Sequence
atgc intronic sequence ATGC exonic sequence...aatgttgaaattttttgtatcgtttgtattatgtgatgaactcaaaattttcttgtgcatgcacttagtcaactaccaattttctgattatgttgggcagGATATTGTCATGTATGTAAATTCTCCAGGAGGGTCGGTTACAGCTG
Basic information
species | Glycine max |
transcript | GLYMA10G01550.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G01550.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G02560.1 (Arabidopsis thaliana), 3'ss of exon 4
aatgttgaaattttttgtatcgtttgtattatgtgatga-actcaaaattttcttgtgcatgcacttagtcaactaccaattttctgattatgttgggcagGATATTGTCATGTATGTAAATTCTCCAGGAGGGTCGGTTACAGCTG
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---gtcagatattgttgaat--tctaattcatgtcttgttacttga----ttcagatgttttgctttag---gattctgatatt-tgcttatgttgaacagGATATTGTCATGTATGTTAATTCTCCTGGTGGATCAGTTACAGCTG
upper sequence: GLYMA10G01550.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv07s0005g01530.t01 (Vitis vinifera), 3'ss of exon 4
-aatgttgaaattttttgtatcgtttgtat-tatgtgatgaactcaaaattttcttgtgcatgcacttagtcaactaccaattttctgattatgttgggcagGATATTGTCATGTATGTAAATTCTCCAGGAGGGTCGGTTACAGCTG
| | | | | || | | || | | ||||| || | || |||| | || || || | |||| || || |||||||||||||||||||| || ||||||||||| || ||||||||||
tttttctatagctctctgactttctattaaacagcttatgaaaattaactaccattatgcaagt-tttcaccattagatcatgtcttgat-attctgaacagGATATTGTCATGTATGTGAACTCTCCAGGAGGATCAGTTACAGCTG
upper sequence: GLYMA10G01550.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ24258 (Selaginella moellendorffii), 3'ss of exon 3
aatgttgaaattttttgtatcgtttgtattatgtgatgaactcaaaattttcttgtgcatgcacttagtcaactaccaattttctgattatgttgggcagGATATTGTCATGTATGTAAATTCTCCAGGAGGGTCGGTTACAGCTG
||| || || ||| | || || | || ||| ||||||||||||||||||||||||| || ||||| || ||||| ||||
----------------------------------------------gtttgtgggttataacatgtagaagatggttaaagctcgattgattttg--tagGATATTGTCATGTATGTAAATTCACCTGGAGGTTCCGTTACCGCTG
upper sequence: GLYMA10G01550.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ35520 (Selaginella moellendorffii), 3'ss of exon 3
aatgttgaaattttttgtatcgtttgtattatgtgatgaactcaaaattttcttgtgcatgcacttagtcaactaccaattttctgattatgttgggcagGATATTGTCATGTATGTAAATTCTCCAGGAGGGTCGGTTACAGCTG
||| || || ||| | || || |||| || | ||||||||||||||||||||||||| || ||||| || ||||| ||||
----------------------------------------------gtttgtgggttataacatgtagaagatggttaaagctc-gattggtttttgtagGATATTGTCATGTATGTAAATTCACCTGGAGGTTCCGTTACCGCTGMapped 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|31561455|gb|CD487293.1|CD487293EST: ACATCATAGTTGCTCAGCTCCTGTACCTCGACGCTGTTGATCCTAACAAG GATATTGTCATGTATGTAAATTCTCCAGGAGGGTCGGTTACAGCTG
genomic: ACATCATAGTTGCTCAGCTCCTGTACCTCGACGCTGTTGATCCTAACAAGgtctgttgtt ... tgttgggcagGATATTGTCATGTATGTAAATTCTCCAGGAGGGTCGGTTACAGCTG
EST:
gi|16279786|gb|BI943616.1|BI943616EST: ACATCATAGTTGCTCAGCTCCTGTACCTCGACGCTGTTGATCCTAACAAG GATATTGTCATGTATGTAAATTCTCCAGGAGGGTCGGTTACAGCTG
genomic: ACATCATAGTTGCTCAGCTCCTGTACCTCGACGCTGTTGATCCTAACAAGgtctgttgtt ... tgttgggcagGATATTGTCATGTATGTAAATTCTCCAGGAGGGTCGGTTACAGCTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattttcttgtgcatgcacttagtcaactaccaattttctgattatgttgggcagGATATTGTCATGTATGTAAATTCTCCAGGAGGGTCGGTTACAGCTG
ttctgat putative branch site (score: 3)
aattttctgattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatgttgaaattttttgtatcgtttgtattatgtgatgaactcaaaattttcttgtgcatgcacttagtcaactaccaattttctgattatgttgggcagGATATTGTCATGTATGTAAATTCTCCAGGAGGGTCGGTTACAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- tgttgaa
- - - - - - - - - - - - - - - -tgtgatg
- - - - - - - - - - - - - - - - - - - -actcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctaccaa