Sequence
atgc intronic sequence ATGC exonic sequence...tccattattgtatcacaattatataaatctcatgctaatgcactataatactctgtgcaatggctgttgtgaagcaaatttccgtctttgcattttgtagGATACAGAGATCATAGATCAAATTGACCGAGATGTAAAGCGCACTCATCCTGATATGCACTTTTTCTCTGGTGATTCCCAATTTGCAAAATCTAATCAG
Basic information
species | Glycine max |
transcript | GLYMA08G11760.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G11760.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g68010.1 (Oryza sativa), 3'ss of exon 4
--tccattat-tgtatcacaattatataaatctcatgctaatgcactataatactctgtgcaatggctgttgtgaagcaaatttc-cgtctttgcattttgtagGATACAGAGATCATAGATCAAATTGACCGAGATGTAAAGCGCACTCATCCTGATATGCACTTTTTCTCTGGTGATTCCCAATTTGCAAAATCTAATCAG
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gttctagtacgcgcaccctatgtttgtatttttcaccagcttgcatcattctg----atgttactactaatttatatcagctttgacatatatctttcgtgcagTATTCAGAGATTATCGAGCAAATTGACCGTGATGTGAAGCGCACTCACCCTGACATGCATTTTTTCTGTGGAGACTCATCTTTTGCAAAGTCCAATCAG
upper sequence: GLYMA08G11760.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g68010.5 (Oryza sativa), 3'ss of exon 2
--tccattat-tgtatcacaattatataaatctcatgctaatgcactataatactctgtgcaatggctgttgtgaagcaaatttc-cgtctttgcattttgtagGATACAGAGATCATAGATCAAATTGACCGAGATGTAAAGCGCACTCATCCTGATATGCACTTTTTCTCTGGTGATTCCCAATTTGCAAAATCTAATCAG-
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gttctagtacgcgcaccctatgtttgtatttttcaccagcttgcatcattctg----atgttactactaatttatatcagctttgacatatatctttcgtgcagTATTCAGAGATTATCGAGCAAATTGACCGTGATGTGAAGCGCACTCACCCTGACATGCATTTTTTCTGTGGAGACTCATCTTTTGCAAAGTCCAATCAGG
upper sequence: GLYMA08G11760.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G13730.2 (Arabidopsis thaliana), 3'ss of exon 4
----------tccattattgtatcacaattatataaatctcatgctaatgcactataatactctgtgcaatggctgttgtgaagcaaatttccgtctttgcattttgtagGATACAGAGATCATAGATCAAATTGACCGAGATGTAAAGCGCACTCATCCTGATATGCACTTTTTCTCTGGTGATTCCCAATTTGCAAAATCTAATCAG
| | | | | | | | ||| || | | |||| ||||| || | |||| | | ||| || | ||| | | | |||| ||||| | | || ||||| || || ||||| | ||| |||||||| |||||||||||||||||||| ||||| | |||||||||||||||||
aaaagatccttttctcttcctgttttagtaaagtaattccgtttttgttgca-tataaagct--gcaaaatgaccttcctga-------tttcaacttgatactgttcagGACACAGAAGTTTTGGAACAAATAGAACGCGATGTGATGCGTACTCATCCAGATATGCACTTTTTCTCTGGGGATTCAGCAGTTGCAAAATCTAATCAG
upper sequence: GLYMA08G11760.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv05s0029g01350.t01 (Vitis vinifera), 3'ss of exon 4
tccattattgtatcacaatta--tataaatctcatgctaatgcactataatactctgtgcaatggctgttgtgaagcaa--atttccgtctttgcattttgtagGATACAGAGATCATAGATCAAATTGACCGAGATGTAAAGCGCACTCATCCTGATATGCACTTTTTCTCTGGTGATTCCCAATTTGCAAAATCTAATCAG
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cccatttctttatgctattggactataaat-tggtattaggagatgata-tatggtcactgatgg-tgttttgaattatttattacaatttgaacatttt-tagGACACAGAGATCATAGAGCAAATTGACCGAGATGTCAAGCGCACTCATCCAGACATGAACTTCTTCTCTGGGGACACGCCATCTGCAAAAACAAATCAG
upper sequence: GLYMA08G11760.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ15182 (Selaginella moellendorffii), 3'ss of exon 4
tccattattgtatcacaattatataaatctcatgctaatgcactataatactctgtgcaatggctgttgtgaagcaaatttccgtctttgcattttgtagGATACAGAGATCATAGATCAAATTGACCGAGATGTAAAGCGCACTCATCCTGATATGCACTTTTTCTCTGGTGATTCCCAATTTGCAAAATCTAATCAG
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---------------------------------------gtttgtttacttcctttgcaatt-ccaatccaaatggaatttcc--------acttcgcagGACACGGAACTTTTCGAGCAGATTGATCGTGATGTTAAGCGAACTCATCCTGATATGCAGTTTTTCTGTGGTGATAACGAGCGCGCGCACGAAAACCAG
upper sequence: GLYMA08G11760.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ09811 (Selaginella moellendorffii), 3'ss of exon 4
tccattattgtatcacaattatataaatctcatgctaatgcactataatactctgtgcaatggctgttgtgaagcaaatttccgtctttgcattttgtagGATACAGAGATCATAGATCAAATTGACCGAGATGTAAAGCGCACTCATCCTGATATGCACTTTTTCTCTGGTGATTCCCAATTTGCAAAATCTAATCAG
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---------------------------------------------gtttgtttacttcctttgcatttccaatccaaata---gaatttccacttcgcagGACACGGAACTTTTCGAGCAGATTGATCGTGATGTTAAGCGAACTCATCCTGATATGCAGTTTTTCTGTGGTGATAACGAGCGCGCGCACGAAAACCAGMapped 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|254324135|gb|GR836260.1|GR836260EST: AGCATCCTTTGAGTCTGGGGAAGACCAGCGTATGGAATCAGTTCTTCCAG GATACAGAGATCATAGATCAA-TTGA
genomic: AGCATCCTTTGAGTCTGGGGAAGACCAGCGTATGGAATCAGTTCTTCCAGgtagaatgca ... cattttgtagGATACAGAGATCATAGATCAAATTGA
EST:
gi|8286250|gb|BE023809.1|BE023809EST: AGCATCCTTTGAGTCTGGGGAAGACCAGCGTATGGAATCAGTTCTTCCAG GATACAGAGATCATAGATCAAATTGACCGAGATGTAAAGCGCACTCATCCT
genomic: AGCATCCTTTGAGTCTGGGGAAGACCAGCGTATGGAATCAGTTCTTCCAGgtagaatgca ... cattttgtagGATACAGAGATCATAGATCAAATTGACCGAGATGTAAAGCGCACTCATCCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taatactctgtgcaatggctgttgtgaagcaaatttccgtctttgcattttgtagGATACAGAGATCATAGATCAAATTGACCGAGATGTAAAGCGCACTCATCCTGATATGCACTTTTTCTCTGGTGATTCCCAATTTGCAAAATCTAATCAG
tctttgc CT-rich tract
attttgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tccattattgtatcacaattatataaatctcatgctaatgcactataatactctgtgcaatggctgttgtgaagcaaatttccgtctttgcattttgtagGATACAGAGATCATAGATCAAATTGACCGAGATGTAAAGCGCACTCATCCTGATATGCACTTTTTCTCTGGTGATTCCCAATTTGCAAAATCTAATCAG
- - - - - - - - - - - - - - -tcatgct
- - - - - - - - - - - - - - - - - - aatgcac
- - - - - - - - - - - - - - - - - - - - - - - - - -tctgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggctgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaagcaaa