Sequence
atgc intronic sequence ATGC exonic sequencegtgagaaccttttcttgttagtatcgagtgttagttggtgttctaacatagatactatttaattgcatctttctgtttcaaaaaaaaatgttgattatttattgtagGTTACTGGAGAGTTGCAAGATCATTTGACTAGCTGGGATGCCCTGCGAGCTGCATTGCCTGTTGGAACTGTCAGTGGAGCGCCAAAG
Basic information
species | Glycine max |
transcript | GLYMA18G03260.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G03260.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os03g61120.1 (Oryza sativa), 3'ss of exon 9
---------------------------------------------------------------------------------------------gtgagaaccttttcttgttagtatcgagtgttagttggtgttctaacatagatactatttaattgcatctttct-gtttcaaaaaaaaatgttgattatttattgtagGTTACTGGAGAGTTGCAAGATCATTTGACTAGCTGGGATGCCCTGCGAGCTGCATTGCCTGTTGGAACTGTCAGTGGAGCGCCAAAG
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gtaagtctacctgtatgatatacagctttgacaatatccaatatccttggacaatcaagtattgtttgtgtacagttgttggagtaactagtagctaggaaccatccttcttactgtca--tatctactaagattc-gtcatgg---ctgtgttattacttattaatagttctcacaaggtctgtttctgcatttctgtagGTTACTGGAGAGTTGCGTGATGATCTGACTTGTTGGGATGCTCTTCGAGCAGCATTGCCCGTTGGAACAGTTAGTGGTGCACCAAAG
upper sequence: GLYMA18G03260.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os03g15780.4 (Oryza sativa), 3'ss of exon 9
gtg-agaaccttttcttgttagtatcgagtgttagttggtgttctaacatagatactatttaattgcatctttctgtttcaaaaaaaaatgttgatt--atttattgtagGTTACTGGAGAGTTGCAAGATCATTTGACTAGCTGGGATGCCCTGCGAGCTGCATTGCCTGTTGGAACTGTCAGTGGAGCGCCAAAG
|| || | ||| || ||| ||| | | || || | || | | || || | || | |||| || | ||| || || || |||| | |||||||||| | |||||| | || ||||||||||||||||| || |||||||||||||| || |||||||| ||||||
-tgtagtgctcttttacgtaagt-----gtgctggctgagcgcct----ttgagattcttgtcttctgtacttacactgaaaaacaatgtattgtttgaatgatttacagGTGAGTGGAGAGTTGGATGATCATCTCCAAAGTTGGGATGCCCTGCGAGCCGCGTTGCCTGTTGGAACAGTTAGTGGAGCACCAAAG
upper sequence: GLYMA18G03260.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G003109_T01 (Zea mays), 3'ss of exon 9
gtgagaaccttttcttgttagtatcgagtgttagttggtgttctaacatagatactatttaattgcatctttctgtttcaaaaaaaaatgttgattatttattgtagGTTACTGGAGAGTTGCAAGATCATTTGACTAGCTGGGATGCCCTGCGAGCTGCATTGCCTGTTGGAACTGTCAGTGGAGCGCCAAAG
||| | ||| ||||| | | | || || || || ||| | | ||| | | | || || | | | || |||| || || ||| | | ||| || | || |||||||||| || |||||||||||||| |||||||| || |||||||| ||||||
----taacacaattatgt-agtatgaacaagttagcagctttttatgatttgtagtatcaa--caattatttataagaaacatgcgtattttaaaaaacttgtgcagGTCACCGGTGAGCTACGTGATGATCTTACGTGCTGGGATGCGCTACGAGCTGCATTGCCAGTTGGAACAGTTAGTGGAGCTCCAAAG
upper sequence: GLYMA18G03260.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv13s0067g00400.t01 (Vitis vinifera), 3'ss of exon 9
gtgagaaccttttcttgttagtatcgagtgttagttgg--tgttctaacatagatactatttaattgcatctttctgtttcaaaaaaaaatgttgattatttattgtagGTTACTGGAGAGTTGCAAGATCATTTGACTAGCTGGGATGCCCTGCGAGCTGCATTGCCTGTTGGAACTGTCAGTGGAGCGCCAAAG
| | ||| | | || | | ||| | || || |||| | | | | | || |||| | |||||| |||| || ||||||| || ||||||||||||||| | ||||||||| |||||||||| | | ||| ||||||| | || |||||||| ||||||
----cattttgttccatgtgatttccaatcttacaagagtcaggagaaaattgatataaacaataagtaaccttttgttac-----aaaatggatgccattttttccagGTTACAGGGGAGTTGCAAGATCATCTCACTAGCTGGAATGCCCTGCGCAGTATACTGCATGTTGGAGCAGTTAGTGGAGCACCAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tactatttaattgcatctttctgtttcaaaaaaaaatgttgattatttattgtagGTTACTGGAGAGTTGCAAGATCATTTGACTAGCTGGGATGCCCTGCGAGCTGCATTGCCTGTTGGAACTGTCAGTGGAGCGCCAAAG
tgttgat putative branch site (score: 4)
tttctgtttcaaaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagaaccttttcttgttagtatcgagtgttagttggtgttctaacatagatactatttaattgcatctttctgtttcaaaaaaaaatgttgattatttattgtagGTTACTGGAGAGTTGCAAGATCATTTGACTAGCTGGGATGCCCTGCGAGCTGCATTGCCTGTTGGAACTGTCAGTGGAGCGCCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG