Sequence
atgc intronic sequence ATGC exonic sequence...ttgggactgacttcataatttgattttaagtctgtatgttacctttaactctaaaagtctaatggtgatgaaatgatttatgattgagtttctattccagGCCCTGTTATGACCAAATTCACCATAGCCTTAAGAGAAATTGGGACATATAAGGAAGTCCTTCGATCACAG
Basic information
species | Glycine max |
transcript | GLYMA18G51810.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G51810.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os08g42530.1 (Oryza sativa), 3'ss of exon 3
ttgggactgacttcataatt--tgattttaagtctgtatgttacctttaactctaa-aagtctaatggtgatgaaatgatttatgattgagtttctattccagGCCCTGTTATGACCAAATTCACCATAGCCTTAAGAGAAATTGGGACATATAAGGAAGTCCTTCGATCACAG
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---cttttcatcccttaattactgttttcattttactagaactgtcttgtctttagtatggtcatttcctctaatatgcatactgaacatttctcctctccagGACCTGTTATGACCAAATTTACAATTGCCTTGAGAGAACTAGGCACATACAAGGAAGTCCTCCGCTCCCAG
upper sequence: GLYMA18G51810.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G872204_T02 (Zea mays), 3'ss of exon 3
----ttgggactgacttcataatttgattttaagtctgtatgttacctttaactctaaaagtctaatggtgatgaaatgatttatgattgagtttctattccagGCCCTGTTATGACCAAATTCACCATAGCCTTAAGAGAAATTGGGACATATAAGGAAGTCCTTCGATCACAG
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tttctcattatttattactctttccccacataagagtaga-gttgagctcaatgtcgtcagttcctc--tactgagcatactgaattttcatcttct-ttccagGGCCTGTAATGACCAAATTTACAATTGCCTTAAGAGAAATTGGAACATACAAGGAAGTCCTGCGCTCCCAG
upper sequence: GLYMA18G51810.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G059225_T02 (Zea mays), 3'ss of exon 3
-----------------------------------------------ttgggactgacttcataatttgattttaagtctgtatgtt---acctttaactctaaaagtctaatggtgatgaaatgatttatgat-tgagtttctattccagGCCCTGTTATGACCAAATTCACCATAGCCTTAAGAGAAATTGGGACATATAAGGAAGTCCTTCGATCACAG
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gttagtaatgtggttctcgtgaaaatacatgtattcgaaacttcaatttgtgacaagcatgataactctttctcctgttttcatgttttgcccttttgctttcctgattggttggttctcttgtacatgacaacatttaccttttttgcagGGCCTGTCATGACCAAATTTACAATTGCTTTAAGAGAAATTGGAACATACAAGGAAGTATTGCGCTCCCAG
upper sequence: GLYMA18G51810.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv01s0150g00030.t01 (Vitis vinifera), 3'ss of exon 3
ttgggactg---acttcataatttgattttaagtctgtatgttacctttaactctaaaagtctaatggtgatgaaatgatttatgattgagtttctattccagGCCCTGTTATGACCAAATTCACCATAGCCTTAAGAGAAATTGGGACATATAAGGAAGTCCTTCGATCACAG
| |||| | | ||| || || | || || | || | || | || ||| || |||| | | | || | | ||||||||||||||||||||||||| || || || ||||| ||||||||||| |||||||| ||||| || |||
-tttaactggaaattgcatgatatggtactagctcctagaaggcctgttcataagtgaaatttactggcattgt--tgatgaaatctctatttgtttcttcagGCCCTGTTATGACCAAATTCACTATTGCATTGAGAGAGATTGGGACATACAAGGAAGTTCTTCGCTCCCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taactctaaaagtctaatggtgatgaaatgatttatgattgagtttctattccagGCCCTGTTATGACCAAATTCACCATAGCCTTAAGAGAAATTGGGACATATAAGGAAGTCCTTCGATCACAG
gtctaat putative branch site (score: 3)
tttctattcc putative PPT
aaatgatttatgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgggactgacttcataatttgattttaagtctgtatgttacctttaactctaaaagtctaatggtgatgaaatgatttatgattgagtttctattccagGCCCTGTTATGACCAAATTCACCATAGCCTTAAGAGAAATTGGGACATATAAGGAAGTCCTTCGATCACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - ctgactt
- - - - - - - - - - - - - - - - tgtatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtgatg