Sequence
atgc intronic sequence ATGC exonic sequencegtgacttttactcattctgtttgcagacaacttttcattttgatgagtttgccatatgaagttctcttagtgatagttgtactgtaaactatttctctgacagAGAAGTATGAACCTGTTCATGCTAAGTGGACTACAGAACGCTGTGCTGTTTGTAGATGGGTTGAAGACTGGGACTACAACAAAATTATCATTTGCAACAG
Basic information
species | Glycine max |
transcript | GLYMA04G41500.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G41500.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os01g46700.1 (Oryza sativa), 3'ss of exon 10
gtgacttttactcattctg---tttgcagacaacttttcattttgatgagtttgccatatgaagttctcttagtgatagttgtactgtaaactatttctctgacagAGAAGTATGAACCTGTTCATGCTAAGTGGACTACAGAACGCTGTGCTGTTTGTAGATGGGTTGAAGACTGGGACTACAACAAAATTATCATTTGCAACAG
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gtaactcaacttcaatttagatcttccaagttgcctgtagtattgaatgatccttctcacaagggaattggattgatggagttaaaatttatt-tacattttacagAACCATATGATACTGTAAATGTAAAATGGACAACAGAAAGATGTGCAGTCTGTAGATGGGTTGAAGACTGGGATTACAACAAAATTGTAATCTGTAACAG
upper sequence: GLYMA04G41500.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G170412_T01 (Zea mays), 3'ss of exon 10
gtgacttttactcattctgtttgcagacaacttttcattttgatgagtttgccatatgaagttctcttagtgatagttgtactgtaaactatttctctgacagAGAAGTATGAACCTGTTCATGCTAAGTGGACTACAGAACGCTGTGCTGTTTGTAGATGGGTTGAAGACTGGGACTACAACAAAATTATCATTTGCAACAG
|| ||||| | | || | | |||||| || | | | || | | | | || | || || | |||| | |||| ||||| ||||| ||| || ||||| |||||| | ||||| || ||||||||||||||||| ||||| |||||||||||| | ||||| || ||
gtataaagctttcattttaatcttagtagcttagttgttttgaagatacttctcccagcagattt----gaattcgtggagcttgaatttgtttcccatgcagACCCATATGATCCTGTAAATGTAAAATGGACGACAGAAAGATGTGCAGTCTGTAGATGGGTTGAAGATTGGGATTACAACAAAATTGTGATTTGTAATAG
upper sequence: GLYMA04G41500.1 (Glycine max), 3'ss of exon 11
lower sequence: AT4G27910.1 (Arabidopsis thaliana), 3'ss of exon 10
gtgacttttactcattctgtttgcagacaacttttcattttgatgagt-ttgccatatgaagt-tctcttagtgatagttgtactgtaaactatttct----ctgacagAGAAGTATGAACCTGTTCATGCTAAGTGGACTACAGAACGCTGTGCTGTTTGTAGATGGGTTGAAGACTGGGACTACAACAAAATTATCATTTGCAACAG
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-------------------gtagaaaaggaaatggaatcctgtaacatgttgcagtgttttgagtgtttttgtgatgcttttgttggcttttcctttcgttgttggcagAGACATATGAGCCGGTCAATGCGAAGTGGACAACAGAACGATGTGCAGTTTGCAGATGGGTTGAAGATTGGGACTACAACAAGATTATTATCTGCAACAG
upper sequence: GLYMA04G41500.1 (Glycine max), 3'ss of exon 11
lower sequence: AT5G53430.1 (Arabidopsis thaliana), 3'ss of exon 10
gtgacttttactcattctgtttgcagacaacttttcattttgatgagtttgccatatgaagttctcttagtgatagttgtactgtaaactatttctctgacagAGAAGTATGAACCTGTTCATGCTAAGTGGACTACAGAACGCTGTGCTGTTTGTAGATGGGTTGAAGACTGGGACTACAACAAAATTATCATTTGCAACAG
|| | |||| | | ||| ||||| || | | ||| | | || | | | | || | | ||| || |||| |||||||| || || | | || ||||| || || || ||||| ||||| |||||||| ||||| |||||||||||||| || || || ||||||||
---gtattaagcaattcggatctcag--aactt---atccaaaactttctgctgcgttttgcgctgcttatactgga-gtgttttttttcattat--tggcagAAAAGTATGAGCCGGTCAACGTGAAATGGACAACCGAGCGATGTGCAGTTTGCAGATGGGTGGAAGATTGGGACTACAACAAGATCATTATCTGCAACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgccatatgaagttctcttagtgatagttgtactgtaaactatttctctgacagAGAAGTATGAACCTGTTCATGCTAAGTGGACTACAGAACGCTGTGCTGTTTGTAGATGGGTTGAAGACTGGGACTACAACAAAATTATCATTTGCAACAG
ctatttctct CT-rich tract
taaactattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgacttttactcattctgtttgcagacaacttttcattttgatgagtttgccatatgaagttctcttagtgatagttgtactgtaaactatttctctgacagAGAAGTATGAACCTGTTCATGCTAAGTGGACTACAGAACGCTGTGCTGTTTGTAGATGGGTTGAAGACTGGGACTACAACAAAATTATCATTTGCAACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA