Sequence
atgc intronic sequence ATGC exonic sequencegttgttacttactcttttgtaaaccatcctacttttcttatttttagcgattttttgttcttttgtgtcaaacttgaagaaatgatgaaatgaagtgataccagactgaatgtttcaccaactgttgtttttgatgtatcagGTTTCTTTTGAAGAACGATGGTCTCTTCCTTGGGAGTTCTTCTGCAATGAACTGTGTTGGAGCAGTAAGAGTAGCGCAAGCAATTGGCCCTGGTCACACA
Basic information
species | Glycine max |
transcript | GLYMA02G46950.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G46950.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os03g11660.1 (Oryza sativa), 3'ss of exon 5
gttgttacttactcttttgtaaaccatcctacttttcttatttttagcgattttttgttcttttgtgtca-aacttgaagaaatgatgaaatgaagtgataccagactgaatgtttcaccaactgttgtttttgatgtatcagGTTTCTTTTGAAGAACGATGGTCTCTTCCTTGGGAGTTCTTCTGCAATGAACTGTGTTGGAGCAGTAAGAGTAGCGCAAGCAATTGGCCCTGGTCACACA
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---------------------------------------gctcatagttgtttattctcttatcttaagataattcaaagaaaagctaaaaatgtatttcaattatct-aacctcaatctacttgtaaatattaac---ttagGTTCTTGTTGAAAAATGATGGGCTGTTCGTTGGGAGTTCTTCAGCCATGAATTGTGTTGGTGCTGTAAGAGTTGCTCAAGATTTAGGTCCAGGACATACA
upper sequence: GLYMA02G46950.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G55880.1 (Arabidopsis thaliana), 3'ss of exon 5
gttgttacttactcttttgtaaaccatcctacttttcttatttttagcgattttttgttcttttgtgtcaaacttgaagaaatgatgaaatgaagtgataccagactgaatgtttcaccaactgttgtttttgatgtatcagGTTTCTTTTGAAGAACGATGGTCTCTTCCTTGGGAGTTCTTCTGCAATGAACTGTGTTGGAGCAGTAAGAGTAGCGCAAGCAATTGGCCCTGGTCACACA
| || || |||| | | || | | |||| ||| | | || | || |||| | | | | | |||| | | || | || |||||||||| ||||||| ||||| ||||| |||| || || || || |||||||||||||| |||||||| || || || | |||| ||||||||||||
----------------------gtagtgctcattcctttatatgttttgacata--actgttttagagagtactgataaagatttcgtaa--aagttggatcttgatatctttctcacta--tattatgttc------ccagGTTTCTTCTGAAGAATGATGGGCTCTTTGTTGGAAGCTCCTCGGCTATGAACTGTGTTGGGGCAGTAAGGGTGGCTCAGACCCTTGGTCCTGGTCACACA
upper sequence: GLYMA02G46950.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv19s0015g00380.t01 (Vitis vinifera), 3'ss of exon 6
gttgttacttactcttttgtaaaccatcctacttttcttatttttagcgattttttgttcttttgtgtcaaacttgaagaaatgatgaaatgaagtgataccagactgaatgtttcaccaactgttgtttttgatgtatcagGTTTCTTTTGAAGAACGATGGTCTCTTCCTTGGGAGTTCTTCTGCAATGAACTGTGTTGGAGCAGTAAGAGTAGCGCAAGCAATTGGCCCTGGTCACACA
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---------------------------------------aattctaaaatttcttggccaccctgaagaacatctttaatagttgtatttttcttgagcattggctcttattctatgttcccatttaaacttt---catcagGTATCTTCTCAAGAATGATGGGCTATTTGTCGGGAGTTCTTCAGCCATGAACTGCGTTGGAGCTGTCAGAGTGGCACAGTCGATCGGCCCTGGTCACACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaatgaagtgataccagactgaatgtttcaccaactgttgtttttgatgtatcagGTTTCTTTTGAAGAACGATGGTCTCTTCCTTGGGAGTTCTTCTGCAATGAACTGTGTTGGAGCAGTAAGAGTAGCGCAAGCAATTGGCCCTGGTCACACA
ttttgat putative branch site (score: 4)
ttgttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgttacttactcttttgtaaaccatcctacttttcttatttttagcgattttttgttcttttgtgtcaaacttgaagaaatgatgaaatgaagtgataccagactgaatgtttcaccaactgttgtttttgatgtatcagGTTTCTTTTGAAGAACGATGGTCTCTTCCTTGGGAGTTCTTCTGCAATGAACTGTGTTGGAGCAGTAAGAGTAGCGCAAGCAATTGGCCCTGGTCACACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA