Sequence
atgc intronic sequence ATGC exonic sequencegtaatgcttgaagcctctatcaagcttagtgagaggtaaattttttaggttacgtggtgtgtttaataaactgggtatttcttgcagAATCTTGAAATAAAGAAAATCAATGATGAAAAAAAAGCATCGATGGCAGCTCAGTTTGCAGCTGAAGCCACTCTTCGAAGGGTCCATGCTGCTCAGAAGG
Basic information
species | Glycine max |
transcript | GLYMA05G34560.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G34560.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G14840.2 (Arabidopsis thaliana), 3'ss of exon 3
gtaatgcttgaagcctctatcaagcttagtgagaggtaaattttttaggttacgtggtgtgtttaataaactgggtatttcttgcagAATCTTGAAATAAAGAAAATCAATGATGAAAAAAAAGCATCGATGGCAGCTCAGTTTGCAGCTGAAGCCACTCTTCGAAGGGTCCATGCTGCTCAGAAGG
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gta-tgcttctaatatctcctttgttctttgatcgcttatttatattgattc-----tatatataatgatgttgtatgttgtcacagAACCTTGAAATCAAGAAGATAAATGAAGAAAAGAAGGCTTCCATGGCAGCTCAGTTTGCAGCAGAAGCTTCTCTTCGTAGGGTTCATGCTGCTCAAAAGG
upper sequence: GLYMA05G34560.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G24764.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaatgcttga-agcctctatcaagcttagtgagaggtaaattttttaggttacgtggtgtgtttaataaactgggtatttcttgcagAATCTTGAAATAAAGAAAATCAATGATGAAAAAAAAGCATCGATGGCAGCTCAGTTTGCAGCTGAAGCCACTCTTCGAAGGGTCCATGCTGCTCAGAAGG
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gtattgttcgataatctttccttggttcgatgatgttcacctttcgtttcttaagcttatagacatatgatatcaaccttgct-gcagAATCTAGAAATCAAGAAAATCAATGAGGAAAAGAAAGCATCAATGGCTGCTCAGTTTGCTGCTGAAGCCACTTTAAGAAGAGTCCATGCTGCTCAAAAGG
upper sequence: GLYMA05G34560.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G68060.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaatgcttgaagcctctatcaagcttagtgagaggtaaattttttaggttacgtggtgtgtttaataaactgggtatttcttgcagAATCTTGAAATAAAGAAAATCAATGATGAAAAAAAAGCATCGATGGCAGCTCAGTTTGCAGCTGAAGCCACTCTTCGAAGGGTCCATGCTGCTCAGAAGG
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gtatgtatcaaaatctccctc---cttac---gatcatgatttggctggatatctga------ttatgaactatg------ttgcagAATCTAGAAATCAAGAAGATCAATGAGGAGAAGAAGGCTTCCATGGCTGCTCAGTTTGCTGCTGAAGCTACCTTAAGAAGGGTCCATGCTGCTCAAAAGG
upper sequence: GLYMA05G34560.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G01750.2 (Arabidopsis thaliana), 3'ss of exon 4
gtaatgcttgaagcctctatcaa--gcttagtgagaggtaaattttttaggttacgtgg----tgtgtttaataaactgggtatttcttgcagAATCTTGAAATAAAGAAAATCAATGATGAAAAAAAAGCATCGATGGCAGCTCAGTTTGCAGCTGAAGCCACTCTTCGAAGGGTCCATGCTGCTCAGAAGG
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gta-tgtttgcaatgtttctcagttgcttttcattttccaatctcttttatttttctggattctgtatttgatgatatcgcatcttgtcacagAACCTTGAAATCAAGAAAATAAACGAAGAAAAAAGGGCTTCAATGGCAGCTCAATTTGCTGCAGAAGCCACTCTTCGAAGGGTTCATGCTGCTCAAAAGG
upper sequence: GLYMA05G34560.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv01s0011g05790.t01 (Vitis vinifera), 3'ss of exon 3
gtaatgcttgaagcctctatcaagcttagtgagaggtaaattttttaggttacgtggtgtgtttaataaactgggtatttcttgcagAATCTTGAAATAAAGAAAATCAATGATGAAAAAAAAGCATCGATGGCAGCTCAGTTTGCAGCTGAAGCCACTCTTCGAAGGGTCCATGCTGCTCAGAAGG
||| ||| |||| || || || || | | | || | | | || || || ||| | | ||| ||||||||||| || || |||||||||||||||||||| || || || ||||| ||||| |||||||| |||||||||||| ||||||| |||||||| |||||||
gtattgcatgaaacc-cttccatttttctttataagttttgtgtgtgtgtgttttgcagt-tttgtcctaacaattgttttttgcagAATCTCGAGATCAAGAAAATCAATGATGAAAAGAAGGCCTCCATGGCTGCTCAATTTGCAGCAGAAGCCACTCTTAGAAGGGTTCATGCTGCGCAGAAGG
upper sequence: GLYMA05G34560.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S136_188V6.1 (Physcomitrella patens), 3'ss of exon 3
-------gtaatgcttgaagcctctatcaagc-ttagtgagaggtaaattttttag--gttacgtggtgtgtt--taataaactgggtat-ttcttgcagAATCTTGAAATAAAGAAAATCAATGATGAAAAAAAAGCATCGATGGCAGCTCAGTTTGCAGCTGAAGCCACTCTTCGAAGGGTCCATGCTGCTCAGAAGG
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gattctcgcattttttgtcttatgtggacgtcgtttctttgtgctaaaattttaagttgtttctttgttacttatcagtatttggggggtgtttttgcagAACCTTGAATTGAAGAAGCTCAATGACGAGAAGAAAGCAGCTCTGGCCGCCCAGTTTGCAGCGGAGGCAACTCTGCGAAGGGTGCATGCAGCTCAGAAAGMapped 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|209727056|gb|BW680336.1|BW680336EST: CAAGGGTTGAGGGGAAGCTGAAGTTAACAGAATCTCTTCTAGAAAGCAAA AATCTTGAAATAAAGAAAATCAATGATGNNNNNNNNGCATCGATGGCAGCT
genomic: CAAGGGTTGAGGGGAAGCTGAAATTAACAGAATCTCTTCTAGAAAGCAAAgtaatgcttg ... tttcttgcagAATCTTGAAATAAAGAAAATCAATGATGAAAAAAAAGCATCGATGGCAGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaggtaaattttttaggttacgtggtgtgtttaataaactgggtatttcttgcagAATCTTGAAATAAAGAAAATCAATGATGAAAAAAAAGCATCGATGGCAGCTCAGTTTGCAGCTGAAGCCACTCTTCGAAGGGTCCATGCTGCTCAGAAGG
gtttaat putative branch site (score: 4)
tatttctt putative PPT
aaattttttaggtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgcttgaagcctctatcaagcttagtgagaggtaaattttttaggttacgtggtgtgtttaataaactgggtatttcttgcagAATCTTGAAATAAAGAAAATCAATGATGAAAAAAAAGCATCGATGGCAGCTCAGTTTGCAGCTGAAGCCACTCTTCGAAGGGTCCATGCTGCTCAGAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT