTGCTGAATATATGGAAATTCCAGTTCGTAGGACTGATGATGAACCTCTTCAGAAGCTTTTTATGTTGGTAAGG
| | | | | || |||| | |||| || | || || | | | | | || || | |||| |||||||||| ||||||||||||||||||||||| ||||||||||| || |||||||| | | |||||||||||| ||||| || | ||| | || ||
ttccgggaaacttctatattggg-tcttaatttacttgctagccttcaaaatcatgtttcattttcccttgcctgatccatgggttgtttccatgt--cacagCAAAGTTATGGATGTCTTCATCAAGGCTGCAGAATATATGGAGATGCCAGTTCGACGCAGTGATGATGAACCCCTTCAAAAATTGTTTGTAGCTGTTAGA
upper sequence: GLYMA15G20400.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G007871_T02 (Zea mays), 3'ss of exon 5
tgagttatccccccgcccccctctccca-attcatacaatagctatcttttatactttaaactttcaaagtttaattatttgtgaata--ttatgtggtacagCAAAGTCATGGATGTCTTCATCAAGGCTGCTGAATATATGGAAATTCCAGTTCGTAGGACTGATGATGAACCTCTTCAGAAGCTTTTTATGTTGGTAAGG
|| | | | | | | || || | | |||| |||| | | |||| || | | ||| | || || |||||||||| || |||||||||||||||||||| ||||||||||| || |||||||| | | |||||||||||| || || || | ||| | || ||
-tagcttccaggaaacttctatttttggtgttaatttacttgctagctttcgaaatcatgtttttccc--ttgtgtgagccatgagttgtttccatgtcacagCAAAGTTATAGATGTCTTCATCAAGGCTGCAGAATATATGGAGATGCCAGTTCGACGCAGTGATGATGAACCCCTGCAAAAATTGTTTGTAGCTGTTAGA
upper sequence: GLYMA15G20400.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G79940.3 (Arabidopsis thaliana), 3'ss of exon 6
-tgagttatccccccgcccccctctcccaattcatacaatagctatcttttatact--ttaaactttcaaa-----gtttaattatttgtgaatattatgtggtacagCAAAGTCATGGATGTCTTCATCAAGGCTGCTGAATATATGGAAATTCCAGTTCGTAGGACTGATGATGAACCTCTTCAGAAGCTTTTTATGTTGGTAAGG
| || | | || | ||| | || | || | | | | | | |||| || | | || | || || | | || ||||||||| ||||| || |||| |||||| ||||| || ||||| |||||||||||||| ||||||||||||||||| |||||||| ||||||| || |||
gtatattcactcatacccatatacattcaagtgatgctattggtgcatgacaaatgggctgtgttttcgtttgtttgtatgacatgttttaaaatttttattgtccagCAAAGTTATGGAAGTTTTCACCAAGGCAGCTGAGTACATGGAGATTCCAGTTCGTAGAACTGATGATGAACCTCTGCAGAAGCTCTTTATGTCTGTTAGG
upper sequence: GLYMA15G20400.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv16s0050g01460.t01 (Vitis vinifera), 3'ss of exon 5
---tgagttatccccccgcccccctctcccaattcatacaatagc-tatcttttatactttaaactttcaaagtttaattatttgtgaatattatgtggtacagCAAAGTCATGGATGTCTTCATCAAGGCTGCTGAATATATGGAAATTCCAGTTCGTAGGACTGATGATGAACCTCTTCAGAAGCTTTTTATGTTGGTAAGG
| | | | | | || ||| | | ||| || | ||| ||| ||||| ||||| | | || ||||||||||| |||||||||||||| |||||||| ||||| |||||||||||||| ||||||||||| |||| || |||||||| || || ||||| ||||||
gaaaaatgggtgtttatgtttatatatgtttttatgtatcttagtgtgtgatttctattataagtttt----gtttatgatgatgtgataacttggttttacagCAAAGTTATGGATGTCTTCATTAAGGCTGCAGAATACATGGAAATTCCAGTCCGTAGGACTGACAATGAGCCCCTTCAGAAACTGTTCATGTTAGTAAGGMapped 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|27426194|gb|CA937714.1|CA937714EST: CAAACACTTTCTACTTACTATTACCTTATGAAGCCTTCTTTGGCCCCCAG CAAAGTCATGGATGTCTTCATCAAGGCTGCTGAATATATGGAAATTCCAGT
genomic: CAAACACTTTCTACTTACTATTACCTTATGAAGCCTTCTTTGGCCCCCAGgtatatatac ... tgtggtacagCAAAGTCATGGATGTCTTCATCAAGGCTGCTGAATATATGGAAATTCCAGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttttatactttaaactttcaaagtttaattatttgtgaatattatgtggtacagCAAAGTCATGGATGTCTTCATCAAGGCTGCTGAATATATGGAAATTCCAGTTCGTAGGACTGATGATGAACCTCTTCAGAAGCTTTTTATGTTGGTAAGG
gtttaat putative branch site (score: 4)
tttaaactttcaaagt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgagttatccccccgcccccctctcccaattcatacaatagctatcttttatactttaaactttcaaagtttaattatttgtgaatattatgtggtacagCAAAGTCATGGATGTCTTCATCAAGGCTGCTGAATATATGGAAATTCCAGTTCGTAGGACTGATGATGAACCTCTTCAGAAGCTTTTTATGTTGGTAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - atccccc
- - - - - - -cgccccc
- - - - - - - - - - ctctccc
- - - - - - - - - - - - - - - tcataca