Sequence
atgc intronic sequence ATGC exonic sequence...tgtgttgagcacattgatgctgtattttttattagatggaaatttgcatgtctattattaatagattcttattagctctccttttttttccctcttcaagATAATGGAAAAGTCTTCTGCTGGGGATGGAACAAGTATGGACAG
Basic information
species | Glycine max |
transcript | GLYMA11G34470.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G34470.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os01g62810.1 (Oryza sativa), 3'ss of exon 9
----tgtgttgagcacattgatgctgtattttttatta--gatggaaatttgcatgtctattattaatagattcttattagctctccttttttttccctcttcaagATAATGGAAAAGTCTTCTGCTGGGGATGGAACAAGTATGGACAG
||| | | ||| | | ||| | | |||| | | || | ||| | | || | | | | | ||| |||| | || | |||||||||||||||||||||||||| ||||||
gttaatctttggcctccctgacaatttgtttaaacatgcccgtagaaagtgctgttcctggt-ctaacatctactgacaaaatgtggtgacatttatgc-----agATGAAGGCGAGGTCTTCTGCTGGGGATGGAACAAGTACGGACAG
upper sequence: GLYMA11G34470.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G337819_T01 (Zea mays), 3'ss of exon 9
tgtgttgagcacattgatgctgtattttttattagatggaaatttgc-atgtctattattaatagattcttattagctctccttttttttcc--ctcttcaagATAATGGAAAAGTCTTCTGCTGGGGATGGAACAAGTATGGACAG
|| | | | | ||| ||| | | | || | || | || | ||||| |||| || || | || | || | || || |||| | || | || |||||||||||||||||||||||||| |||
-aggtggtggaaaaaaatg-tgtccatagaaatggaaaggggttaactatctatattaccaataagttttt-ccatctgacaagggttacacaactattgcagATGAAGGTGAGGTATTCTGCTGGGGATGGAACAAGTATGGCCAG
upper sequence: GLYMA11G34470.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G337819_T02 (Zea mays), 3'ss of exon 9
tgtgttgagcacattgatgctgtattttttattagatggaaatttgc-atgtctattattaatagattcttattagctctccttttttttcc--ctcttcaagATAATGGAAAAGTCTTCTGCTGGGGATGGAACAAGTATGGACAG--------------------------------------------------------
|| | | | | ||| ||| | | | || | || | || | ||||| |||| || || | || | || | || || |||| | || | || |||||||||||||||||||||||||| |||
-aggtggtggaaaaaaatg-tgtccatagaaatggaaaggggttaactatctatattaccaataagttttt-ccatctgacaagggttacacaactattgcagATGAAGGTGAGGTATTCTGCTGGGGATGGAACAAGTATGGCCAGGTGGGTGCCCCTTAACATACCTTTTGCATAAACATATTGGATTGTAAAATTAGCTG
upper sequence: GLYMA11G34470.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv13s0019g02280.t01 (Vitis vinifera), 3'ss of exon 9
tgtgttgagcacattgatgctgtattttttattagatggaaatttgcatgtctattattaatagattcttattagctctc-----cttttttttccctcttcaagATAATGGAAAAGTCTTCTGCTGGGGATGGAACAAGTATGGACAG
| || ||||| | |||| | | || | | || ||||||| | | | || ||| | || | | || || |||||||| | |||| ||||||||||||||||||||| |||
----tcatattcactgatgtttagaattttgatgtctagat-tctagatacagattattactgaagtaccatgttttcttgacgtttgcttctgttttgttacagCCGATGGAAAAATGTTCTCCTGGGGATGGAACAAGTATGGTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcatgtctattattaatagattcttattagctctccttttttttccctcttcaagATAATGGAAAAGTCTTCTGCTGGGGATGGAACAAGTATGGACAG
tattaat putative branch site (score: 2)
ttcttattagctctcc putative PPT
tctattattaatagat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtgttgagcacattgatgctgtattttttattagatggaaatttgcatgtctattattaatagattcttattagctctccttttttttccctcttcaagATAATGGAAAAGTCTTCTGCTGGGGATGGAACAAGTATGGACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- tgttgag
- - - - - - - tgatgct
- - - - - - - - - - - - - - - - - - - - - - -gcatgtc