Sequence
atgc intronic sequence ATGC exonic sequence...ttgctggtttctcaactttgcagttactgatataatgatattgcttttaccattgaagctctgttcaaataatctaaagatattttttgtacatcttcagGCTATATTTCTACTCTGAGAAACAATGTACGTTCCCGTGCTTGGGGTGCTGCAATTGGTTGTAGTTATAAAGTTGAGCGGTGCTGCATTGTAAAG
Basic information
species | Glycine max |
transcript | GLYMA16G33300.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G33300.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os07g29450.1 (Oryza sativa), 3'ss of exon 6
ttgctggtttctcaactttg-cagtt--actgatataatgatattgcttttaccattgaagctctgttca-aataatctaaagatattttttgtacatcttcagGCTATATTTCTACTCTGAGAAACAATGTACGTTCCCGTGCTTGGGGTGCTGCAATTGGTTGTAGTTATAAAGTTGAGCGGTGCTGCATTGTAAAG
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--gtaagccttcattctttgtcagtccaattattagacttaaaaaggtcagagcaatatggctaaattagtagtacttgtataacacttgatctacct-tccagGCTATACTTCAACTTTAAGGAACAATGTCCGCTCACGTGCTTGGGGTGCTGGTATTGGTTGTAGCTTTCGCATAGAACGCTGCTGCATTGTTAAG
upper sequence: GLYMA16G33300.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G146118_T02 (Zea mays), 3'ss of exon 6
ttgctggtttctcaactttgcagttactgatataatgatattgcttttac-cattgaagctctgttcaaataatctaaagatattttttgtacatcttcagGCTATATTTCTACTCTGAGAAACAATGTACGTTCCCGTGCTTGGGGTGCTGCAATTGGTTGTAGTTATAAAGTTGAGCGGTGCTGCATTGTAAAG
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-----------gtaagtttcca----taaatttcgtgacagttcagtcacactttgttggtacg---gacttcacttataagacttggtatctgtcc-cagGTTATACTTCAACACTGAGGAACAATGTGCGTTCACGTGCTTGGGGTGCTGGGATTGGTTGTAGCTTTCGGATTGAACGTTGCTGCATTTTCAAG
upper sequence: GLYMA16G33300.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G464000_T02 (Zea mays), 3'ss of exon 5
ttgctggtttctcaactttgcagttactgatataatgatattgcttttaccattgaagctctgttcaaataatctaaagatattttttgtacatcttcagGCTATATTTCTACTCTGAGAAACAATGTACGTTCCCGTGCTTGGGGTGCTGCAATTGGTTGTAGTTATAAAGTTGAGCGGTGCTGCATTGTAAAG
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--gtaagtttccattctttttgtgaaagctcaatctgacatggttaagacatatga----ttgaataagtactcgtataatgtggtatttat---cccagGTTATACTTCAACATTGAGGAACAACGTACGCTCACGTGCTTGGGGTGCTGGGATTGGTTGTAGCTTCCGCATAGAACGCTGCTGCATAGTTAAG
upper sequence: GLYMA16G33300.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv07s0130g00270.t01 (Vitis vinifera), 3'ss of exon 5
----------ttgctggtttctcaactttgcagttactgatataatgatattgcttttaccattgaagctctgttcaaataatctaaagatattttttgtacatcttcagGCTATATTTCTACTCTGAGAAACAATGTACGTTCCCGTGCTTGGGGTGCTGCAATTGGTTGTAGTTATAAAGTTGAGCGGTGCTGCATTGTAAAG
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aagttgggttttattttttccttattattgcagttggggttattct-atgttgctcattgtacttgattcatgt----gtaacacgttaacttttcttgt-----tctagGCTACATTTCTACACTGAGAAACAATGTCCGATCCCGTGCTTGGGGGGCTGCAATTGGTTGTAGCTACCGTGTCGAACGGTGCTGCATTGTGAAGMapped 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|192298007|gb|FG993241.1|FG993241EST: GGCTGTACAAGAGTTGCGCACAACCATTCGAGTGCTACCTCCGCAAGATT GCTATATTTCTACTCTGAGAAACAATGTACGTTCCCGTGCTTGGGGTGCTG
genomic: GGCTGTACAAGAGTTGCGCACAACCATTCGAGTGCTACCTCCGCAAGATTgtatgtcctt ... acatcttcagGCTATATTTCTACTCTGAGAAACAATGTACGTTCCCGTGCTTGGGGTGCTG
EST:
gi|193490705|gb|FK457748.1|FK457748EST: ACAAGAGTTGCGCACAACCATTCGAGTGCTACCTCCGCAAGATT GCTATATTTCTACTCTGAGAAACAATGTACGTTCCCGTGCTTGGGGTGCTG
genomic: ACAAGAGTTGCGCACAACCATTCGAGTGCTACCTCCGCAAGATTgtatgtcctt ... acatcttcagGCTATATTTCTACTCTGAGAAACAATGTACGTTCCCGTGCTTGGGGTGCTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttaccattgaagctctgttcaaataatctaaagatattttttgtacatcttcagGCTATATTTCTACTCTGAGAAACAATGTACGTTCCCGTGCTTGGGGTGCTGCAATTGGTTGTAGTTATAAAGTTGAGCGGTGCTGCATTGTAAAG
atctaaa putative branch site (score: 3)
catcttc putative PPT
ttcaaataatctaaag 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgctggtttctcaactttgcagttactgatataatgatattgcttttaccattgaagctctgttcaaataatctaaagatattttttgtacatcttcagGCTATATTTCTACTCTGAGAAACAATGTACGTTCCCGTGCTTGGGGTGCTGCAATTGGTTGTAGTTATAAAGTTGAGCGGTGCTGCATTGTAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
-tgctggt
- - - - - - - -ctttgca
- - - - - - - - - - - gttactg