Sequence
atgc intronic sequence ATGC exonic sequence...gtatttcactagtgggcacttgtcgatggtaccatatcttgaatatcgttctgtgatactgttaaaattaatcatcttcaagttttcaaataatgtgtagGTTGGAAGCCAATTTAACTGGCGTGTTGCATTTTGGGTTGAGGCAATTTTGATGCTTCCTTTTCCCATTTTGGGTTTTGTAATAAAGCCTTTGCAATTGA
Basic information
species | Glycine max |
transcript | GLYMA09G33680.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G33680.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os04g44430.1 (Oryza sativa), 3'ss of exon 5
------------------------------gtatttcactagtgggcacttgtcgatggtaccatatcttgaatatcgttctgtgatactgttaaaattaatcatcttcaagttttcaaataatgtgtagGTTGGAAGCCAATTTAACTGGCGTGTTGCATTTTGGGTTGAGGCAATTTTGATGCTTCCTTTTCCCATTTTGGGTTTTGTAATAAAGCCTTTGCAATTGA
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gtaagtcttatgctacacatgatctttcttctatttttttagttgtcaagt-taagcagttttgagtaacaattg-catttt-cgatattaacttacctcatgccctcttctattcaaaatcacat-cagGTTGGAAATAGTCTGCACTGGCGTGCTGCTTTCTGGGGAGAGTCGATTTTGATGCTTCCTTTTGTTATTCTGGGCTTTGTAATAAAGCCATTAGAGCTCA
upper sequence: GLYMA09G33680.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv07s0205g00120.t01 (Vitis vinifera), 3'ss of exon 6
-gtatttcactagtgggcacttgtcgatggtaccatatcttgaatatcgttctgtgatac-tgttaaaattaatcatcttcaagttttcaaataatgtgtagGTTGGAAGCCAATTTAACTGGCGTGTTGCATTTTGGGTTGAGGCAATTTTGATGCTTCCTTTTCCCATTTTGGGTTTTGTAATAAAGCCTTTGCAATTGA
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tgtcgcaaacatgttggctttcattcttggttgaat-tggtgaaatcctctaaatgctatgtgttttctgtgaaaatgtatttcttgtgcaacccttt-tagGTTGGAGAGCATTTTAACTGGCGATATGCATTCTGGGGTGAAGCAATTTTGATGCTTCCATTTGCTGTTCTGGGTTTTGTTATGAAACCTTTGCAGTTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcgttctgtgatactgttaaaattaatcatcttcaagttttcaaataatgtgtagGTTGGAAGCCAATTTAACTGGCGTGTTGCATTTTGGGTTGAGGCAATTTTGATGCTTCCTTTTCCCATTTTGGGTTTTGTAATAAAGCCTTTGCAATTGA
aattaat putative branch site (score: 3)
atactgttaaaattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttcactagtgggcacttgtcgatggtaccatatcttgaatatcgttctgtgatactgttaaaattaatcatcttcaagttttcaaataatgtgtagGTTGGAAGCCAATTTAACTGGCGTGTTGCATTTTGGGTTGAGGCAATTTTGATGCTTCCTTTTCCCATTTTGGGTTTTGTAATAAAGCCTTTGCAATTGA
- - - - - - - - cacttgt
- - - - - - - - - - - - gatggta
- - - - - - - - - - - - - - - - - - - - - - - - - - - gatactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaattaa