Sequence
atgc intronic sequence ATGC exonic sequencegtatgttaagtgtgccatgtgtcattttgttgttcagttaacaagtttttttgttttattaaccatctattctttgtgtgcagTGGGTTCAATGTGATAAGTGTGAAGCATGGCAACATCAAATTTGTGCCTTATTTAATGGTAGAAGAAATGATGGTGGACAAGCTGAATATACTTGCCCTA
Basic information
species | Glycine max |
transcript | GLYMA08G24290.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G24290.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os02g04490.1 (Oryza sativa), 3'ss of exon 7
gtatgttaagtgtgccatgt--gtcattttgttgttcagttaacaagtttt-------tttgttttattaaccatctattctt------tgtgt---gcagTGGGTTCAATGTGATAAGTGTGAAGCATGGCAACATCAAATTTGTGCCTTATTTAATGGTAGAAGAAATGATGGTGGACAAGCTGAATATACTTGCCCTA
||| ||| | | | | | || ||||||| | | | ||| ||| || |||| | | | | || || ||| | |||||||||||| ||||| ||||||||| ||||| || || || ||||| |||||||||||||||| |||||||| || ||||| || || || ||||| |
gtaagttcctttttcatttttggtgattttgtgtctgtatcatcaaaatttgggtatcttccttttgtatattaaatctttttaaatgatgtattctgcagTGGGTTCAGTGTGACAAGTGTGAATGCTGGCAGCACCAGATATGTGCTCTATTTAATGGTAGAAGGAATGATGGAGGGCAAGCAGAGTACACCTGCCCAA
upper sequence: GLYMA08G24290.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G139977_T01 (Zea mays), 3'ss of exon 6
----gtatgttaagtgtgcc-atgtgtcattttgtt---gttcag----ttaacaagtttttttgttttattaaccatctat-----tctttgtgtgcagTGGGTTCAATGTGATAAGTGTGAAGCATGGCAACATCAAATTTGTGCCTTATTTAATGGTAGAAGAAATGATGGTGGACAAGCTGAATATACTTGCCCTA
||| | | || ||| ||| | | ||| || | ||||| | || | ||| ||| | | | ||||||||||||||||||| || |||||| |||||||||||||||||||| ||||||||||| ||||| || ||||| ||||||||||||||||||||||| |
gtaagtactgcagttccattgatatgtggtttcataaaagctcaagagtttctgatatttttcttttgtgctaaacattttcaaaccacacattctgcagTGGGTTCAATGTGACAAATGTGAATGTTGGCAACATCAAATTTGTGCTTTATTTAATGGAAGAAGGAACGATGGAGGACAAGCTGAATATACTTGCCCCA
upper sequence: GLYMA08G24290.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G470556_T01 (Zea mays), 3'ss of exon 6
gtatgttaagt-gtgccatgtgt-cattttgttgttca---gttaacaa-gtttttttgttttattaaccatctattctttgtg-----tgcagTGGGTTCAATGTGATAAGTGTGAAGCATGGCAACATCAAATTTGTGCCTTATTTAATGGTAGAAGAAATGATGGTGGACAAGCTGAATATACTTGCCCTA
||||||| | || |||| | || | | ||| ||| || ||||| | | | ||| ||| | | || ||||||||||||||||||| || ||| || |||||||||||||||||||| |||||||||| ||||| || | ||| |||||||||||||||||||||||
gtatgttttgcagttccattgatacacataaaagctcaaaagtttctaatatttttctttggtgctaaacattttcaaatcatgcattctgcagTGGGTTCAATGTGACAAATGTCAATGCTGGCAACATCAAATTTGTGCTCTATTTAATGGAAGAAGGAACGGTGGAGGACAAGCTGAATATACTTGCCCCC
upper sequence: GLYMA08G24290.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G55970.1 (Arabidopsis thaliana), 3'ss of exon 5
---------------------gtatgttaagtgtgccatgtgtcattttgttgttcagttaacaagtttttttgttttattaaccat-ctattctttgtgtgcagTGGGTTCAATGTGATAAGTGTGAAGCATGGCAACATCAAATTTGTGCCTTATTTAATGGTAGAAGAAATGATGGTGGACAAGCTGAATATACTTGCCCTA
| | || | | | ||| |||| || | ||| | |||| | | | | ||||| | | | || | |||||||||| |||||||||||||||||||||||||| ||| ||||||||| || || || | |||||||| |||| | | | | || ||||||||||
gtatgtatgcctcatgatttcggaaatttgtttcttcctttgtttttttttttctttgttttctttttttgtgtgtgtctgaaccaaaccaatggttttctgcagTGGGTGCAATGTGATAAGTGTGAAGCATGGCAGCATATAATTTGTGCTTTGTTCAACAGCCGAAGAAATCATGGAGAATCCACCAAGTACACTTGCCCTA
upper sequence: GLYMA08G24290.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G79000.2 (Arabidopsis thaliana), 3'ss of exon 8
-------------------gtatgttaagtgtgc-catgtgtcattttgttgttcagttaacaagtttttttgttttattaaccatctattctttgtgtgcagTGGGTTCAATGTGATAAGTGTGAAGCATGGCAACATCAAATTTGTGCCTTATTTAATGGTAGAAGAAATGATGGTGGACAAGCTGAATATACTTGCCCTA
||| | | | || ||| || | |||| || |||| | | | || | | | | | |||||||||| ||||||||||| ||||| || ||||| ||||| || ||||| ||||||||||| ||||| ||||| || || || ||||| ||||| |||||
gtaaaagcctatccactctgtagacttattttgtgtttgtctcccgtctttgtatgtttttttagttcatgctatattttgtttctatgtatgatttttgcagTGGGTCCAATGTGATAAATGTGAGGCGTGGCAGCATCAGATATGTGCTTTATTTAATGGGAGAAGGAATGACGGAGGGCAGGCTGAGTATACCTGCCCAT
upper sequence: GLYMA08G24290.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G16710.1 (Arabidopsis thaliana), 3'ss of exon 7
---------gtatgttaagtgtgccatgtgtcattttgttgttcagttaacaagtttttttgt-tttattaac--catctattctttgtgtgcagTGGGTTCAATGTGATAAGTGTGAAGCATGGCAACATCAAATTTGTGCCTTATTTAATGGTAGAAGAAATGATGGTGGACAAGCTGAATATACTTGCCCTA
| | | | | | | |||| || || |||||| || ||| | | | | | | ||| | || ||||||| ||||||||||| ||| | || ||||| |||||||| ||||| |||||||||| | || |||||||| || |||||||| ||||| |||||
gtaagactatcctatcagtagagttgtattgtcatttgcatctcgttttgttggtttttctgagtttgtctatttcgtttgatgttt-tttgtagTGGGTCCAATGTGATAAATGTCAGGCCTGGCAGCATCAAATATGTGCTCTATTTAATGGGCGGAGGAATGATGGGGGGCAAGCTGAGTATACCTGCCCAT
upper sequence: GLYMA08G24290.1 (Glycine max), 3'ss of exon 9
lower sequence: AT3G12980.1 (Arabidopsis thaliana), 3'ss of exon 7
------------gtatgttaagtgtgccatgtgtcattttgttgttcagtta-acaagtttttttgttttattaaccatctattctttgtgtgcagTGGGTTCAATGTGATAAGTGTGAAGCATGGCAACATCAAATTTGTGCCTTATTTAATGGTAGAAGAAATGATGGTGGACAAGCTGAATATACTTGCCCTA---
| | ||| || ||| | | | || ||| | || | ||| | | || | | ||| || |||||||||||| ||||||||||| ||| |||||||||| |||||||||||||| || || || || | || ||| |||| ||||| || || ||||||||||
gtatgcctcttcagttactgagttctgcaattgttttatagggattattttatattagctgctttactctttttctgaaccattaattctgtgcagTGGGTGCAATGTGATAAATGTCAAGCATGGCAGCATCAAATTTGTGCTTTGTTCAACGGCCGTAGGAATCATGG---GCAAGCCGAGTACACTTGCCCTAATT
upper sequence: GLYMA08G24290.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv09s0054g01780.t01 (Vitis vinifera), 3'ss of exon 6
---------gtatgttaagtgtgccatgtgtcattttgttgttcagttaacaagtttttttgttttat---taaccatctattctttgtgtgcagTGGGTTCAATGTGATAAGTGTGAAGCATGGCAACATCAAATTTGTGCCTTATTTAATGGTAGAAGAAATGATGGTGGACAAGCTGAATATACTTGCCCTA
| || | | || ||||||| ||||| || | | | |||| | | ||| | | | | ||||||||||||||||||| || |||||||| ||||||||||||||||||||||| || |||||| | || ||||||||||| || |||||||||||||||||||
gtatgttttattcatttcttttagtatctgtcattatgttggattattgtctgagcaatcgctcttatgtttgaacatttgcttctattttgcagTGGGTTCAATGTGACAAATGTGAAGCTTGGCAACATCAAATTTGTGCCTTGTTCAATGGTCGGAGGAATGATGGTGGGCAGGCTGAATATACTTGCCCTA
upper sequence: GLYMA08G24290.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ09423 (Selaginella moellendorffii), 3'ss of exon 2
gtatgttaagtgtgccatgtgtcattttgttgttcagttaacaagtttttttgttttattaaccatctattctttgtgtgcagTGGGTTCAATGTGATAAGTGTGAAGCATGGCAACATCAAATTTGTGCCTTATTTAATGGTAGAAGAAATGATGGTGGACAAGCTGAATATACTTGCCCTA
| ||| || | | || | ||| ||| | | | ||| ||| | |||||||||||||||||| ||||| | | |||||| |||||||| ||||||||||||||||||||||||||||| ||||| | | |||| || ||||||
----------------gtatgtgcttctatattttttctc-----tttccttgaaacgtctgacttgtatggtttat--gcagTGGGTTCAATGTGACAAGTGCAATGTATGGCAGCATCAAATCTGTGCCTTATTTAATGGTAGAAGAAATGAAGGTGGTGACACGGAATTTATTTGCCCCT
upper sequence: GLYMA08G24290.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ34595 (Selaginella moellendorffii), 3'ss of exon 5
gtatgttaagtgtgccatgtgtcattttgttgttcagttaacaagtttttttgttttattaaccatctattctttgtg-----tgcagTGGGTTCAATGTGATAAGTGTGAAGCATGGCAACATCAAATTTGTGCCTTATTTAATGGTAGAAGAAATGATGGTGGACAAGCTGAATATACTTGCCCTA
|||||| |||| || || | | | |||| | || | || | || | | || ||||||||||||||||||| ||||| | | |||||| |||||||| ||||||||||||||||||||||||||||| ||||| | | |||| || ||||||
--------------gtatgtgtttttttttttttacttctatattttttctctttccttgaaacgtccgacttgtatggtttatgcagTGGGTTCAATGTGACAAGTGCAATGTATGGCAGCATCAAATCTGTGCCTTATTTAATGGTAGAAGAAATGAAGGTGGTGACACGGAATTTATTTGCCCCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttgttcagttaacaagtttttttgttttattaaccatctattctttgtgtgcagTGGGTTCAATGTGATAAGTGTGAAGCATGGCAACATCAAATTTGTGCCTTATTTAATGGTAGAAGAAATGATGGTGGACAAGCTGAATATACTTGCCCTA
tattaac putative branch site (score: 1)
tctattcttt putative PPT
agttaacaagtttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgttaagtgtgccatgtgtcattttgttgttcagttaacaagtttttttgttttattaaccatctattctttgtgtgcagTGGGTTCAATGTGATAAGTGTGAAGCATGGCAACATCAAATTTGTGCCTTATTTAATGGTAGAAGAAATGATGGTGGACAAGCTGAATATACTTGCCCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA