Sequence
atgc intronic sequence ATGC exonic sequence...ttaaaatatcaagggtttgatgtgtgttgatttgccaaatggcttgaattaaaatataaagggtctgtctgatttgtgtactttggtttatggtttgtagATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCCGGAAAGATGAGATCATGAAAGCTATTGGGAAGAAGTTGGACCGCTACAG
Basic information
species | Glycine max |
transcript | GLYMA17G02640.1 |
intron # | 21 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 21
lower sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 21
-----------------------------------------------------ttaaaatatcaagggtttgatgtgtgttgatttgccaaatggcttgaattaaaatataaagggt-ctgtctgatttgtgtactttggtttatggtttgtagATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCCGGAAAGATGAGATCATGAAAGCTATTGGGAAGAAGTTGGACCGCTACAG
|||| ||| | | | | || || ||||| ||| || | | | ||| | || ||||| | | || | | |||||||||||||||||| || || |||||||| || ||||| || ||||| ||||| ||||| || |||| ||| || ||||||||||| |||||||| |
gtaagcaagtgtttcaattgagtatacatgattaataaattgttaattagtacataaatcttcaccaaacagctaatttcttatgtggtgaatgg--tgagttgagaactgaagattattggctgatcattattattgactgtccaacc---agATTATGATAGAATTATCAAGAATATTGAAAGGGGAGAGGCCAGGATATCACGGAAGGATGAAATTATGAGAGCCATCGGGAAGAAGTTAGACCGCTATAA
upper sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 21
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 21
----------------------------------------------------------------------------ttaaaatatcaagggtttgatgtgtgttgatttgccaaatggcttgaattaaaatataaagggtctgtctgatttgtgtactttggtttatggtttgtagATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCCGGAAAGATGAGATCATGAAAGCTATTGGGAAGAAGTTGGACCGCTACAG
|||| | | | | | || | | ||| | | | ||| | ||| | ||||| | | || || | | ||||||||| || ||||||| |||||||| | ||| || ||||| |||| |||||| |||||||| ||||||||||||||||| ||| | |||||||| |
gtatattttgtaaccttttctcttactgtttgtattccctactgatgacctatttaatgtgtagctgactttgttattaacttgtaaccaagtaatggattgcttacatgctgagctgagt-aatggtcagatacaaaatctgttttgactaaatatgatgtcctcatcctatcagATTATGACCGAGTTATTAAGAACATTGAGAAAGGAGAAGCAAGGATATACCGGAAGGATGAGATTATGAAAGCTATTGGGAAAAAGCTAGACCGCTATAA
upper sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 21
lower sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 21
--ttaaaatatcaa---gggtttgatgtgtgttgatttgccaaatggcttgaattaaaatataaagggtctgtctgatttgtgtactttggtttatggtttg-tagATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCCGGAAAGATGAGATCATGAAAGCTATTGGGAAGAAGTTGGACCGCTACAG
||| || | || ||| || ||||| | || || ||| | | | ||| | ||||| ||| |||| | || | ||||||||||||||||||| ||||| |||||||| ||||| |||||||||||||| || |||||||| ||||| ||||||||||||||||| ||||||||||
ttataacattttaattaaaagcaactgtttgcaattttgcatactga---agatcaaacttttcata--ctgacagattt-tgtgttttgatcattgttcaactagATTATGATAGAATTATAAAAAATATTGAAAGGGGGGAAGCAAGAATATCCCGCAAGGATGAGATTATGAAGGCTATTGGGAAGAAGTTAGACCGCTACAA
upper sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 21
lower sequence: GRMZM2G010085_T02 (Zea mays), 3'ss of exon 13
-ttaaaatatcaagggtttgatgtgtgttgatttgccaaatggcttgaattaaaatataaagggtctgtctgatt-tgtgtactttggtttatg-gtttgtagATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCCGGAAAGATGAGATCATGAAAGCTATTGGGAAGAAGTTGGACCGCTACAG
| |||| ||| || | | | || || ||| | | | ||| |||| ||| | |||| | || |||||||||||||||||| ||||| |||||||| ||||| ||||| |||||||| || |||||||| ||||| ||||||||||||||| | ||||||||||
accattatattttttttttaataaaagc-aactgtttgcatactgaagatcaaactttccata--ctgatggattgtgtatgttttgatcattgtacaaccagATTATGATAGAATTATAAAAAATATTGAAAGGGGGGAAGCAAGGATATCCCGCAAGGATGAGATTATGAAGGCTATTGGGAAGAAGCTAGACCGCTACAA
upper sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 21
lower sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 21
----------ttaaaatatcaag--ggtttgatgtgtgttgatt-tgccaaatggcttgaattaaaatataaagggtctgtctgatttgtgtactttggtttatggtttgtagATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCCGGAAAGATGAGATCATGAAAGCTATTGGGAAGAAGTTGGACCGCTACAG
||| | | | ||| || ||| ||||| ||| | | | | || | | ||| || ||| | ||| | | || |||||||||| || ||||| || || || ||||| |||||||| |||||||| || |||||||||| ||||||||||||||||||||||| |||| ||||||||
gttagtaactttagattgttaagtaaagttaatgagtgtttgcagtgcgacaaagttggatatttatcctaagtaagct--ctgcctcttgttttcctttgtaaaaattgtagATTACGACAGAATCATCAAGAATATTGAGAGAGGGGAAGCAAGAATCTCTAGGAAAGATGAAATCATGAAAGCTATTGGGAAGAAACTGGATCGCTACAG
upper sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 21
lower sequence: AT3G06400.3 (Arabidopsis thaliana), 3'ss of exon 21
------------ttaaaatatcaagg-gtttgatgtgtgttgat-ttgccaaatggcttgaattaaaatataaagggtctgtctgatttgtgta----ctttggtttatggtttgtagATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCCGGAAAGATGAGATCATGAAAGCTATTGGGAAGAAGTTGGACCGCTACAG
|| ||| ||| | ||| | | || || | || | | | | | | || | || | || || |||| | | |||||| ||||||||||| ||||| |||||||| || || |||||||| || || ||||||| || |||||||| || || |||||||| |||| ||||||||
gtaagtaacacctttcaatgctaagttatgcagtgtttttacatgtttctaagtaattcctacctccaaaaagagcttatgctaagtaagtttatcatctttccctctaaatatgtagACTATGATAGAATCATTAAGAACATTGAGAGGGGAGAGGCAAGGATCTCTAGGAAAGACGAAATCATGAAGGCCATAGGGAAGAAACTGGATCGCTACAG
upper sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 21
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 21
--ttaaaatatcaagggtttgatgtgtgttg-atttgccaaatggcttgaattaaaata-taaagggtctgtctgatttgtgtactttggtttatggtttgtagATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCCGGAAAGATGAGATCATGAAAGCTATTGGGAAGAAGTTGGACCGCTACAG
|| | |||| || |||| | || | ||| || || || ||||| | | | ||||| ||| || | | | | |||||||||||| || || || |||||||||||||| ||||| ||||| || |||||||||||||||||||||| ||||||||||||||||| |||||||
ggttgatatatt----gtcagatgcatcttacaacatccatttgtttttcatcaaaatggtgattttttcgtctgcttttaaccattaaatacaatttctccagATTATGATAGGATCATCAAGAACATTGAAAGAGGAGAGGCTAGAATTTCTAGGAAAGATGAGATCATGAAAGCAATTGGGAAGAAGTTGGATCGCTACAA
upper sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 21
lower sequence: EFJ31365 (Selaginella moellendorffii), 3'ss of exon 21
ttaaaatatcaagggtttgatgtgtgttgatttgccaaatggcttgaattaaaatataaagggtctgtctgatttgtgtactttggtttatggtttgtagATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCCGGAAAGATGAGATCATGAAAGCTATTGGGAAGAAGTTGGACCGCTACAG
| | || | | ||| | | | ||| | ||| | | || | |||| || || |||||| | | ||||||| | |||||||| | || | | |||||||| ||||||| | |||||||||||||| ||||||| ||||
-----------------------------------------gtaagcttttccttgtcaagaaac-atattgtttaagctgttttgctgctgtaatttagACTACGACAGAATTTTGCGAGCCATTGAACGCGGGGAGGCTCGCATCGCAAGAAAAGATGAAATCATGAGAACTATTGGGAAGAAGCTGGACCGATACAA
upper sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 21
lower sequence: EFJ06565 (Selaginella moellendorffii), 3'ss of exon 21
ttaaaatatcaagggtttgatgtgtgttgatttgccaaatggcttgaattaaaatataaagggtctgtctgatttgtgtactttggtttatggtttgtagATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCCGGAAAGATGAGATCATGAAAGCTATTGGGAAGAAGTTGGACCGCTACAG
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-----------------------------------------gtaagcttttccttgtcaagaaac-atattgtttaagctgttctgctactgtaatttagACTACGACAGAATTTTGCGAGCCATTGAACGCGGGGAGGCTCGCATCGCAAGAAAAGATGAAATCATGAGAACTATTGGGAAGAAGCTGGACCGATACAAMapped 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|23734541|gb|BU765507.1|BU765507EST: GAAAGATACAAGGAATTAAATG ATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCC
genomic: GAAAGATACAAGGAATTAAATGgtaagttaca ... tggtttgtagATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCC
EST:
gi|193367197|gb|FK330315.1|FK330315EST: CTTCAAAGAAAGATACAAGGAATTAAATG ATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCC
genomic: CTTCAAAGAAAGATACAAGGAATTAAATGgtaagttaca ... tggtttgtagATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCC
EST:
gi|208083528|gb|GD883996.1|GD883996EST: AGTTGAAAGATATGCAAAAGTCTTCAAAGAAAGATACAAGGAATTAAANG ATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCC
genomic: AGTTGAAAGATATGCAAAAGTCTTCAAAGAAAGATACAAGGAATTAAATGgtaagttaca ... tggtttgtagATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaattaaaatataaagggtctgtctgatttgtgtactttggtttatggtttgtagATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCCGGAAAGATGAGATCATGAAAGCTATTGGGAAGAAGTTGGACCGCTACAG
gtctgat putative branch site (score: 4)
aaaatataaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttaaaatatcaagggtttgatgtgtgttgatttgccaaatggcttgaattaaaatataaagggtctgtctgatttgtgtactttggtttatggtttgtagATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCCGGAAAGATGAGATCATGAAAGCTATTGGGAAGAAGTTGGACCGCTACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - gggtttg
- - - - - - - - - - tgtgtgt
- - - - - - - - - - - - - - - - tgccaaa
- - - - - - - - - - - - - - - - - - - -tggcttg
- - - - - - - - - - - - - - - - - - - - - - - - - -aaatataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgtac