Sequence
atgc intronic sequence ATGC exonic sequence...gtcaaggtcagaaatttggcctcttctcacacatctatttcatgttagattttgtgtctttttaatttatttattttttggtgatgggggttctctgcagGCACCGATGGACAGGAAGATATGAAGCGCATCTATGGGACAATAGTTGCAGAAGGGAGGGTCAAGCTAGAAAAGGGCGTCAAG
Basic information
| species | Glycine max |
| transcript | GLYMA09G33240.1 |
| intron # | 3 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G33240.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G10510.3 (Arabidopsis thaliana), 3'ss of exon 2
------------------------------------------------------------------gtcaaggtcagaaatttggcctcttc--tcacacatctatttca-tgttagattttgtgtctttttaatt-tatttattttttggtgatgggggttctctgcagGCACCGATGGACAGGAAGATATGAAGCGCATCTATGGGACAATAGTTGCAGAAGGGAGGGTCAAGCTAGAAAAGGGCGTCAAG
| || | | || | |||| | | ||||| | | || | |||||| | || ||| | || |||| | | || | | || || || ||||||| |||||||||||||| ||||||||||| ||||| || || || || ||||| || || || || |||||||
gtaagtatataattaagaatccaataagttgtgattaggaattaattaagtactgttttgtgatttgccattgactaaaggtcaaagacttcaatactattactattgaagttttggtttttgttttgttctaagtgtaagtattaat-gtaaatatttgattgatgtagACATAGATGGACGGGAAGATATGAAGCACATCTATGGGATAATAGCTGTAGGAGAGAAGGTCAGGCCAGGAAGGGACGTCAAG
upper sequence: GLYMA09G33240.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G65510.1 (Arabidopsis thaliana), 3'ss of exon 2
gtcaaggtcagaaatttggcctcttctcacacatctatttcatgttagattttgtgtcttttta-atttatttattttttggtgatgggggttctctgcagGCACCGATGGACAGGAAGATATGAAGCGCATCTATGGGACAATAGTTGCAGAAGGGAGGGTCAAGCTAGAAAAGGGCGTCAAG
|| | | |||||| | | | |||| | || ||||| |||| | || || | || | || | | | ||||| || ||||||| |||||||| ||||||||||||||||| || || || || ||||| |||||||| |||||||| |||||||
-caaacttttgttttttggctgtgggtgggaaaaagatttgacatttgatttaagcaattttgatatgagttcaattatatgtatgtgttgattgatgcagACATAGATGGACTGGAAGATACGAAGCGCATCTATGGGATAACAGCTGTAGGAGGGAAGGTCAAGCCAGAAAAGGACGTCAAG
upper sequence: GLYMA09G33240.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv00s1291g00010.t01 (Vitis vinifera), 3'ss of exon 2
-gtcaaggtcagaaatttggcctcttctcacacatctatttcatgttagattttgtgtctttttaatttatttattttttggtgatgggggttctctgcagGCACCGATGGACAGGAAGATATGAAGCGCATCTATGGGACAATAGTTGCAGAAGGGAGGGTCAAGCTAGAAAAGGGCGTCAAG
|| | ||| | || | | |||| ||||| | || | | ||| ||| | | | || ||||| ||| | ||||| || ||||||||||||||||| ||||| || || ||||||||||||| || || || || ||||||||||
taacagcattcactgtttcaagtgtttgggttc-ctgggaacttgttcatcagtgtgtatagggaacaaactagtttattgctttctgtattgctttgcagACACAGGTGGACGGGTAGATATGAAGCGCATCTGTGGGATAACAGCAGCAGAAGGGAGGGCCAGGCCAGGAAGGGGCGTCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagattttgtgtctttttaatttatttattttttggtgatgggggttctctgcagGCACCGATGGACAGGAAGATATGAAGCGCATCTATGGGACAATAGTTGCAGAAGGGAGGGTCAAGCTAGAAAAGGGCGTCAAG
ttttaat putative branch site (score: 3)
ttctctgc putative PPT
tttgtgtctttttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcaaggtcagaaatttggcctcttctcacacatctatttcatgttagattttgtgtctttttaatttatttattttttggtgatgggggttctctgcagGCACCGATGGACAGGAAGATATGAAGCGCATCTATGGGACAATAGTTGCAGAAGGGAGGGTCAAGCTAGAAAAGGGCGTCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - -cctcttc
- - - - - - - - - - - - - -cacacat
- - - - - - - - - - - - - - - - - - - -tcatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtgatg
