Sequence
atgc intronic sequence ATGC exonic sequence...tacctgatattccattgtttgtttcagaactgtcttattagaagttttgccaactataattaatgataatatgatacttaacaaataacaacacctgcagGCAGGATAATCCCAGAGAGTGTGATCTACAGTTATGGAACTGTTCTTCTGGATCTTCTAAGTGGCAAGCATATTCCTCCAAGCCAT
Basic information
species | Glycine max |
transcript | GLYMA05G06140.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G06140.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os10g42110.1 (Oryza sativa), 3'ss of exon 5
--------------------------------------------------------------------tacctgatattccattgtttgtttcagaactgtcttattagaagttttgccaactataattaat-gataatat--gatacttaacaaataacaac-acctg-cagGCAGGATAATCCCAGAGAGTGTGATCTACAGTTATGGAACTGTTCTTCTGGATCTTCTAAGTGGCAAGCATATTCCTCCAAGCCAT
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gtaggaatttacacatgatccttattaccgcactcatgggcaccttactctattgatgttttccagcaaaaatgaaacatgtcaacttatttcaagcttgctatatatttactcccaagtactaacattgtttgactgcaccgaacaatttgtgcatgacacttgtatgacagGCAGAGTCATCGCCGAGAGTGTGATATATAGCTATGGAACAGTTCTTTTGGATCTTTTGAGTGGGAAGCACATACCTCCTAGCCAT
upper sequence: GLYMA05G06140.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G46570.1 (Arabidopsis thaliana), 3'ss of exon 4
tacctgatattccattgtttgtttcagaactgtcttattagaagttttgccaactataattaatgataatatgatacttaacaaataacaacacctgcagGCAGGATAATCCCAGAGAGTGTGATCTACAGTTATGGAACTGTTCTTCTGGATCTTCTAAGTGGCAAGCATATTCCTCCAAGCCAT
| ||| || | | | || || | |||| |||| | |||| ||| | || | | || | | | |||||| || | || || || |||||||| | ||||||||||||| ||||| | |||||| |||| ||||| || ||||| || ||||||
--------gtaaaattcttgatcttgtga--atcgtagtcgaagacaaaccaatt--cattattga--agattaaagttctctggttttt-cttttgcagGTAGAGTCATTCCTGAAAGTGTGATATTCAGTTATGGAACTATTCTTTTAGATCTTTTAAGCGGCAAACACATTCCACCTAGCCAT
upper sequence: GLYMA05G06140.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv02s0012g01140.t01 (Vitis vinifera), 3'ss of exon 5
tacctgatattccattgtttgtttcagaactgtcttattagaagttttgccaactataattaatgataatatgatacttaa-caaataacaacacc-tgcagGCAGGATAATCCCAGAGAGTGTGATCTACAGTTATGGAACTGTTCTTCTGGATCTTCTAAGTGGCAAGCATATTCCTCCAAGCCAT
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--gatcctgtcccattgatatgatatgaaatgtatttgatttgatgttgacatttgagattccatatgaaagcaaatttgatcaggtcatgaaactgtgcagGGAGGGTCATTCCAGAGAGTGTGATATACAGTTATGGAACAGTTCTATTGGACCTGTTGAGTGGGAAGCATATCCCTCCAAGTCAT
upper sequence: GLYMA05G06140.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ20301 (Selaginella moellendorffii), 3'ss of exon 4
tacctgatattccattgtttgtttcagaactgtcttattagaagttttgccaactataattaatgataatatgatacttaacaaataacaacacctgcagGCAGGATAATCCCAGAGAGTGTGATCTACAGTTATGGAACTGTTCTTCTGGATCTTCTAAGTGGCAAGCATATTCCTCCAAGCCAT
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-----------------------gtaaagctctcgtgcc------tttgtcacct-tgcgtattcaaagctttgttttc------------tgtttgcagGTAGAGTAACACCCGAGAGTGTTATTTATAGTTATGGTACTGTTCTCTTGGATCTTCTTAGCGGGAAGCACATTCCTCCAAGCCAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgccaactataattaatgataatatgatacttaacaaataacaacacctgcagGCAGGATAATCCCAGAGAGTGTGATCTACAGTTATGGAACTGTTCTTCTGGATCTTCTAAGTGGCAAGCATATTCCTCCAAGCCAT
aaataac putative branch site (score: 2)
aactataattaatgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tacctgatattccattgtttgtttcagaactgtcttattagaagttttgccaactataattaatgataatatgatacttaacaaataacaacacctgcagGCAGGATAATCCCAGAGAGTGTGATCTACAGTTATGGAACTGTTCTTCTGGATCTTCTAAGTGGCAAGCATATTCCTCCAAGCCAT
- cctgata
- - - - - - - -tgtttgt
- - - - - - - - - - - - - - -ctgtctt