Sequence
atgc intronic sequence ATGC exonic sequencegtaatgcttgaagcctctatcaagcttagcgaggagtaaatttctgaggttacgtggtgtgtttttactaaactggatatttcttgcagAATCTTGAAATAAAGAAAATTAATGATGAAAAGAAAGCATCGATGGCAGCTCAGTTTGCAGCTGAAGCCACTCTTCGAAGGGTCCATGCTGCTCAGAAGG
Basic information
species | Glycine max |
transcript | GLYMA08G05100.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g50320.2 (Oryza sativa), 3'ss of exon 3
gtaatgcttgaagcctctatcaagcttagcgaggagtaaatttctgaggttacgtggtgtgtttttactaaactggatatttcttgcagAATCTTGAAATAAAGAAAATTAATGATGAAAAGAAAGCATCGATGGCAGCTCAGTTTGCAGCTGAAGCCACTCTTCGAAGGGTCCATGCTGCTCAGAAGG
| | | | | ||| | | |||||| | | || | | | | | | ||||||||||| ||| | ||||||| |||||||| || || || | ||||| |||||||||||||| ||||| ||||| ||||| || ||||| || || || |
---------gtatctatctttatactttttaaagtt---gtttctgcccccctctttttgattgctccctgatggagaacattttgcagAATCTAGAACTCAAGAAAACAAATGATGAGAAAAAGGCGGCTATGGCTGCTCAGTTTGCAGCAGAAGCAACTCTGCGAAGAGTGCATGCAGCCCAAAAAG
upper sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os06g14080.1 (Oryza sativa), 3'ss of exon 3
--gtaatgcttgaagcctctatcaagcttagcgaggagtaaatttctgaggttacgtggtgtgtttttactaaactggatatttcttgcagAATCTTGAAATAAAGAAAATTAATGATGAAAAGAAAGCATCGATGGCAGCTCAGTTTGCAGCTGAAGCCACTCTTCGAAGGGTCCATGCTGCTCAGAAGG
| ||| | | | | | || | || | | | || | | | | | |||| || | | |||||||||| ||| | ||||| ||||||||||| || || || | ||||| |||||||||||||| ||||| ||| | || || || ||||| || || ||||
gtatgtatcttataatttgtgtttatctgtatccgttgtctctgttttagctgatct----tttctttaacaatgataaaaacaaatgcagAATCTAGAAGTCAAGAAGATTAATGATGAGAAAAAGGCTGCAATGGCTGCTCAGTTTGCAGCAGAAGCGACTTTGCGGAGAGTACATGCAGCCCAAAAGG
upper sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os12g44340.1 (Oryza sativa), 3'ss of exon 3
gtaatgcttgaagcctctatcaagcttagcgaggagtaaatttctgaggttacgtggtgtgtttttactaa-actggatatttcttgcagAATCTTGAAATAAAGAAAATTAATGATGAAAAGAAAGCATCGATGGCAGCTCAGTTTGCAGCTGAAGCCACTCTTCGAAGGGTCCATGCTGCTCAGAAGG
|||||| | ||| | | | || || | || || | ||| | || || ||| | |||||| ||||| |||||| || || ||||||||||||||| | | ||||| || |||||||| || || || ||||||||||| ||||| || |||||||
gtaatggagcagccctattcttttcctctttcacagctcatatt----gtctcgagaacagttactgatagcacacgatgct----gcagAACCTTGAGGCAAAGAAGATAAACGATGAAAAGAAAGCAGCACTTGCAGCCCAATTTGCAGCAGAGGCTACACTTCGAAGGGTTCATGCAGCACAGAAGG
upper sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G14840.2 (Arabidopsis thaliana), 3'ss of exon 3
gtaatgcttgaagcctctatcaagcttagcgaggagtaaatttctgaggttacgtggtgtgtttttactaaactggatatttcttgcagAATCTTGAAATAAAGAAAATTAATGATGAAAAGAAAGCATCGATGGCAGCTCAGTTTGCAGCTGAAGCCACTCTTCGAAGGGTCCATGCTGCTCAGAAGG
||| ||||| | ||| | | || | | || | || | | | | | || || || | ||||| |||||||| ||||| || ||||| |||||||| || || |||||||||||||||||||| ||||| ||||||| ||||| ||||||||||| ||||
gta-tgcttctaatatctcctttgttctttgatcgcttatttatattgattctata------tataatgatgttgtatgttg-tcacagAACCTTGAAATCAAGAAGATAAATGAAGAAAAGAAGGCTTCCATGGCAGCTCAGTTTGCAGCAGAAGCTTCTCTTCGTAGGGTTCATGCTGCTCAAAAGG
upper sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G24764.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaatgcttga-agcctctatcaagcttagcgaggagtaaatttctgaggttacgtggtgtgtttttactaaactggatatttcttgcagAATCTTGAAATAAAGAAAATTAATGATGAAAAGAAAGCATCGATGGCAGCTCAGTTTGCAGCTGAAGCCACTCTTCGAAGGGTCCATGCTGCTCAGAAGG
||| || | || | || | | | || | | |||| | || | | | | | | || |||||||||| ||||| |||||||| ||||| |||||||||||||| ||||| ||||||||||| |||||||||||| | |||| |||||||||||||| ||||
gtattgttcgataatctttccttggttcgatgatgttcacctttc---gtttcttaagcttatagacatatgatatcaaccttgctgcagAATCTAGAAATCAAGAAAATCAATGAGGAAAAGAAAGCATCAATGGCTGCTCAGTTTGCTGCTGAAGCCACTTTAAGAAGAGTCCATGCTGCTCAAAAGG
upper sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G68060.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaatgcttgaagcctctatcaagcttagcgaggagtaaatttctgaggttacgtggtgtgtttttactaaactggatatt-tcttgcagAATCTTGAAATAAAGAAAATTAATGATGAAAAGAAAGCATCGATGGCAGCTCAGTTTGCAGCTGAAGCCACTCTTCGAAGGGTCCATGCTGCTCAGAAGG
|| | | | | | | | | | || | || | | | | | ||||||||||| ||||| ||||| || ||||| || ||||| || || ||||| ||||||||||| |||||||| || | ||||||||||||||||||| ||||
---------------------gtatgtatcaaaatctccctccttacgatcatgatttggctggatatctgattatgaactatgttgcagAATCTAGAAATCAAGAAGATCAATGAGGAGAAGAAGGCTTCCATGGCTGCTCAGTTTGCTGCTGAAGCTACCTTAAGAAGGGTCCATGCTGCTCAAAAGG
upper sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G01750.2 (Arabidopsis thaliana), 3'ss of exon 4
gtaatgcttgaagcctctatcaa--gcttagcgaggagtaaatttctgaggttacgtgg--tgtgtttttactaaactggatatttcttgcagAATCTTGAAATAAAGAAAATTAATGATGAAAAGAAAGCATCGATGGCAGCTCAGTTTGCAGCTGAAGCCACTCTTCGAAGGGTCCATGCTGCTCAGAAGG
||| || ||| | | | ||| |||| | || | | || ||| | ||| ||| | | | | || | ||||| |||||||| |||||||| || || ||||| | || || ||||||||||| ||||| || |||||||||||||||||||| ||||||||||| ||||
gta-tgtttgcaatgtttctcagttgcttttcattttccaatctcttttatttttctggattctgtatttgatgatatcgcatcttgtcacagAACCTTGAAATCAAGAAAATAAACGAAGAAAAAAGGGCTTCAATGGCAGCTCAATTTGCTGCAGAAGCCACTCTTCGAAGGGTTCATGCTGCTCAAAAGG
upper sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv01s0011g05790.t01 (Vitis vinifera), 3'ss of exon 3
gtaatgcttgaagcctctatcaagcttagcgaggagtaaatttctgaggttacgtggtgtgtttttactaaactggatatttcttgcagAATCTTGAAATAAAGAAAATTAATGATGAAAAGAAAGCATCGATGGCAGCTCAGTTTGCAGCTGAAGCCACTCTTCGAAGGGTCCATGCTGCTCAGAAGG
||| ||| |||| || || || || | ||| ||| || | | || || |||| | | ||| ||||||||||| || || |||||||| |||||||||||||| || || ||||| ||||| |||||||| |||||||||||| ||||||| |||||||| |||||||
gtattgcatgaaacc-cttccatttttctttataagt---tttgtgtgtgtgtgttttgcagttttgtcctaacaattgttttttgcagAATCTCGAGATCAAGAAAATCAATGATGAAAAGAAGGCCTCCATGGCTGCTCAATTTGCAGCAGAAGCCACTCTTAGAAGGGTTCATGCTGCGCAGAAGG
upper sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S136_188V6.1 (Physcomitrella patens), 3'ss of exon 3
-------gtaatgcttgaagcctctatcaagcttagcgaggag-taaatttctgag--gttacgtggtgtgtttttactaaactggatat-ttcttgcagAATCTTGAAATAAAGAAAATTAATGATGAAAAGAAAGCATCGATGGCAGCTCAGTTTGCAGCTGAAGCCACTCTTCGAAGGGTCCATGCTGCTCAGAAGG
| | | ||| | | | | | | | |||| || | || ||| | | || || | | || || | || |||||||| |||||| | ||||| | ||||| || ||||||||| | |||| || ||||||||||| || || ||||| |||||||| ||||| |||||||| |
gattctcgcattttttgtcttatgtggacgtcgtttctttgtgctaaaattttaagttgtttctttgttacttatcagtatttggggggtgtttttgcagAACCTTGAATTGAAGAAGCTCAATGACGAGAAGAAAGCAGCTCTGGCCGCCCAGTTTGCAGCGGAGGCAACTCTGCGAAGGGTGCATGCAGCTCAGAAAG
upper sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S342_2V6.1 (Physcomitrella patens), 3'ss of exon 3
----------------------------------gtaatgcttgaagcctctatcaagc---ttagcgaggagtaaat---ttctgaggt-tacgtggtgtgtttt----tactaaactggatat-ttcttgcagAATCTTGAAATAAAGAAAATTAATGATGAAAAGAAAGCATCGATGGCAGCTCAGTTTGCAGCTGAAGCCACTCTTCGAAGGGTCCATGCTGCTCAGAAGG
||| || | || | || || || || |||| || |||| | ||| | || | | ||| | | | || | |||||||||||| | |||||||| |||||||||| ||||||| | | ||||| ||| ||||| || || ||||| ||||||| || || |||| ||||
gtactgatatcagagactcctagactcattttttgtattgtcaaagtccccgatgcggccatttctttagtagtacatcggttctataatgtaccagatgcagtcaacaatttgaaattcggtgcgttttcacagAATCTTGAAGTGAAGAAAATGAATGATGAAAGGAAAGCAGCACTAGCAGCACAGACCGCAGCAGAGGCGACTCTAAGAAGGGTTCAGGCGTCTCAAAAGGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|24205768|gb|BU965021.1|BU965021EST: CAAGGGTTGAGGGGAAGCTGAAGTTAACAGAATCTCTTCTAGAAAGCAAA AATCTTGAAATAAAGAAAATTAATGATGAAAAGAAAGCATCGATGGCAGCT
genomic: CAAGGGTTGAGGGGAAGCTGAAGTTAACAGAATCTCTTCTAGAAAGCAAAgtaatgcttg ... tttcttgcagAATCTTGAAATAAAGAAAATTAATGATGAAAAGAAAGCATCGATGGCAGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtaaatttctgaggttacgtggtgtgtttttactaaactggatatttcttgcagAATCTTGAAATAAAGAAAATTAATGATGAAAAGAAAGCATCGATGGCAGCTCAGTTTGCAGCTGAAGCCACTCTTCGAAGGGTCCATGCTGCTCAGAAGG
tactaaa putative branch site (score: 1)
tatttctt putative PPT
tttttactaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgcttgaagcctctatcaagcttagcgaggagtaaatttctgaggttacgtggtgtgtttttactaaactggatatttcttgcagAATCTTGAAATAAAGAAAATTAATGATGAAAAGAAAGCATCGATGGCAGCTCAGTTTGCAGCTGAAGCCACTCTTCGAAGGGTCCATGCTGCTCAGAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT