Sequence
atgc intronic sequence ATGC exonic sequence...gcttttgtatgttgtctgtttgcaattttctagttgatttgctaatataagcttacatgctgtttactgcaaatgcataattgtaatttttatgtggcagGTTATACTGATCCTGCAAAGCCTGATCTCCCTCGAATGCATGAGTGGCATTTCAGATCTGGGCTTGATCGCTACATCTGGATAATTGGAATGATTTATGC
Basic information
| species | Glycine max |
| transcript | GLYMA08G08730.1 |
| intron # | 9 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G08730.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os05g50510.1 (Oryza sativa), 3'ss of exon 8
---gcttttgtatgttgtctgttt--gcaattttctagttgatttgctaatataagcttacatgctgtttactgcaaatgcataattgtaatttttatgtggcagGTTATACTGATCCTGCAAAGCCTGATCTCCCTCGAATGCATGAGTGGCATTTCAGATCTGGGCTTGATCGCTACATCTGGATAATTGGAATGATTTATGC
|| || ||||| ||||| | ||| | |||| || | ||| | ||||| | || | || | || || || || || | || ||| | ||| | | | || | | ||||||||||||||| ||||||| |||||||| ||||| ||||| |||||||||||
gtgagttatgcatgttttctgtcttagcattattctcattaacc-atggataggattttacaccattttcctttcatgtacagGAT----------ATAAGG------ATCCAGAGCCTTCCAAGGCAAACTTACCCCTGCTACATGAGTGGCATTTCCGATCTGGCCTTGATCGATACATATGGATTATTGGAATGAT------
upper sequence: GLYMA08G08730.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os01g44040.1 (Oryza sativa), 3'ss of exon 8
gcttttgtatgttgtctgtttgcaattttctagttgatttgctaatataagcttacatgctgtttactgcaaatgcataattgtaatttttatgtggcagGTTATACTGATCCTGCAAAGCCTGATCTCCCTCGAATGCATGAGTGGCATTTCAGATCTGGGCTTGATCGCTACATCTGGATAATTGGAATGATTTATGC
||| | || | || | || | | || || | | | || | | || |||| || | || || | | | | || | | | || ||| |||| | | | || | ||||||||||||||||| ||||||| |||||||| || || ||||| |||||||||||
---gttggttattcttatatttcgatgtgtcattttccttaccattcctagataa-atcatgttaacatgtgttttgtacttttgtgatgcagGCTACAAGG-ACCCAGAGCCTTCAAAAGCAAACTTACCACTGTTGCATGAGTGGCATTTCCGATCTGGCCTTGATCGTTATATATGGATTATTGGAATGAT------
upper sequence: GLYMA08G08730.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G147351_T01 (Zea mays), 3'ss of exon 2
gcttttgtatgttgtctgtttgcaattttctagttgatttgctaatataagcttacatgctgtttactgcaaatgcataattgtaatttttatgtgg-cagGTTATACTGATCCTGCA------AAGCCTGATCTCCCTCGAATGCATGAGTGGCATTTCAGATCTGGGCTTGATCGCTACATCTGGATAATTGGAATGATTTATGC
||| ||| | | | | |||| || ||| | || || |||||| | | || | || | ||||| || | | |||| |||| ||||| || ||| | | | || | ||||||||||||||| ||||||| || ||||| ||||| ||||| |||||||||||
------gtaagttattgat--gtagttttgtatgacattctccc-taccagt---catgctcaggagttcagaacca--accttaattattttctattcagGCTATAAAGATCCATCACCATCCAAGGCACACTTACCCGTGCTACATGAGTGGCATTTCTGATCTGGCCTCGATCGATACATATGGATTATTGGAATGAT------
upper sequence: GLYMA08G08730.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G458538_T01 (Zea mays), 3'ss of exon 3
gcttttgtatgttgtctgtttgcaattttctagttgatttgctaatataagcttacat-gctgtttactgcaaatgcataattgtaatttttatgtggcagGTTATACTGATCCTGCA------AAGCCTGATCTCCCTCGAATGCATGAGTGGCATTTCAGATCTGGGCTTGATCGCTACATCTGGATAATTGGAATGATTTATGC
||| ||| | | | | |||| || ||| | | | | | | | ||| | | || | ||||| | ||| ||| |||| |||| ||||| | ||| | | | || | | ||||||||||||||| ||||||| || ||||| ||||| ||||| |||||||||||
------gtaagttattgat--gtagttttgtatgacattctccctaccagtcatgcttaggagttcaggaccaac-cttaattat--tttctatt---cagGCTATAAAGATCCATCGCCATCCAAGGCACACTTACCCCTGCTACATGAGTGGCATTTCCGATCTGGCCTCGATCGATACATATGGATTATTGGAATGAT------
upper sequence: GLYMA08G08730.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G370741_T01 (Zea mays), 3'ss of exon 3
gcttttgtatgttgtctgtttgcaattttctagttgatttgctaatataagcttacat-gctgtttactgcaaatgcataattgtaatttttatgtggcagGTTATACTGATCCTGCA------AAGCCTGATCTCCCTCGAATGCATGAGTGGCATTTCAGATCTGGGCTTGATCGCTACATCTGGATAATTGGAATGATTTATGC
||| ||| | | | | |||| || ||| | | | | | | | ||| | | || | ||||| | ||| ||| ||| |||| ||||| || ||| | | | || | | ||||||||||||||| ||||||| || ||||| ||||| || || |||||||||||
------gtaagttattgat--gtagttttgtatgacattctccctaccagtcatgcttaggagttcaggaccaac-cttaattat--tttctatt---cagACTATAAAGATCCATCACCATCCAAGGCACACTTACCCCTGCTACATGAGTGGCATTTCCGATCTGGCCTCGATCGATACATATGTATTATTGGAATGAT------
upper sequence: GLYMA08G08730.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G463445_T01 (Zea mays), 3'ss of exon 3
gcttttgtatgttgtctgtttgcaattttctagttgatttgctaatataagcttacat-gctgtttactgcaaatgcataattgtaatttttatgtggcagGTTATACTGATCCTGCA------AAGCCTGATCTCCCTCGAATGCATGAGTGGCATTTCAGATCTGGGCTTGATCGCTACATCTGGATAATTGGAATGATTTATGC
||| ||| | | | | |||| || ||| | | | | | | ||||| | || | ||||| | ||| ||| |||| |||| ||||| || ||| | | | || | | ||||||||||||||| ||||||| || |||| ||||| ||||| |||||||||||
------gtaagttattgat--gtagttttgtatgacattctccctaccagtcatgctcaggagtttaggaccaac-cttaattat--tttctatt---cagGCTATAAAGATCCATCACCATCCAAGGCACACTTACCCCTGCTACATGAGTGGCATTTCCGATCTGGCCTCAATCGATACATATGGATTATTGGAATGAT------
upper sequence: GLYMA08G08730.1 (Glycine max), 3'ss of exon 9
lower sequence: AT2G34410.1 (Arabidopsis thaliana), 3'ss of exon 8
------------------------------------------------------------gcttttgtatgttgtctgtttgcaat-tttctagttgatttgctaatataagcttacatgctgtttactg-caaatgcataattgtaatttttatgtgg---cagGTTATACTGATCCTGCAAAGCCTGATCTCCCTCGAATGCATGAGTGGCATTTCAGATCTGGGCTTGATCGCTACATCTGGATAATTGGAATGATTTATGC
||| || | | |||| ||| | || || | | | || | ||| | || | || || || | | ||| |||| || |||||||| || || || || || || | | ||||| ||||| |||||||| || ||||| |||||||| ||||| ||||||||||| |||||
gtcagtatcagactcttctcatatcttttactgtgttcggcatggtcgactgcatatccgtcttgtgctaaaaaaatcctgccaatgtttgttgtcacttggtcactggaattagtgtttttgtatgttgactaacatttagtttttttccttacacaagtacagGATACACTGATCCAGCTAAACCAGAACTACCACTTTTACATGAATGGCACTTCAGATCAGGACTTGACCGCTACATATGGATCATTGGAATGATATATGC
upper sequence: GLYMA08G08730.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G29890.2 (Arabidopsis thaliana), 3'ss of exon 7
