Sequence
atgc intronic sequence ATGC exonic sequence...ctccatttggtgggagcttcttgcattgggtttccttttgatgtctcttggtccactctaatgaatacaatctaaaagtctgcattacttgaattttcagATTTGTGTTATTTGTAAGCAAATTCATGGTTCGTGTACACAATGTTGCAAGTGTTCTACTTATTTCCATGCCATGTGTGCTTCAAGGGCCGGTTATCGAA
Basic information
species | Glycine max |
transcript | GLYMA06G13330.1 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G13330.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os01g46700.1 (Oryza sativa), 3'ss of exon 13
---------------------ctccatttggtgggagcttcttgcattgggtttccttttgatgtctcttgg--tccactctaatgaatacaatctaaaagtctgcatt---acttgaattttcagATTTGTGTTATTTGTAAGCAAATTCATGGTTCGTGTACACAATGTTGCAAGTGTTCTACTTATTTCCATGCCATGTGTGCTTCAAGGGCCGGTTATCGAA
| | | | || | | ||| || |||||| | | | | || | | | ||||| | ||| | | ||||| ||||| ||||||| |||||| ||||||||||||||||| || | || ||| || ||||||| ||||||||| ||||| |||||||| || ||| | |
gtagtataattggatgatatattaagtgtcttaagaagat-taatcttgaacaatattaaaatgtcttgtatattgaagttgaactacaaaactctaattatgcttattctcatccattgctccagATGTGTGTCATTTGTAGGCAAATACATGGTTCGTGTACACAGTGCTACAGGTGCTCAACTTATTACCATGCCATCTGTGCATCAAGGGCAGGCTATAGGA
upper sequence: GLYMA06G13330.1 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G170412_T01 (Zea mays), 3'ss of exon 13
------------------ctccatttggtggg--agcttcttgcattgggtttccttttgatgtctcttggtccactctaatgaata-caatctaaaagtctgcattacttgaattttcagATTTGTGTTATTTGTAAGCAAATTCATGGTTCGTGTACACAATGTTGCAAGTGTTCTACTTATTTCCATGCCATGTGTGCTTCAAGGGCCGGTTATCGAA
| | | | | || | | ||| || | | | || || | | || || |||| | | | | | ||||| ||||| |||||||||||||| |||||||| ||||| ||||| | || ||| |||||||| | ||||||||| ||||| |||||||| || |||||||
gttgtttatctttcgtagtttcgtactataatttatgttgctcaagtggattgaccaacaagtaatacatttctgtgctgaagtatggcagtctatgctctatgctcatctatctctgcagATGTGTGTGATTTGTAAGCAAATACATGGTTCATGTACTCAATGCTACAGGTGCTCTACTTACTACCATGCCATTTGTGCATCAAGGGCAGGCTATCGAA
upper sequence: GLYMA06G13330.1 (Glycine max), 3'ss of exon 14
lower sequence: AT5G53430.1 (Arabidopsis thaliana), 3'ss of exon 13
-----------------------------------ctccatttggtgggagc--ttcttgcattgg---gtttc----cttttgatgtctcttggtccactctaatgaatacaatctaaaagtctgcattacttg----aattttcagATTTGTGTTATTTGTAAGCAAATTCATGGTTCGTGTACACAATGTTGCAAGTGTTCTACTTATTTCCATGCCATGTGTGCTTCAAGGGCCGGTTATCGAA
|| | | || || |||| | ||||| |||||| | | | | || | | | | ||| | | || | || ||||||||||| || || |||||||| ||||| || || || || ||||||||||| ||||| |||| ||||||||||||||||| | || || ||| |||
gtacatacctgattcctggatatcatattcggcctatcgtgataataagattagctcctgcagttacttgtttctaaccttttgggaagtttcactatgtgcaaaactaaaaagccagaaaccttatcctgtttttgatatattccagATTTGTGTAATATGCAAGCAAATACATGGCTCATGCACTCAGTGTTGCAAGTGCTCTACGTATTATCATGCCATGTGTGCTTCCCGAGCTGGGTATAGAA
upper sequence: GLYMA06G13330.1 (Glycine max), 3'ss of exon 14
lower sequence: AT4G27910.1 (Arabidopsis thaliana), 3'ss of exon 13
ctccatttggtgggagcttcttgcattgggttt----ccttttgatgtctcttggtccactctaatgaatacaatctaaaagtctgcattacttgaattttcagATTTGTGTTATTTGTAAGCAAATTCATGGTTCGTGTACACAATGTTGCAAGTGTTCTACTTATTTCCATGCCATGTGTGCTTCAAGGGCCGGTTATCGAA
| |||| | | ||| ||| || ||| ||||| || || | | | | ||| || || ||| | || |||||||| ||||| || || || ||||| ||||| |||||||| || ||||||||||||||||| || | |||||||||||||| || | || |||||| |||
gtaaatttaatattaacttattgtctttaattttggacctttccataactgtctgcgaccaaagctaaattgcatgaaatcttcttcgttttgatggatttcagATATGTGTAATATGCAAACAAATACATGGCTCGTGTACTCAGTGTTGCAAGTGTTCTACATACTATCATGCCATGTGTGCCTCCCGAGCTGGTTATAGAA
upper sequence: GLYMA06G13330.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv16s0098g00350.t01 (Vitis vinifera), 3'ss of exon 14
-ctccatttggtggga--gcttcttgcattgggtttccttttgatgtctcttggtccactctaatgaatacaatctaaaagtctgcattacttgaatt---ttcagATTTGTGTTATTTGTAAGCAAATTCATGGTTCGTGTACACAATGTTGCAAGTGTTCTACTTATTTCCATGCCATGTGTGCTTCAAGGGCCGGTTATCGAA
| | || | | | | | |||| ||| ||| | | | || | | | || |||| | || ||| || || || |||||||||| || || ||||||||||| |||||||| || ||||| |||||||||||||||||||| | |||||| |||||||| |||||||| || ||||| |
tttgaaaatgttagcatgatgtttaatattgagttggttttc--ttgcacatgaatc--ttcagctgatgtgatctga--gtttgccttgttttcatgaaattcagATTTGCGTAATCTGTAAGCAAATACATGGTTCATGCACACAGTGTTGCAAGTGTTCTACTTACTACCATGCAATGTGTGCATCAAGGGCGGGGTATCGTAMapped 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|208262289|gb|GE059664.1|GE059664EST: TCTTTTGTAAAG ATTTGTGTTATTTGTAAGCAAATTCATGGTTCGTGTACACAATGTTGCAAG
genomic: TCTTTTGTAAAGgtaaagtatc ... gaattttcagATTTGTGTTATTTGTAAGCAAATTCATGGTTCGTGTACACAATGTTGCAAG
EST:
gi|193409864|gb|FK373840.1|FK373840EST: TGGAGCCTGCTTTGGGTATTCTAAGTATTCCATCAAATTCTTTTGTAAAG ATTTGTGTTATTTGCAAGCAAATTCATGGTTCGTGTACACAATGTTGCAAG
genomic: TGGAGCCTGCTTTGGGTATTCTAAGTATTCCATCAAATTCTTTTGTAAAGgtaaagtatc ... gaattttcagATTTGTGTTATTTGTAAGCAAATTCATGGTTCGTGTACACAATGTTGCAAG
EST:
gi|208238085|gb|GE040433.1|GE040433EST: TGGAGCCTGCTTTGGGTATTCTAAGTATTCCATCAAATTCTTTTGTAAAG ATTTGTGTTATTTGTAAGCAAATTCATGGTTCGTGTACACAATGTTGCAAG
genomic: TGGAGCCTGCTTTGGGTATTCTAAGTATTCCATCAAATTCTTTTGTAAAGgtaaagtatc ... gaattttcagATTTGTGTTATTTGTAAGCAAATTCATGGTTCGTGTACACAATGTTGCAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttggtccactctaatgaatacaatctaaaagtctgcattacttgaattttcagATTTGTGTTATTTGTAAGCAAATTCATGGTTCGTGTACACAATGTTGCAAGTGTTCTACTTATTTCCATGCCATGTGTGCTTCAAGGGCCGGTTATCGAA
atctaaa putative branch site (score: 3)
ttttc putative PPT
aatacaatctaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctccatttggtgggagcttcttgcattgggtttccttttgatgtctcttggtccactctaatgaatacaatctaaaagtctgcattacttgaattttcagATTTGTGTTATTTGTAAGCAAATTCATGGTTCGTGTACACAATGTTGCAAGTGTTCTACTTATTTCCATGCCATGTGTGCTTCAAGGGCCGGTTATCGAA
ctccatt
- - - -tggtggg
- - - - - - - - - -cttgcat
- - - - - - - - - - - - - - - - -ccttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - ccactct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcattac