Sequence
atgc intronic sequence ATGC exonic sequence...aacatatatttagattcacatatatgctagtttctacttttcttacaacaatagccgtgtctattgagtgcatctctattaatcatcatttcaaatacagATGCGATGTTTATAGTTTTGGAGTCATCTTATGGGAGCTTGCCACTCTAAGGTTGCCGTGGAGTGGAATGAATCCTATGCAAGTTGTTGGTGCCGTTGGT
Basic information
species | Glycine max |
transcript | GLYMA10G30070.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G30070.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os03g06410.1 (Oryza sativa), 3'ss of exon 11
-----aacatatatttagattcacatatatgctagtttctacttttcttacaacaatagccgtgtctattgagtgcatctctattaatcatcatttcaaat----acagATGCGATGTTTATAGTTTTGGAGTCATCTTATGGGAGCTTGCCACTCTAAGGTTGCCGTGGAGTGGAATGAATCCTATGCAAGTTGTTGGTGCCGTTGGT
|| | || | | | | |||| |||| ||| || | ||| | ||| ||||| | | ||||| | |||| ||| || |||||||| || ||||| |||||||| ||||| | || || || ||| |||| ||||||||||||||||| |||||||||||||| || || ||
gtagaaatggaacacccatctccctcacaaacc--tttcagctttccttgtt-tgattggtgtggc-----agta-atctcactcagacatcacctgaaatttctgcagGTGTGATGTTTACAGCTTTGGTGTCATCTTGTGGGAATTAGCAACACTTAGGATGCCATGGAGTGGAATGAATCCAATGCAAGTTGTTGGGGCAGTCGGC
upper sequence: GLYMA10G30070.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os10g29540.1 (Oryza sativa), 3'ss of exon 11
aacatatatttagattcacatatatgctagtttctacttttcttacaacaatagccgtgtctattgagtgcatctctattaatcatcatttcaaat---acagATGCGATGTTTATAGTTTTGGAGTCATCTTATGGGAGCTTGCCACTCTAAGGTTGCCGTGGAGTGGAATGAATCCTATGCAAGTTGTTGGTGCCGTTGGT
| ||| | || | | | | | || || | || ||| ||| | ||||| | | ||||| || || | | ||| || |||||||| || ||||| |||||||||||||| || || || ||| |||| |||||||| ||||| || ||||||||||| ||||| ||||||
ctgaagaattcaagttgaatttctctccggcctttatttctgttggcacactagaca-acacattgacaac--tgcagctaatcgtcgttgagagttttgcagGTGTGATGTTTACAGCTTTGGTGTCATCTTATGGGAACTAGCAACACTACAAATGCCATGGAGTGGCATGAACCCCATGCAAGTTGTGGGTGCAGTTGGT
upper sequence: GLYMA10G30070.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G038982_T01 (Zea mays), 3'ss of exon 7
aacatatatt-tagattcacatatatgctagtttctacttttcttacaacaatagccgtgtctattgagtgcatctctattaatcatcatttcaaatacagATGCGATGTTTATAGTTTTGGAGTCATCTTATGGGAGCTTGCCACTCTAAGGTTGCCGTGGAGTGGAATGAATCCTATGCAAGTTGTTGGTGCCGTTGGT
||| || | | | | |||| ||| | | ||||| | | | || || || | | | ||||| ||||| ||||| || ||||| ||||| ||||||||||| || || || || |||| |||||||| |||||||| ||||| ||||| || || ||||||
-ttatactttgcaaaaactgaagtatgataggatactcacctcttaacttagttaaattcagtaacgatcttgatgctgccactacctgaattttgtacagGTGCGACGTTTACAGCTTTGGTGTCATATTATGGGAGCTGGCAACGCTTAGAATGCCATGGAGTGGGATGAATCCAATGCAGGTTGTGGGGGCAGTTGGT
upper sequence: GLYMA10G30070.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv14s0030g01440.t01 (Vitis vinifera), 3'ss of exon 11
aacatatatttagattcacatatatgctagtttctacttttcttacaacaatagccgtgtctattgagtgcatctctattaatcatcatttcaaatacagATGCGATGTTTATAGTTTTGGAGTCATCTTATGGGAGCTTGCCACTCTAAGGTTGCCGTGGAGTGGAATGAATCCTATGCAAGTTGTTGGTGCCGTTGGT
| | | | || | | | | || | ||| | | || | | | | | | | | || | | |||||| ||||| || ||||| ||||| |||||| |||| | ||||||||||| ||| |||||||||| |||||||| |||||||| ||||||||||| || || || |||
gccctgtttggttgttgagaataaggagagagaaaagtttcaatcttataacaatcattgcaactaaaaattgatataacatgccaaatttcacttacagGTGTGATGTCTATAGCTTTGGAATCATTCTGTGGGAGCTTGCAACTTTAAGGTTGCCTTGGAGTGGGATGAATCCAATGCAAGTTGTGGGAGCAGTAGGTMapped 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|21888577|gb|BQ741790.1|BQ741790EST: ATGGATGGCTCCTGAAGTTCTCCGCAATGAGCCCTCAAATGAGAA ATGCGATGTTTATAGTTTTGGAGTCATCTTATGGGAGCTTGCCACTCTAAG
genomic: ATGGATGGCTCCTGAAGTTCTCCGCAATGAGCCCTCAAATGAGAAgtgagttgtt ... tcaaatacagATGCGATGTTTATAGTTTTGGAGTCATCTTATGGGAGCTTGCCACTCTAAG
EST:
gi|17153163|gb|BM143096.1|BM143096EST: CCGGAATGGATGGCTCCTGAAGTTCTCCGCAATGAGCCCTCAAATGAGAA ATGCGATGTTTATAGTTTTGGAGTCATCTTATGGGAGCTTGCCACTCTAAG
genomic: CCGGAATGGATGGCTCCTGAAGTTCTCCGCAATGAGCCCTCAAATGAGAAgtgagttgtt ... tcaaatacagATGCGATGTTTATAGTTTTGGAGTCATCTTATGGGAGCTTGCCACTCTAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caacaatagccgtgtctattgagtgcatctctattaatcatcatttcaaatacagATGCGATGTTTATAGTTTTGGAGTCATCTTATGGGAGCTTGCCACTCTAAGGTTGCCGTGGAGTGGAATGAATCCTATGCAAGTTGTTGGTGCCGTTGGT
tattaat putative branch site (score: 2)
tcatttc putative PPT
tattaatcatcatttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aacatatatttagattcacatatatgctagtttctacttttcttacaacaatagccgtgtctattgagtgcatctctattaatcatcatttcaaatacagATGCGATGTTTATAGTTTTGGAGTCATCTTATGGGAGCTTGCCACTCTAAGGTTGCCGTGGAGTGGAATGAATCCTATGCAAGTTGTTGGTGCCGTTGGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - -attcaca
- - - - - - - - - - tatatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - agccgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgagtgc