Sequence
atgc intronic sequence ATGC exonic sequence...aatcatatagtcccttcatgtctctttttcatcattttgtttatttaagaaattatgccttgtaattgatgtgtgattcaaattttgaatgtgtgtgtagCTGAATATCGTGGAAGGGAAGATGCAATATCTTTATGATGATAGTGGGAGGCGTTACCTTGATGCATTTGCGGGAATAGTTACTGTTTCTTGCGGACATT
Basic information
species | Glycine max |
transcript | GLYMA05G31630.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G31630.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G39660.1 (Arabidopsis thaliana), 3'ss of exon 1
--aatcatatagtcccttcatgtctctttttcatcattttgtttatttaagaaattatgccttg--taattgatgtgtgatt--caaattttgaatgtgtgt-gtagCTGAATATCGTGGAAGGGAAGATGCAATATCTTTATGATGATAGTGGGAGGCGTTACCTTGATGCATTTGCGGGAATAGTTACTGTTTCTTGCGGACATT
| |||| ||| || | | ||||| | ||| | || || ||| | ||||| | | |||| | ||| | |||| || ||||| |||||||||||||| || | |||||||| ||||| ||||| || || ||||| ||||| |||||||| ||||| || ||||| || |
cgattcat-tagctcccgaagac------taagaggatttgtggacttagaagccagcttgatgatccatggatctctgattattcagtgttgatgttatgttgcagCTTAACATCGTTGAAGGGAAGATGCAGTACTTGTATGATGAGAGTGGTAGGCGATATCTGGATGCCTTTGCTGGAATAGTCACTGTGTCGTGCGGTCACT
upper sequence: GLYMA05G31630.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv07s0031g01330.t01 (Vitis vinifera), 3'ss of exon 1
aatcatatagtcccttcatgtctctttttcat-cattttgtttatttaagaaattatgccttgtaattg-atgtgtgattcaaattttgaatgtgtgtgtagCTGAATATCGTGGAAGGGAAGATGCAATATCTTTATGATGATAGTGGGAGGCGTTACCTTGATGCATTTGCGGGAATAGTTACTGTTTCTTGCGGACATT
|||||| | | ||| || || | | || | ||| |||| | |||| || || | || |||| | | ||| || | ||| | || |||||||||||||| ||| | | |||||| | ||| | ||| || |||||||| ||||| |||||||||||||| || || || ||||
-atcata-aactaatatatgaacagacttgatgtactcagtacacctaataaatatcatcccaacattgcatacatgttctaacttttcattatgtacacagGTCAATGTTGTTGAAGGGAAGATGCAGTATTTGTTTGATGAGAATGGCAAGCGCTATCTTGATGCCTTTGCTGGAATAGTTACTGTGTCATGTGGGCATT
upper sequence: GLYMA05G31630.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ12384 (Selaginella moellendorffii), 3'ss of exon 1
aatcatatagtcccttcatgtctctttttcatcattttgtttatttaagaaattatgccttgtaattgatgtgtgattcaaattttgaatgtgtgtgtagCTGAATATCGTGGAAGGGAAGATGCAATATCTTTATGATGATAGTGGGAGGCGTTACCTTGATGCATTTGCGGGAATAGTTACTGTTTCTTGCGGACATT
| | ||| || || ||| |||||| || | | | | || | || |||| ||||| |||||||||||||||||||||||||| ||||| ||||| | | | ||| | ||||| ||||| || || || |||||||| || ||||
----------------------------------------gtgagtgtgaatttgtgtcttt---ttgatggatggattga-tcgcgggcgtct-tgcagCTCAATATTGTGGAAGGGAAGATGCAATATCTTTACGATGAGAGTGGAAAGAGGTACTTGGATGCGTTTGCTGGGATTGTCACTGTTTCCGTGGGTCATT
upper sequence: GLYMA05G31630.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ33785 (Selaginella moellendorffii), 3'ss of exon 1
aatcatatagtcccttcatgtctctttttcatcattttgtttatttaagaaattatgccttgtaattgatgtgtgattcaaattttgaatgtgtgtgtagCTGAATATCGTGGAAGGGAAGATGCAATATCTTTATGATGATAGTGGGAGGCGTTACCTTGATGCATTTGCGGGAATAGTTACTGTTTCTTGCGGACATT
| | |||| || || | | |||||| | || | | | || | || |||| ||||| |||||||||||||||||||||||||| ||||| ||||| | | | ||| | ||||| ||||| || || || |||||||| || ||||
----------------------------------------gtgagtgagaatttgtgtcctt---ttgatggatcgatcga-tcgcgggcgtct-tgcagCTCAATATTGTGGAAGGGAAGATGCAATATCTTTACGATGAGAGTGGAAAGAGGTACTTGGATGCGTTTGCTGGGATTGTCACTGTTTCCGTGGGTCATTMapped 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|208197183|gb|GD999370.1|GD999370EST: AGCGCAAA-CGTTCCTCGGTCCTTCCGTCTTCCACTACTATAAGAAACCT CTGAATATCGTGGA
genomic: AGCGCAAAACGTTCCTCGGTCCTTCCGTCTTCCACTACTATAAGAAACCTgtgagtctcc ... gtgtgtgtagCTGAATATCGTGGA
EST:
gi|208302368|gb|GE100427.1|GE100427EST: CCGTCTTCCACTACTATAAGAAACCT CTGAATATCGTGGAAGGGAAGATGCAATATCTTTATGATGATAGTGGGAGG
genomic: CCGTCTTCCACTACTATAAGAAACCTgtgagtctcc ... gtgtgtgtagCTGAATATCGTGGAAGGGAAGATGCAATATCTTTATGATGATAGTGGGAGG
EST:
gi|208029480|gb|GD827896.1|GD827896EST: ACTATAAGAAACCT CTGAATATCGTGGAAAGGAAGATGCAATATCTTTATGATGATAGTGGGAGG
genomic: ACTATAAGAAACCTgtgagtctcc ... gtgtgtgtagCTGAATATCGTGGAAGGGAAGATGCAATATCTTTATGATGATAGTGGGAGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taagaaattatgccttgtaattgatgtgtgattcaaattttgaatgtgtgtgtagCTGAATATCGTGGAAGGGAAGATGCAATATCTTTATGATGATAGTGGGAGGCGTTACCTTGATGCATTTGCGGGAATAGTTACTGTTTCTTGCGGACATT
aattgat putative branch site (score: 4)
attcaaattttgaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatcatatagtcccttcatgtctctttttcatcattttgtttatttaagaaattatgccttgtaattgatgtgtgattcaaattttgaatgtgtgtgtagCTGAATATCGTGGAAGGGAAGATGCAATATCTTTATGATGATAGTGGGAGGCGTTACCTTGATGCATTTGCGGGAATAGTTACTGTTTCTTGCGGACATT
- - - - - tcccttc
- - - - - - - - - - - - - - - - - - - - - - - - - - -tatgcct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgtga