Sequence
atgc intronic sequence ATGC exonic sequence...gccatgggcattgctgtttcattcatggggctgtccttttgcgtcttcttcgggtgaacctttttggatttccctaacattatggttatttgtcttgcagAGATTAGCAATCAAATGTTGGAACTGTATGAGCAAAACAGAGTGCCTCCACCTCAAGGGAGTGAAATGGAAGTTAACGCCAGTGGTGGACTAAACCATAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv00s0125g00270.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os12g30020.2 (Oryza sativa), 3'ss of exon 6
gccatgggcatt-gctgtttcattcatggggctgtccttttgcgtcttcttcgggtgaacctttttggatttccctaacat-tatggttatttgtcttgcagAGATTAGCAATCAAATGTTGGAACTGTATGAGCAAAACAG---------AGTGCCTCCACCTCAAGGGAGTGAAATGGAAGTTAACGCCAGTGGTGGACTAAACCATAG
|| ||| ||| | || | | | ||| | | ||| || || | || ||| | | ||||||| ||||||||||||||||||| ||||||||||||||| | | | || | || || | |||| |||| | | | | ||| |
--tatacttatttaactttttgataatacaatttgatcatgacacattcctttctgggttcttgttaaatcagataataatgcatgtctcccttgattgcagAAGTTAGCAATCAAATGTTGGAGCTGTATGAGCAAAACTGTGCAGCACAGGCACAACCGTCCCATGGAAATGAAGCTGAAGGGAGCTCTGCTAGTGTTCC---------
upper sequence: Vv00s0125g00270.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AC233979.1_FGT009 (Zea mays), 3'ss of exon 5
gccatgggcattgc--tgtttcattcatggggctgtccttttgcgtcttcttcgggtgaacctttttggatttccctaacattat-ggttatttgtcttgcagAGATTAGCAATCAAATGTTGGAACTGTATGAGCAAAACAGAGT------GCCTCCACCTCAAGGGAGTGAAATGGAAGTTAACGCCAGTGGTGGACTAAACCATAG
| | ||| | |||| || |||| | || | | || || || | | ||| | || | ||||| | ||| ||||| ||||||| || |||||||||||||||||||||||| | || || ||| | ||||| | ||| | |||| | | ||| ||
-tcttcacttttgacatatttctgctttgaaagatcatttttatgaattataccatcaaagctacatgcttatgccttatgtttttggttactc--ctttcagAGGTTAGCAACCAGATGTTGGAACTGTATGAGCAAAACCGTGTTCAACCACCACCATCACAAGGCAATGATACTGAAGGCAGTTCTGCAAGTGTTGCGAA------
upper sequence: Vv00s0125g00270.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA20G02860.1 (Glycine max), 3'ss of exon 6
---gccatgggcattgctgtttcattcatggggctgtccttttgcgtcttcttcgggtgaacctttttggatttccctaacattatggttatttg-tcttgcagAGATTAGCAATCAAATGTTGGAACTGTATGAGCAAAACAGAGTGCCTCCACCTCAAGGGAGTGAAATGGAAGTTAACGCCAGTGGTGGACTAAACCATAG
|| | || | || | ||||| ||||||||||| || | | || || | | ||| | || ||| ||||| |||||||||| |||||||||||||||||||||| |||||||| || ||| | || ||| | || || |||||| | |||| | || | || | | |
cagtttattgctatgagtagtttaacaatggg-ctgtccttttgtgtgtctgt---atgcttctgtatatccttctcagttcttgtgggtattttctcttgcagAGGTTAGCAATCAAATGTTGGAACTCTATGAGCAGAATAGACTTCCACCAGCACAGGGAAGTGAAGTAGAAGGAAGTGCTGGAGGAACAAGAGCTGCTTC
upper sequence: Vv00s0125g00270.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA20G02880.1 (Glycine max), 3'ss of exon 5
---gccatgggcattgctgtttcattcatggggctgtccttttgcgtcttcttcgggtgaacctttttggatttccctaacattatggttatttg-tcttgcagAGATTAGCAATCAAATGTTGGAACTGTATGAGCAAAACAGAGTGCCTCCACCTCAAGGGAGTGAAATGGAAGTTAACGCCAGTGGTGGACTAAACCATAG
|| | || | || | ||||| ||||||||||| || | | || || | | ||| | || ||| ||||| |||||||||| || ||||||||||||||||||| |||||||| | ||| | || ||| | || || |||||| | |||| | || || || | | |
cagtttattgctatgagtagtttaacaatggg-ctgtccttttgtgtgtctgt---atgcttctgtatatccttctcagttcttgtgggtattttctcttgcagAGGTTTGCAATCAAATGTTGGAACTCTATGAGCAGAGTAGACTTCCACCAGCACAGGGAAGTGAAGTAGAAGGAAGTGCTAGAGGAACAAGAGCTGCTTC
upper sequence: Vv00s0125g00270.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA07G35010.1 (Glycine max), 3'ss of exon 5
---gccatgggcattgctgtttcattcatggggctgtccttttgcgtcttcttcgggtgaacctttttggatttccctaacattatggttatttg-tcttgcagAGATTAGCAATCAAATGTTGGAACTGTATGAGCAAAACAGAGTGCCTCCACCTCAAGGGAGTGAAATGGAAGTTAACGCCAGTGGTGGACTAAACCATAG
|| | || | || | ||||| |||||||||| || | | || || | | ||| | || ||| ||||| ||||||||| |||||||||||||||||||||| || ||||| || ||| | || ||| | || || |||||| | |||| | || | || | | |
cagtttattgctatgagtagtttaacaatggg-ttgtccttttgtgtgtctgt---atgcttctgtatatccttctcagttcttgtgggtattttctcttgcagAAGTTAGCAATCAAATGTTGGAACTCTACGAGCAGAATAGACTTCCACCAGCACAGGGAAGTGAAGTAGAAGGAAGTGCTGGAGGAACAAGAGCTGCTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcttcgggtgaacctttttggatttccctaacattatggttatttgtcttgcagAGATTAGCAATCAAATGTTGGAACTGTATGAGCAAAACAGAGTGCCTCCACCTCAAGGGAGTGAAATGGAAGTTAACGCCAGTGGTGGACTAAACCATAG
ccctaac putative branch site (score: 2)
tttgtctt putative PPT
taacattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gccatgggcattgctgtttcattcatggggctgtccttttgcgtcttcttcgggtgaacctttttggatttccctaacattatggttatttgtcttgcagAGATTAGCAATCAAATGTTGGAACTGTATGAGCAAAACAGAGTGCCTCCACCTCAAGGGAGTGAAATGGAAGTTAACGCCAGTGGTGGACTAAACCATAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- catgggc
- - - - - -tgctgtt
- - - - - - - - - -cattcat
- - - - - - - - - - - - - -gggctgt
- - - - - - - - - - - - - - - - - ccttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccctaac