Sequence
atgc intronic sequence ATGC exonic sequence...tttgaccgaaaattgagggacctaaagcacattctacccctacttcattttatgctacattatgcatatggagtctaaagtttcagacatccttttacagGCCCGTGAGTTTGCAAATGAACTTCGTGCTAGTACTAAAGCATCTAGAAATCCAACTGTTTGGCTTGAAGGTTCCACAGGTTCTGGTCAGAATGTAAATG
Basic information
species | Glycine max |
transcript | GLYMA09G18840.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G18840.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os03g42750.1 (Oryza sativa), 3'ss of exon 13
-----tttgaccgaaaattgagggacctaaagcacattctacccctacttcattttatgctacattatgcatatggagtctaaagtttcagacatccttttacagGCCCGTGAGTTTGCAAATGAACTTCGTGCTAGTACTAAAGCATCTAGAAATCCAACTGTTTGGCTTGAAGGTTCCACAGGTTCTGGTCAGAATGTAAATG
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atgaatgtacacacactctatctggtccttgttaattgatttttttaacttgtccattccaacagc-taaacatgtaatct----ttccccataatttgatttagGCACGTGAATTCGCCAATGAACTTCGAGCAAGCACGAAAGCACCTAAAAATCCAGCTGTTTGGCTTGAAGGTTCTAATAGTGGCGGTCAGAATGGCAGTA
upper sequence: GLYMA09G18840.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G099056_T01 (Zea mays), 3'ss of exon 13
tttgaccgaaaattgagggac--ctaaagcacattctacc--cctacttcattttatgctacattatgcatatggagtctaaagtttcagacatccttt--tacagGCCCGTGAGTTTGCAAATGAACTTCGTGCTAGTACTAAAGCATCTAGAAATCCAACTGTTTGGCTTGAAGGTTCCACAGGTTCTGGTCAGAATGTAAATG
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---gtcctctgcttaatggacagttactttacaatccatttgccttctttatttgattttaaaggattcaca---attttgaagtttactgtttgatttggttcagGCACGCGAATTTGCCAATGAACTTCGTGCAAGTACAAAAGCACCGAAGAATCCTGCTGTTTGGCTTGAAGGTTCTGGCGGCTCTGGTCATAATGGAAGCA
upper sequence: GLYMA09G18840.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 13
-tttgaccgaaaattgagggacctaaagcacattctacccctacttcattttatgctacatt-atgcatatggagtctaaagtttcagacat-ccttttacagGCCCGTGAGTTTGCAAATGAACTTCGTGCTAGTACTAAAGCATCTAGAAATCCAACTGTTTGGCTTGAAGGTTCCACAGGTTCTGGTCAGAATGTAAATG
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acttgataggtccttaattaatt---actagatcttgtgccagtttagaaattcagtatgtttgaatatgtggtgtctgaaagttcttttatatcatctatagGCTCGTGAGTTTGCAAATGAGCTTCGTGCTAGTACCAAAGCATCAAGAAATCCAACTGTCTGGCTTGAAGCTTCTACAGGCTCTGGTCAAAATATGAACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cattttatgctacattatgcatatggagtctaaagtttcagacatccttttacagGCCCGTGAGTTTGCAAATGAACTTCGTGCTAGTACTAAAGCATCTAGAAATCCAACTGTTTGGCTTGAAGGTTCCACAGGTTCTGGTCAGAATGTAAATG
gtctaaa putative branch site (score: 3)
catcctttt putative PPT
tacattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttgaccgaaaattgagggacctaaagcacattctacccctacttcattttatgctacattatgcatatggagtctaaagtttcagacatccttttacagGCCCGTGAGTTTGCAAATGAACTTCGTGCTAGTACTAAAGCATCTAGAAATCCAACTGTTTGGCTTGAAGGTTCCACAGGTTCTGGTCAGAATGTAAATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - -tgaggga
- - - - - - - - - - - - - - - - -ctacccc
- - - - - - - - - - - - - - - - - - - - - - - - - - tgctaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcatat