Sequence
atgc intronic sequence ATGC exonic sequence...tcttacagtcccatgtattttaattttcttatttgttaatgcgcatacaattgagtagggtcaatatattctaatatttctttccacatggttatgcaggGAAAGAAAGAATGCTTTGCCTCGTGTCTATTTGTTTGCTATGATTTGATCCGGGCAGACATTGCTCTTGAATTGGCCTGGATGAACAATATGATTGACTT
Basic information
species | Glycine max |
transcript | GLYMA18G02960.1 |
intron # | 26 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 26
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 27
---------tcttacagtcccatgtattttaattttcttatttgttaatgcgcatacaattgagtagggtcaatatattctaatatttctttccacatggttatgcaggGAAAGAAAGAATGCTTTGCCTCGTGTCTATTTGTTTGCTATGATTTGATCCGGGCAGACATTGCTCTTGAATTGGCCTGGATGAACAATATGATTGACTT
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caattgaagtgaaacaagcaagctcacctgattttttttattatttag---gcata-atctgtattgcattctgatgag-taacatctataattgtgtatt---gcagGGAAAGAAAGAATGCTTTGCTTCTTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACT-
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 26
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 27
--tcttacagtcccatgtattttaattttcttatttgttaatgcgcataca-attgagtagggtcaatatattctaatatttctttccacatggttatgcaggGAAAGAAAGAATGCTTTGCCTCGTGTCTATTTGTTTGCTATGATTTGATCCGGGCAGACATTGCTCTTGAATTGGCCTGGATGAACAATATGATTGACTT
| | | || | | | | | || ||| ||| | | || | | ||| | || | | | | ||| | || | ||||||||||||||||||||||||| || ||||| ||| |||| ||||| |||||||| || || |||||||||| | || ||||||||||| ||| | ||||
aattgaagtgaaacaagcaagctcacctgattttttattattatttaggcataatctgtattg-cattctgatgagtaacatctataattgtgtat-tgcagGGAAAGAAAGAATGCTTTGCTTCTTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACT-
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 26
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 27
------------tcttacagtccc---atgt--attttaattttcttatttgttaatgcgcatacaattgagtagggtcaatatattctaatatttctttccacatg--gttatgcaggGAAAGAAAGAATGCTTTGCCTCGTGTCTATTTGTTTGCTATGATTTGATCCGGGCAGACATTGCTCTTGAATTGGCCTGGATGAACAATATGATTGACTT
| ||| | | ||| | || | |||| | | | | | ||||| | | | || ||| | | | || ||||| ||||| || || ||||||||||| | ||||| ||||| || ||||| || ||||| ||||| | ||||| ||| | |||||||| ||||||||||| ||||
gtatgatgatggttaaacatttacgagatgctagtgctagccattcagtttggttagttgaaaagaattggtccagac--gttgaacgtagtatcccgtgtcttctgctgttatacagGGCAAAAAGGAATGCTTTGCTACATGTCTCTTTGTATGTTATGACTTAATCCGACCAGACGTGGCTCTAGAACTTGCCTGGATCAACAATATGATGGACT-
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 26
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 27
tcttacagtcccatgtattttaattttcttatttgttaatgcgcatacaattgagtagggtcaatatattctaat----atttctttccacatggttatgcaggGAAAGAAAGAATGCTTTGCCTCGTGTCTATTTGTTTGCTATGATTTGATCCGGGCAGACATTGCTCTTGAATTGGCCTGGATGAACAATATGATTGACTT
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-ttaatgtgggcatg-gttctaatat-ctttttgttgaatttctgtggtatggtgcttatttttattattttaagtctaatttatattgatgtacttttgcagGGAAAGAAAGAATGCTTTGCATCTTGCCTCTTTGTGTGCTACGACTTAATTCGTCCAGACATTGCTCTTGAACTTGCCTGGATTAACAATATGGTTGACT-Mapped 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|18712840|gb|BM522687.1|BM522687EST: TGGTGACCGTGAACTTGCTGAGGAGTTGCTTGTTTATTTCATTGATCAGG GAAAGAAAGAATGCTTTGCCTCGTGTCTATTTGTTTGCTATGATTTGATCC
genomic: TGGTGACCGTGAACTTGCTGAGGAGTTGCTTGTTTATTTCATTGATCAGGtgccaaattc ... gttatgcaggGAAAGAAAGAATGCTTTGCCTCGTGTCTATTTGTTTGCTATGATTTGATCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacaattgagtagggtcaatatattctaatatttctttccacatggttatgcaggGAAAGAAAGAATGCTTTGCCTCGTGTCTATTTGTTTGCTATGATTTGATCCGGGCAGACATTGCTCTTGAATTGGCCTGGATGAACAATATGATTGACTT
ttctaat putative branch site (score: 2)
tcaatatattctaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcttacagtcccatgtattttaattttcttatttgttaatgcgcatacaattgagtagggtcaatatattctaatatttctttccacatggttatgcaggGAAAGAAAGAATGCTTTGCCTCGTGTCTATTTGTTTGCTATGATTTGATCCGGGCAGACATTGCTCTTGAATTGGCCTGGATGAACAATATGATTGACTT
- - -cagtccc
- - - - - - - - - - - - - - - - - -ttaatgc
- - - - - - - - - - - - - - - - - - - - - gcataca