--------------------------------gcttttgt-atgttgtctgtttgcaattttctagttgatttgctaatataagcttacatgct---------gtttactgcaaatgcata-attgtaatttttatgtgg---cagGTTATACTGATCCTGCAAAGCCTGATCTCCCTCGAATGCATGAGTGGCATTTCAGATCTGGGCTTGATCGCTACATCTGGATAATTGGAATGATTTATGC
|||||| |||| | | || | || | | | | || | | | |||||| || | || | | ||| | ||| | |||| || || ||||| || || || || || || || | || || ||||||||||||||||| |||||||||||||| ||||| || || ||||| |||||
gtcagtaacaaatttctctcatttttcataccatttttgtcatgtggctgatctgtagttctgtcttctacacaaatattttggatggcatgcttgaataaaaattggtaactaacgttgatattctgtctttaacacaaatacagGGTACACAGATCCAGCTAAACCAGACCTTCCACGTCTACACGAATGGCATTTCAGATCTGGACTTGATCGCTACATATGGATCATCGGCATGATATATGC
upper sequence: GLYMA08G08730.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G46340.1 (Arabidopsis thaliana), 3'ss of exon 9
-------gcttttgt-atgttgtctg--tttgcaattttctagttgatttgctaatataagcttacatgctgtttactgcaaatgcataattgtaatttttatgtggcagGTTATACTGATCCTGCAAAGCCTGATCTCCCTCGAATGCATGAGTGGCATTTCAGATCTGGGCTTGATCGCTACATCTGGATAATTGGAATGATTTATGC
|||| | | ||| || || |||| | | |||| | || ||| | | |||| | || ||| | | | || ||||||| | ||| ||||| ||||| ||||| | ||| ||||||| ||||| || ||||| || |||||||||||||| ||||| || ||||||||||||||
gtggttagcttatccgaaattgattgaattcccaatgtggaatgagattattcataatggaattagaagaagtttctaatatttgtatattacttgtgaata-actccagGTTACAATGACCCTGCCAAGCCCGATCTTCATCGGCTGCATGAATGGCACTTTAGATCAGGCCTTGATCGCTACATATGGATCATCGGAATGATTTATGC
upper sequence: GLYMA08G08730.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv10s0003g02830.t01 (Vitis vinifera), 3'ss of exon 3
gcttttgtatgttgtctgtttgcaatt--ttctagttgatttgctaatataagcttacatgctgtttactgcaaatgcataattgtaatttttatgtggcagGTTATACTGATCCTG------CAAAGCCTGATCTCCCTCGAATGCATGAGTGGCATTTCAGATCTGGGCTTGATCGCTACATCTGGATAATTGGAATGATTTATGC
| | ||| ||||| | ||| | | | ||| | | ||| | ||||| | | || | | ||| |||| |||||||||| | |||||| | | || | | |||||||||| ||||||| |||||||| |||||||||||||||||||| || ||||| || ||||||||
attactatattgaactggtttgttgctagttcaatctagtggcttaacaccaagttaagttgtgttttccaagttttcaaactagta--ttttcaatggcagGTTACAGTGATCCAGATCCTTCTAAACAAGGTCTCCCTCGACTGCATGAATGGCATTTTAGATCTGGGCTTGATCGCTATATTTGGATCATCGGAATGAT------ atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tataagcttacatgctgtttactgcaaatgcataattgtaatttttatgtggcagGTTATACTGATCCTGCAAAGCCTGATCTCCCTCGAATGCATGAGTGGCATTTCAGATCTGGGCTTGATCGCTACATCTGGATAATTGGAATGATTTATGC
agcttac putative branch site (score: 3)
tttttat putative PPT
aaatgcataattgtaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcttttgtatgttgtctgtttgcaattttctagttgatttgctaatataagcttacatgctgtttactgcaaatgcataattgtaatttttatgtggcagGTTATACTGATCCTGCAAAGCCTGATCTCCCTCGAATGCATGAGTGGCATTTCAGATCTGGGCTTGATCGCTACATCTGGATAATTGGAATGATTTATGC
gcttttg
- - - - -tgttgtc
- - - - - - - - tgtttgc
- - - - - - - - - - - - - - - - - tgatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - acatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tactgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcataa
