Sequence
atgc intronic sequence ATGC exonic sequencegcaagtacttgagttacaccattttgtccctttcttgcttacttttggttatcagacttgtattcatgctcatctaatatgatgttttctcttttgtttcagATCCATCTGGCTTCATCTTGTTTCCTCTTGTTGTTCACTCATTCGATCTGATAGTTTCATCAGCTGGAATATTTTCTATCAGGGGTACACGTGAAACTGG
Basic information
species | Glycine max |
transcript | GLYMA08G24120.2 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G24120.2 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os02g33490.1 (Oryza sativa), 3'ss of exon 8
gcaagtacttgagttacaccattttgtccctttcttgcttacttttggttatcagacttgtattcatgctcatctaatatgat--gttttctcttttgtttcagATCCATCTGGCTTCATCTTGTTTCCTCTTGTTGTTCACTCATTCGATCTGATAGTTTCATCAGCTGGAATATTTTCTATCAGGGGTACACGTGAAACTGG
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----gtgcctggttttgagtaaaatcgagattcatcttttcttctgcaataacttttttttggtaatatttctactttataatcagcattctttgctaatgcagATCCCTCAGGCTTTATACTGTTTCCTCTTGTTGTTCATTCATTTGATCTGGTGATCTCATCAGTTGGAATACTCTCAATTCGGGGAACACGTGACTCTGG
upper sequence: GLYMA08G24120.2 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G075900_T01 (Zea mays), 3'ss of exon 8
gcaagtacttgagttacaccattttgtccctttcttgcttacttttggttatcagacttgtattcatgctcatctaat--atgat--gttttctcttttgtttcagATCCATCTGGCTTCATCTTGTTTCCTCTTGTTGTTCACTCATTCGATCTGATAGTTTCATCAGCTGGAATATTTTCTATCAGGGGTACACGTGAAACTGG
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------gctttgttgttgctgttgtgtttttggtacaatggcacacatatcgcacctttgtaatcgctctattatggtccataatcagctttgtttattattgcagATCCGTCTGGCTTTATTTTGTTTCCTCTTGTTGTGCATTCATTTGATTTGGTGGTGTCATCAGTCGGAATTCTCTCAATCAGAGGAACACGTGACTCTGG
upper sequence: GLYMA08G24120.2 (Glycine max), 3'ss of exon 8
lower sequence: Vv09s0054g00700.t01 (Vitis vinifera), 3'ss of exon 8
-gcaagtactt-gagttacaccattttgtccctttcttgcttacttttggttatcagacttgtattcatgctcatctaatatgatgttttctcttttgtttcagATCCATCTGGCTTCATCTTGTTTCCTCTTGTTGTTCACTCATTCGATCTGATAGTTTCATCAGCTGGAATATTTTCTATCAGGGGTACACGTGAAACTGG
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tgatcgtgctttgacctttgccata--gatccattactgctttcgtcggtttgtttgttttctat--agattgatcctttcaaatattgattatgttcatgcagATCCATCTGGTTTCATCCTGTTTCCTCTTGTCATTCACTCTTTTGACCTGGTAATATCATCGGTTGGAATATTTTCAATAAGGGGGACACGTGACTCTGGMapped 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|105633719|gb|DW247082.1|DW247082EST: TAGTGCCATGATACTTGGTGGAACAATGGCACAACGCTGTAAAATTGCAG ATCCATCTGGCTTCAGCTTGTTTCCTCTTGTTGTTCACTCATTCGATCTGA
genomic: TAGTGCCATGATACTTGGTGGAACAATGGCACAACGCTGTAAAATTGCAGgcaagtactt ... tttgtttcagATCCATCTGGCTTCATCTTGTTTCCTCTTGTTGTTCACTCATTCGATCTGA
EST:
gi|193436498|gb|FK400830.1|FK400830EST: TAGTGCCGTGATACTTGGTGGAACAATGGCACAACGCTGTAAAATTGCAG ATCCATCTGGCTTCATCTTGTTTCCTCTTGTTGTTCACTCATTCGATCTGA
genomic: TAGTGCCATGATACTTGGTGGAACAATGGCACAACGCTGTAAAATTGCAGgcaagtactt ... tttgtttcagATCCATCTGGCTTCATCTTGTTTCCTCTTGTTGTTCACTCATTCGATCTGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttatcagacttgtattcatgctcatctaatatgatgttttctcttttgtttcagATCCATCTGGCTTCATCTTGTTTCCTCTTGTTGTTCACTCATTCGATCTGATAGTTTCATCAGCTGGAATATTTTCTATCAGGGGTACACGTGAAACTGG
atctaat putative branch site (score: 3)
tgttttctcttttgtt putative PPT
taatatgatgtttt 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
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gcaagtacttgagttacaccattttgtccctttcttgcttacttttggttatcagacttgtattcatgctcatctaatatgatgttttctcttttgtttcagATCCATCTGGCTTCATCTTGTTTCCTCTTGTTGTTCACTCATTCGATCTGATAGTTTCATCAGCTGGAATATTTTCTATCAGGGGTACACGTGAAACTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA