Sequence
atgc intronic sequence ATGC exonic sequence...ttttttgctgaaattaatataaattgtcatctaacttcactgttgagttatgctacaaatatgattcaagatctgattaggccattatgttattgtccagGAGCTTTTTGTAAAACTGAATCGAATGGCCAATATAGCAGCAGATATGTTTGTAGGGAGGGAAAGATTTGCTACGCTGCTCTTGATGAGACTTACAGAAA
Basic information
species | Glycine max |
transcript | GLYMA08G23840.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G23840.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os07g10110.1 (Oryza sativa), 3'ss of exon 4
-----ttttttgctgaaattaatataaattgtcatctaacttc--actgttgagttatgctacaaatatgattcaagatctgattaggccattatgttattgtccagGAGCTTTTTGTAAAACTGAATCGAATGGCCAATATAGCAGCAGATATGTTTGTAGGGAGGGAAAGATTTGCTACGCTGCTCTTGATGAGACTTACAGAAA
|| || ||| | | ||| | | || | | | || | | | || || ||| | ||||| | ||| | |||| |||||||| | || ||| || ||| | ||||||| ||| || |||||||||||||| || || |||||||||||||| ||||| ||||| |||| || || |
ttattcttcatgatgatggctctctgaatcaatgtagatattaggattctagaacttgcccaaaagtagtattttgtagctgat----ctgctat-tcattg--cagGAGCTGTATGCAAAGCTAAATAGGATGGCCAGTATTGCGGCAGATATGTTTGTCGGCAGAGAAAGATTTGCTACTCTGCTAATGATGCGACTCACTGAGA
upper sequence: GLYMA08G23840.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G090573_T01 (Zea mays), 3'ss of exon 4
--------ttttttgctgaaattaatataaattgtcatctaacttcactgttgagttatgctacaaa-tatgattcaagatctgattaggccattatgttattg--tccagGAGCTTTTTGTAAAACTGAATCGAATGGCCAATATAGCAGCAGATATGTTTGTAGGGAGGGAAAGATTTGCTACGCTGCTCTTGATGAGACTTACAGAAA
| ||| || || | | | ||| || || || || | | | ||| ||| |||| | | ||| || | ||||| | | || ||| ||||| ||||| | | || ||||| |||||||| || |||||||| ||||| |||||||| ||||||||||||| ||
gtgtttccatattttttggcat-gctgtgacaagtctgctccctccaaaatttccacacacaaaaaaatatctcctgtcttctgcgtcatctcacctgtagttcattgcagGAATTGTATGCGAAATTGAATAAGATGGCAAGCGTTGCGGCAGACATGTTTGTTGGTAGGGAAAGGTTTGCCACGCTGCTTATGATGAGACTTACGGAGG
upper sequence: GLYMA08G23840.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G49830.1 (Arabidopsis thaliana), 3'ss of exon 4
ttttttgctgaaat-taatataaattgtcatctaacttcactgttgagttatgctacaaatatgattcaagatctgattaggccattatgttattgtc---cagGAGCTTTTTGTAAAACTGAATCGAATGGCCAATATAGCAGCAGATATGTTTGTAGGGAGGGAAAGATTTGCTACGCTGCTCTTGATGAGACTTACAGAAA
| |||| | | || | | | | | | | || || | | || |||| | | || || || || ||| ||||| ||||||| ||||| || | ||||| | | |||||||||||||||||||||| || |||||||| || | | |||||| || | ||||| |
-tgtttgtcatagtctactgtccacttcaagaacatgatttttttctgtcttttttagcttaatattct---tatactttgggtgttgcgtcgttggaaaacagGAACTTTTTGCCAAACTTAACAGGATGGCAAGTCTAGCAGCAGATATGTTTGTAGGAAGAGAAAGATTCGCCATATCTTTGTTGATGCGATTAACAGAGA
upper sequence: GLYMA08G23840.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv09s0018g01920.t01 (Vitis vinifera), 3'ss of exon 4
ttttttgctgaaattaatataaattgtcatctaacttca--ctgttgagttatgctacaa-atatgattcaagatctgattaggccattatgttattgtccagGAGCTTTTTGTAAAACTGAATCGAATGGCCAATATAGCAGCAGATATGTTTGTAGGGAGGGAAAGATTTGCTACGCTGCTCTTGATGAGACTTACAGAAA
| || | || || | || | | || | | || ||| || ||| |||| | | | || ||| || || |||| | ||||| |||||| ||| ||||| | ||||||| ||||||||||| ||||||||||| |||||||||| |||||| |||| || ||| |||| || ||||
-gctctgagcattttgatggagatatt--ttgaattaaaacctattgctctacagcacatcatattaatttgggcctttttacccctttttgtttccattcagGAACTTTTTACAAAGCTGAACAGGATGGCCAGCATAGCAGCAGACATGTTTGTAGGCAGGGAAAGATATGCTACATTGCTATTAATGCGACTCACTGAAAMapped 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|193729947|gb|FK667819.1|FK667819EST: ATATGGATGGAAACGCAGAAGTTGAATGGACTCCATCTTCGATTTTTCAG GAGCTTTTTGTAAAA
genomic: ATATGGATGGAAACGCAGAAGTTGAATGGACTCCATCTTCGATTTTTCAGgtaatttgga ... tattgtccagGAGCTTTTTGTAAAA
EST:
gi|193654058|gb|FK596472.1|FK596472EST: ATATGGATGGAAACGCAGAAGTTGAATGGACTCCATCTTCGATTTTTCAG GAGCTTTTTGTAAAA
genomic: ATATGGATGGAAACGCAGAAGTTGAATGGACTCCATCTTCGATTTTTCAGgtaatttgga ... tattgtccagGAGCTTTTTGTAAAA
EST:
gi|21888131|gb|BQ741344.1|BQ741344EST: ATATGGATGGAAACGCAGAAGTTGAATGGACTCCATCTTCGATTTTTCAG GAGCTTTTTGTAAAACTGAATCGAATGGCCAATATAGCAGCAGATATGTTT
genomic: ATATGGATGGAAACGCAGAAGTTGAATGGACTCCATCTTCGATTTTTCAGgtaatttgga ... tattgtccagGAGCTTTTTGTAAAACTGAATCGAATGGCCAATATAGCAGCAGATATGTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agttatgctacaaatatgattcaagatctgattaggccattatgttattgtccagGAGCTTTTTGTAAAACTGAATCGAATGGCCAATATAGCAGCAGATATGTTTGTAGGGAGGGAAAGATTTGCTACGCTGCTCTTGATGAGACTTACAGAAA
atctgat putative branch site (score: 4)
attatgttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttttgctgaaattaatataaattgtcatctaacttcactgttgagttatgctacaaatatgattcaagatctgattaggccattatgttattgtccagGAGCTTTTTGTAAAACTGAATCGAATGGCCAATATAGCAGCAGATATGTTTGTAGGGAGGGAAAGATTTGCTACGCTGCTCTTGATGAGACTTACAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - -tgctgaa
- - - - - - - - - - - - tgtcatc
- - - - - - - - - - - - - - - - - - - actgttg
- - - - - - - - - - - - - - - - - - - - - - - - - tgctaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggccatt