Sequence
atgc intronic sequence ATGC exonic sequencegtaattgttgccattattggtatcaatttacagtattgttatatttggtttcatttgtttgcattttgatttaagcatattgcagtcatggcttactaaattgcaatagctttgtccgttgtatatgatagGTGGTCAAGCGAAAACCCTTATGTTTGTACAGCTTAATCCTGATGTTGCTTCATATTCTGAAACTGTAAGCACCTTGAAGTTTGCTGAACGGGTTTCTGG
Basic information
species | Glycine max |
transcript | GLYMA05G37800.1 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G37800.1 (Glycine max), 3'ss of exon 17
lower sequence: LOC_Os05g44560.1 (Oryza sativa), 3'ss of exon 17
gtaattgttgccattattggtatcaatttacagtattgttatatttggtttcatttgtttgcattttgatttaagcata-ttgcagtcatggcttactaaattgcaatagctttgtccgttgtatatgatagGTGGTCAAGCGAAAACCCTTATGTTTGTACAGCTTAATCCTGATGTTGCTTCATATTCTGAAACTGTAAGCACCTTGAAGTTTGCTGAACGGGTTTCTGG
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----------------------------------------gtaatcaatt--atttagttgaaaaatcatgcatgtggagttagatttatggtttttgtaactataat--cttataaaataatctcttgcagGTGGACAAGCAAAGACACTAATGTTTGTTCAAATAAATCCTGATGTTGAGTCATATTCAGAGACTATAAGCACTCTAAAGTTTGCTGAAAGGGTTTCTGG
upper sequence: GLYMA05G37800.1 (Glycine max), 3'ss of exon 17
lower sequence: GRMZM2G173700_T01 (Zea mays), 3'ss of exon 14
gtaattgttgccattattggtatcaatttacagtattgttatatttggtttcatttgtttgc-attttgat-ttaagcatattgcagtcatggcttactaaattgcaatagctttgtccgttgtatatgatagGTGGTCAAGCGAAAACCCTTATGTTTGTACAGCTTAATCCTGATGTTGCTTCATATTCTGAAACTGTAAGCACCTTGAAGTTTGCTGAACGGGTTTCTGG
|| | | |||| ||| | | | ||| |||| ||||| || | ||| | || || || |||| | | | | |||||| ||||| ||||| || |||||||| ||| | ||||||||||||| |||||||| |||||| |||| || || |||||||||||| |||| |||||
----------------------------------------gtaatcaaat--atttatttactacctagatgttaaatatattaatgtt-tatcttccaaattttatgtaccttt-----tattttcttccagGTGGACAAGCAAAAACTCTAATGTTTGTTCAGATAAATCCTGATGTTGAGTCATATTCAGAAACTATAAGTACTTTAAAGTTTGCTGAAAGGGTGTCTGG
upper sequence: GLYMA05G37800.1 (Glycine max), 3'ss of exon 17
lower sequence: GRMZM5G845682_T02 (Zea mays), 3'ss of exon 4
gtaattgttgccattattggtatcaatttacagtattgttatatttggtttcatttgtttgcattttgatttaagcatattgcagtca-tggcttactaaattgcaatagctttgtccgttgtatatgatagGTGGTCAAGCGAAAACCCTTATGTTTGTACAGCTTAATCCTGATGTTGCTTCATATTCTGAAACTGTAAGCACCTTGAAGTTTGCTGAACGGGTTTCTGG
||| | ||||| || | | | | |||| | ||| || | | ||| | ||| | || |||| | | | | ||||| ||||| ||||| || ||||| || || | ||||||||||||| |||||||| |||||| ||||||| || |||||||||||| |||| |||||
--------------------------------gtaatcaagtatttatttactaccagtaa-actagatcttaaatagatttatgtgaatattttaaatatttgtactaccttttgctttcttcca-----gGTGGACAAGCAAAAACTCTAATGTTCGTTCAAATAAATCCTGATGTTGAGTCATATTCAGAAACTATAAGCACTTTAAAGTTTGCTGAAAGGGTGTCTGG
upper sequence: GLYMA05G37800.1 (Glycine max), 3'ss of exon 17
lower sequence: GRMZM2G323622_T01 (Zea mays), 3'ss of exon 8
gtaattgttgccattattggtatcaatttacagt-attgttatatttggtttcatttgtttgcattttgatttaagcatattgcagtcatggcttactaaattgcaatagctttgtccgttgtatatgatagGTGGTCAAGCGAAAACCCTTATGTTTGTACAGCTTAATCCTGATGTTGCTTCATATTCTGAAACTGTAAGCACCTTGAAGTTTGCTGAACGGGTTTCTGG
|| || ||| || | | | | | | | || |||| || | | || |||| | | || ||| | | | | | | || ||| || ||||| || || | |||||||| || ||||||| ||| || |||||||| ||||| ||||||| ||||||||||||||| ||||||||||
----------------------gtaacatatagttgttcctcaaaaaagggacgtcaaatag----ttagtttatatatgcagacat-attactta-tgagttatgataattctcttctgttttcttg-cagGCGGACAAGCAAAGACATTGATGTTTGTTCAAATTAATCCGGATACTGAATCATATTCAGAAACAATAAGCACTTTGAAGTTTGCTGAAAGGGTTTCTGG
upper sequence: GLYMA05G37800.1 (Glycine max), 3'ss of exon 17
lower sequence: GRMZM2G124883_T01 (Zea mays), 3'ss of exon 8
gtaattgttgccattattggtatcaatttacagtattgttatatttggtttcatttgtttgcattttgatttaagcatat-tgcagtcatggcttactaaattgcaatagctttgtccgttgtatatgatagGTGGTCAAGCGAAAACCCTTATGTTTGTACAGCTTAATCCTGATGTTGCTTCATATTCTGAAACTGTAAGCACCTTGAAGTTTGCTGAACGGGTTTCTGG
||| |||| | ||| ||| | | | | | | | || |||| ||| | ||| ||| | | | ||| | ||| ||| | ||| |||||| ||||| || || || |||||||| || ||||||| ||| || |||||||| ||||| ||||||| ||||||||||||||| ||||||||||
-------------------gtaacaat--aacatatagttgttcctcggaaaaaaggggcaccaaatagttggtttatatatgcggacata--ttattta-tgataat--tctcgtctgtttt-catg-cagGTGGGCAAGCAAAGACACTGATGTTTGTTCAAATTAATCCGGATACTGGATCATATTCAGAAACAATAAGCACTTTGAAGTTTGCTGAAAGGGTTTCTGG
upper sequence: GLYMA05G37800.1 (Glycine max), 3'ss of exon 17
lower sequence: AT5G41310.1 (Arabidopsis thaliana), 3'ss of exon 15
gtaattgttgccattattggtatcaatttacagtattgttatatttggtttcatttgtttgcattttgatttaagcatattgcagtcatggcttactaaattgcaatagctttgtccgttgtatatgatagGTGGTCAAGCGAAAACCCTTATGTTTGTACAGCTTAATCCTGATGTTGCTTCATATTCTGAAACTGTAAGCACCTTGAAGTTTGCTGAACGGGTTTCTGG
||| | | | || | |||| | || || || | ||||| | |||| || || | | || || || | |||| || ||||||||||| ||||||||||| || |||||||||||| | ||||||| |||| |||||||| || ||||| ||||| ||| | ||||||||
--------------------------------gtactataagata-gacttcaataaaaaaaatattacttga----tattg------ttgcttgcttctttac-------tcctctttttaattttttagGAGGGCAAGCGAAAACTCTTATGTTTGTTCAAATTAATCCTGATGAAGATTCATATGCTGAGACTGTAAGTACTTTGAAATTTGCGGAAAGAGTTTCTGG
upper sequence: GLYMA05G37800.1 (Glycine max), 3'ss of exon 17
lower sequence: Vv02s0025g03480.t01 (Vitis vinifera), 3'ss of exon 18
--gtaattgttgccattattggtatcaatttacagtattgttatatttggtttcatttgtttgcattttga-tttaagcatattgcagtcatggcttactaaattgcaatagctt-------tgtccgttgtatatgatagGTGGTCAAGCGAAAACCCTTATGTTTGTACAGCTTAATCCTGATGTTGCTTCATATTCTGAAACTGTAAGCACCTTGAAGTTTGCTGAACGGGTTTCTGG
| | | | | || | || | | | | |||| | || ||| || ||| | | | | || | || || || | | || | | | || | ||||| ||||||||||| |||||||||||||||||||||||||||||||| | ||| || || |||||| |||| |||||||||||||| || | || |||||
gtacatatccttctggtttttgagtcttgtggttgaaccataccgtttgtcagtgtgctttaagattgggaatttgactttgtagttgttaacattttcttgcctgggcttgtttgaccgtttctttttcctactttatagGAGGTCAAGCGAAGACCCTTATGTTTGTACAGCTTAATCCTGATGTGGATTCCTACTCCGAAACTATAAGTACCTTGAAGTTTGCCGAGAGAGTCTCTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atattgcagtcatggcttactaaattgcaatagctttgtccgttgtatatgatagGTGGTCAAGCGAAAACCCTTATGTTTGTACAGCTTAATCCTGATGTTGCTTCATATTCTGAAACTGTAAGCACCTTGAAGTTTGCTGAACGGGTTTCTGG
tactaaa putative branch site (score: 1)
ttactaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattgttgccattattggtatcaatttacagtattgttatatttggtttcatttgtttgcattttgatttaagcatattgcagtcatggcttactaaattgcaatagctttgtccgttgtatatgatagGTGGTCAAGCGAAAACCCTTATGTTTGTACAGCTTAATCCTGATGTTGCTTCATATTCTGAAACTGTAAGCACCTTGAAGTTTGCTGAACGGGTTTCTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG