Sequence
atgc intronic sequence ATGC exonic sequencegtttgtgggtcaggcataggcattgcaattacttaagtcactgtttatatattttgcgtgtataacattttctttttgggttaaatcagAGATTTAAAAGAACACTTAAGGAGGTTGCAGCAACAGTCTGATTCAAGACGAAGAGCTGCTGTAATGGAGATGATGAGGCAGAGAGCTGCAGAAGTTGCC
Basic information
species | Glycine max |
transcript | GLYMA15G00250.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G00250.1 (Glycine max), 3'ss of exon 16
lower sequence: LOC_Os02g04490.1 (Oryza sativa), 3'ss of exon 16
gtttgtgggtcaggcataggcattgcaattac-ttaagtcactgtttatatattttgcgtgtataacattttctttttggg---ttaaat------cagAGATTTAAAAGAACACTTAAGGAGGTTGCAGCAACAGTCTGATTCAAGACGAAGAGCTGCTGTAATGGAGATGATGAGGCAGAGAGCTGCAGAAGTTGCC
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----gtgtgttggtgcttctcacttttgttccgtcaccttgccttgtgcttgatctggaataacaccctgaccacttacggaaactatacactatgcagGGATCTCAAGGAGCATCTTCGAAGGTTGCAACAGCAATCTGATTCTAGGAGGAGGGCTGCTGTAAATGAAATGATGAGACAGAGAGCAGCAGAAGTTGCT
upper sequence: GLYMA15G00250.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM2G470556_T01 (Zea mays), 3'ss of exon 15
----------------gtttgtgggtcaggcataggcattgcaattactta--agtcactgtttatatattttgcgtg-tataacatt-ttctttttgggttaaat------cagAGATTTAAAAGAACACTTAAGGAGGTTGCAGCAACAGTCTGATTCAAGACGAAGAGCTGCTGTAATGGAGATGATGAGGCAGAGAGCTGCAGAAGTTGCC
| ||| | | | | ||| | ||| ||| | | | | | |||| | | | || | |||| ||| ||| | || || || | || ||||||||||| ||||||||||| | | || |||||||| | |||||||||||||||||||| || ||||| |||
gtttgtccacgccctccatcccatctcatcctcttgtgtctctgcggtttactactcagtgtagcattgccatctgcgatgtaacctgatcccgcctgtggtaaactatgcacagGGATCTGAAGGAGCATCTCAGAAGGTTGCAGCAGCAGTCTGATTCCCGGAGGAGGGCTGCTGTGAATGAGATGATGAGGCAGAGAGCGGCGGAAGTGGCC
upper sequence: GLYMA15G00250.1 (Glycine max), 3'ss of exon 16
lower sequence: AT1G79000.2 (Arabidopsis thaliana), 3'ss of exon 17
-------------------gtttgtgggtcaggcat---aggcattgcaattacttaagtcact-gtttatatattttgcgtgtataacattttctttttgggttaaatcagAGATTTAAAAGAACACTTAAGGAGGTTGCAGCAACAGTCTGATTCAAGACGAAGAGCTGCTGTAATGGAGATGATGAGGCAGAGAGCTGCAGAAGTTGCC
| | | ||| || | | | || || || | | || | | || | | | ||| | | | |||| || |||| || || | || || || ||||| || || |||||| | || ||||| ||||||||||| |||||||| || |||||||||||||| ||
gtaaacaaacctcatgaaattacatcaaccttacatttaagacgtgaaacatatttggtccatttgattttgtgttgatgatcattgtgaacatctctgtctctctgttcagGGACCTAAAGGAGCATCTGAGAAGATTACAGCAGCAATCAGATTCACGGCGCAGAGCAGCTGTAATGGAAATGATGAGACAAAGAGCTGCAGAAGTCGCT
upper sequence: GLYMA15G00250.1 (Glycine max), 3'ss of exon 16
lower sequence: AT3G12980.1 (Arabidopsis thaliana), 3'ss of exon 16
gtttgtgggtcaggcat-----aggca---ttgcaattacttaagtca--ctgtttatatattttgcgtgtataacattttctttttgggttaaat-----cagAGATTTAAAAGAACACTTAAGGAGGTTGCAGCAACAGTCTGATTCAAGACGAAGAGCTGCTGTAATGGAGATGATGAGGCAGAGAGCTGCAGAAGTTGCC
|| ||| | | | ||| || |||||| | | |||| | | | |||| ||| | | | ||| | | |||||| || | || || || || || |||||||||| | ||||||||||| ||||| || || ||||||||| || |||||||||| || || |
gtatgtaatctaactacttataaagcaaattttcaattatcagaatagatttgttcaagaaggtgatgtgtttaataatgatctgacaagtttattttttgcagAGAGTTGAGAGCTCATTTTAGTAGAAAGCAGCAACAGGCAGATTCAAGACGCAGAGCAGCGGTGATGGAGATGGTGCGGCAGAGAGCCGCTGATACAACG
upper sequence: GLYMA15G00250.1 (Glycine max), 3'ss of exon 16
lower sequence: AT1G16710.1 (Arabidopsis thaliana), 3'ss of exon 16
-------------gtttgtgggtcaggcata-ggcattgcaattacttaagtcactgtttatatattttgcgtgtataacattttctttttgggttaaatcagAGATTTAAAAGAACACTTAAGGAGGTTGCAGCAACAGTCTGATTCAAGACGAAGAGCTGCTGTAATGGAGATGATGAGGCAGAGAGCTGCAGAAGTTGCC
| ||| |||| |||| || || || | || || |||| | || | | | || | || |||| || |||| ||||| | || ||||| || || || || ||||| || || |||||||| || |||||||||||||| ||||||||||||||||| ||
tttggatatattagaaccggggcataacatatggcaaagcttttttgaaaaaaatggtccgcatgatttgtattgatcattgtaaatcttc---tcaattcagGGACCTAAAGGAACATCTGAGAAGGTTACAACAGCAATCAGATTCTAGGCGGAGAGCTGCCGTCATGGAGATGATGAGACAGAGAGCTGCAGAAGTCGCT
upper sequence: GLYMA15G00250.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv09s0054g01780.t01 (Vitis vinifera), 3'ss of exon 15
gtttgtgg--gtcaggc-ataggcattgcaattacttaagtcactgtttatatattttgcgtgtataacattttcttt--ttgggttaaatcagAGATTTAAAAGAACACTTAAGGAGGTTGCAGCAACAGTCTGATTCAAGACGAAGAGCTGCTGTAATGGAGATGATGAGGCAGAGAGCTGCAGAAGTTGCC
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gtttgtagttgtcaacttgtggtcaatgccat--cttaaat-attgtctatgaatatcacatataaatcttatactttatcttaactcattcagAGATCTGAAGGAGCATTTGAGGAGGCTGCAGCAGCAGTCTGATTCTAGGCGAAGAGCTGCTGTGATGGAGATGATGAGACAGAGAGCTGCAGAGGTTGCTMapped 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|31473368|gb|CD415381.1|CD415381EST: CTCCATGCTCGTGCTTGCAAGGAATCTGAATGCCATGTACCACGTTGCAG AGATTTAAAAGAACACTTAAGGAGGTTGCAGCAACAGTCTGATTCAAGACG
genomic: CTCCATGCTCGTGCTTGCAAGGAATCTGAATGCCATGTACCACGTTGCAGgtttgtgggt ... gttaaatcagAGATTTAAAAGAACACTTAAGGAGGTTGCAGCAACAGTCTGATTCAAGACG
EST:
gi|6069353|gb|AW099041.1|AW099041EST: CTCCATGCTCGTGCTTGCAAGGAATCTGAATGCCATGTACCACGTTGCAG AGATTTAAAAGAACACTTAAGGAGGTTGCAGCAACAGTCTGATTCAAGACG
genomic: CTCCATGCTCGTGCTTGCAAGGAATCTGAATGCCATGTACCACGTTGCAGgtttgtgggt ... gttaaatcagAGATTTAAAAGAACACTTAAGGAGGTTGCAGCAACAGTCTGATTCAAGACG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagtcactgtttatatattttgcgtgtataacattttctttttgggttaaatcagAGATTTAAAAGAACACTTAAGGAGGTTGCAGCAACAGTCTGATTCAAGACGAAGAGCTGCTGTAATGGAGATGATGAGGCAGAGAGCTGCAGAAGTTGCC
gtataac putative branch site (score: 3)
tataacattttctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtgggtcaggcataggcattgcaattacttaagtcactgtttatatattttgcgtgtataacattttctttttgggttaaatcagAGATTTAAAAGAACACTTAAGGAGGTTGCAGCAACAGTCTGATTCAAGACGAAGAGCTGCTGTAATGGAGATGATGAGGCAGAGAGCTGCAGAAGTTGCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT