Sequence
atgc intronic sequence ATGC exonic sequencegttggttgagttgtctgcacatcattacagcacgcatgttcagacatgcatgtcgtcacaatagttgcacatcatgagggcatgatttctggtcatgcaggtgtagtaatgcatgtgaatctttcatactcttagctgaccctgagttgaggcttgctgtcgggctttctggtctgcagGGGCCTGCCCGGGAGAAGGAGAAACGGGAAAAGGAAAGGAGCGAGTTGCGCGATCTT
Basic information
species | Glycine max |
transcript | GLYMA11G08390.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G08390.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G17790.1 (Arabidopsis thaliana), 3'ss of exon 5
----------------gttggttg---agttgtctgcacatcattacagcacgcatgttcagacat--gcatgtcgtcacaatagttgcacatcatgagggcatgatttctggtcatgcaggtgtagtaatgcatgtgaatctttcatactcttagctgaccctgagttgaggcttgctgtcgggctttctggtctgcagGGGCCTGCCCGGGAGAAGGAGAAACGGGAAAAGGAAAGGAGCGAGTTGCGCGATCTT
| | ||| | ||| | ||| | | | || || | | ||| || | || | ||||| |||||||| ||| |||||||||||| ||| ||| |||||||| || || ||| | ||| |||||||||| |||| || |||||||||||||||||||||| ||||| || || ||||||| |||||| || || ||| ||||| | || || |||
gtgagttatgatttaagattgttatacacccttctactcattttggaaacgagcttgccagaatgtttgcacttcatggagatttaattggactatgagagcatgatt-ctgatcatgcaggtgttgtattgcttgtgaatcatt---accctttgatgatcctgagttgaagcttcctatcgggctttctggtctgcagGGACCTGCTCGAGAAAAGGAGAGACGGGAGAAAGAGAGGGGCGAGCTTCGTGACCTT
upper sequence: GLYMA11G08390.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv04s0023g03870.t01 (Vitis vinifera), 3'ss of exon 5
gttggttgagttgtctgcacatcattacagcacgcatgttcagacatgcatgtcgtcacaatagttgcacatcatgagggcatgatttctggtcatgcaggtgtagtaatgca--tgtgaatctttcatactcttagctgaccctgagttgaggcttgctgtcgggctttctggtctgcagGGGCCTGCCCGGGAGAAGGAGAAACGGGAAAAGGAAAGGAGCGAGTTGCGCGATCTT
||||||| ||||||||||||||| || ||| |||||||| ||||||||||||||||| ||||||||||||||||| |||| ||||||||||||||||| ||||| ||||| ||||||||||||||||| ||| |||||||| | || |||||
---------------------------------------------------------------------------------atgatttgtggtcatgcaggtgttatagtgctcttgtgaatcattcatactcttagctgatcctgagttgaggcttgcaatcggcctttctggtctgcagGGACCTGCACGGGAAAAGGAGAAACGGGAAAAAGAACGGAGCGAGCTTCGTGATCTC
upper sequence: GLYMA11G08390.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S456_14V6.1 (Physcomitrella patens), 3'ss of exon 5
gttggttgagttgtctgcacatcattacagcacgcatgttcagacatgcatgtcgtcacaatagttgcacatcatgagggcatgatttctggtcatgcaggtgtag-taatgcatgtgaatctttcatactcttagctgaccctgagttgaggcttgctgtcgggctttctggtctgcagGGGCCTGCCCGGGAGAAGGAGAAACGGGAAAAGGAAAGGAGCGAGTTGCGCGATCTT
| | ||| | || ||| ||| | || | | | | |||||| | || || ||| | | | | | | | || ||| || | | || || ||| | | | | | |||| | |||| ||||| |||||||||||||| |||||||||||| | || || | || ||| |
--------------------gtaagcaca--attgatactca--tatgtacgttgcgatga-gataaaacatcactatt-cagtatgcttggactcgttgcagaaaattctagttgggaacgttctccaattttttcttacctcgcttcctaatgggattgcattctttgtcccaccaagGGTCCTGCTCGGGAGAAGGAGAAGCGGGAAAAGGAACGAAGTGAACTTCGTGATTTG
upper sequence: GLYMA11G08390.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S313_104V6.1 (Physcomitrella patens), 3'ss of exon 5
gttggttgagttgtctgcacatcattacagcacgcatgttcagacatgcatgtcgtcacaatagttgcacatcatgagggcatgatttctggtcatgcaggtgtagtaatgcatgtgaatctttcatactcttagctgaccctga-gttgaggcttgctgtcgggctttctggtctgcagGGGCCTGCCCGGGAGAAGGAGAAACGGGAAAAGGAAAGGAGCGAGTTGCGCGATCTT
| || ||| || || || | || | || | || | | || || | | || | ||| | | | || || || | ||||| ||||| ||||||||||||||||| ||||||||| ||||||||||||| || |
----------------------------------------------------------------------gtttggaaagcagcatcg------gtgtagagttcgtca---atcgagacgttgtggattatttgcgcatgccgaagctgacgttggttgatcatattgatg-taaacagGGCCCTGCTCGGGAGAAGGAGAAACGAGAAAAGGAACGGAGCGAGTTGCGTGACTTGMapped 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|254342605|gb|GR858767.1|GR858767EST: TCCAAAATTTCACTGAAATGAACAAACTTTGGGTGCGAATGCAACATCAG GGGCCTGCCCGGGAGAAGGAGAAACGGGAAAAGGAAAGGAGCGAGTTGCGC
genomic: TCCAAAATTTCACTGAAATGAACAAACTTTGGGTGCGAATGCAACATCAGgttggttgag ... tggtctgcagGGGCCTGCCCGGGAGAAGGAGAAACGGGAAAAGGAAAGGAGCGAGTTGCGC
EST:
gi|120531471|gb|EH259604.1|EH259604EST: TCCAAAATTTCACTGAAATGAACAAACTTTGGGTGCGAATGCAACATCAG GGGCCTGCCCGGGAGAAGGAGAAACGGGAAAAGGAAAGGAGCGAGTTGCGC
genomic: TCCAAAATTTCACTGAAATGAACAAACTTTGGGTGCGAATGCAACATCAGgttggttgag ... tggtctgcagGGGCCTGCCCGGGAGAAGGAGAAACGGGAAAAGGAAAGGAGCGAGTTGCGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catactcttagctgaccctgagttgaggcttgctgtcgggctttctggtctgcagGGGCCTGCCCGGGAGAAGGAGAAACGGGAAAAGGAAAGGAGCGAGTTGCGCGATCTT
agctgac putative branch site (score: 3)
ctttct putative PPT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttggttgagttgtctgcacatcattacagcacgcatgttcagacatgcatgtcgtcacaatagttgcacatcatgagggcatgatttctggtcatgcaggtgtagtaatgcatgtgaatctttcatactcttagctgaccctgagttgaggcttgctgtcgggctttctggtctgcagGGGCCTGCCCGGGAGAAGGAGAAACGGGAAAAGGAAAGGAGCGAGTTGCGCGATCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG