Sequence
atgc intronic sequence ATGC exonic sequence...cagtttattgctatgagtagtttaacaatgggctgtccttttgtgtgtctgtatgcttctgtatatccttctcagttcttgtgggtattttctcttgcagAGGTTAGCAATCAAATGTTGGAACTCTATGAGCAGAATAGACTTCCACCAGCACAGGGAAGTGAAGTAGAAGGAAGTGCTGGAGGAACAAGAGCTGCTTC
Basic information
species | Glycine max |
transcript | GLYMA20G02860.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G02860.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os12g30020.2 (Oryza sativa), 3'ss of exon 6
----------cagtttattgctatgagtagtttaacaatgggctgtccttttgtgtgtctgtatgcttctgtatatccttctcagttcttgtgggtattttctcttgcagAGGTTAGCAATCAAATGTTGGAACTCTATGAGCAGAATAGACTTCCACCAGCACAGGGAAGTGAAGTAGAAGGAAGTGCTGGAGGAACAAGAGCTGCTTC
| || ||| || | | ||| | ||| | | ||| || || | | ||| | | | ||| | ||||||| |||||||||||||||||||| || |||||||| || | ||| ||||| | | | | | | || || | | || | |
tatacttatttaactttttgataata-caatttgatcatgacacattcctttctgggttcttgttaaatcagataat------aatgcatgt---ctcccttgattgcagAAGTTAGCAATCAAATGTTGGAGCTGTATGAGCAAAACTGTGCAGCACAGGCACAACCGTCCCATGGAAATGAAGCTGAAGGGAGCTCTGCTAGTGTTCC
upper sequence: GLYMA20G02860.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G308570_T02 (Zea mays), 3'ss of exon 14
cagtt-tattgctatgagtagtttaacaatgggctgtccttttgtgtgtctgtatgcttctgtatatcctt---ctcagttcttgtgggtattttctcttgcagAGGTTAGCAATCAAATGTTGGAACTCTATGAGCAGAA------TAGACTTCCACCAGCACAGGGAAGTGAAGTAGAAGGAAGTGCTGGAGGAACAAGAGCTGCTTC
|| || | |||||| | | | | | | || || | || | | || ||| || | || ||| | | |||| ||||||||||||| || ||||||||||||||||||||||| | || |||||| |||| || | ||| ||||| ||| ||| | |
cacttctgatgctat-atttttgttttggaagatcatttttatgaataataccat-cgaacacacatgcttatgctttatgtttttggtttactcctct--cagAGGTTAGCAACCAGATGTTGGAACTCTATGAGCAGAACCGTGTTCAACCACCACCATCACAAGGTAATGATACTGAAGGCAGTTCTGTAACTGCTGTGAA------
upper sequence: GLYMA20G02860.1 (Glycine max), 3'ss of exon 6
lower sequence: AC233979.1_FGT009 (Zea mays), 3'ss of exon 5
cagtttattgctatgagtagtttaacaatgggctgtccttttgtgtgtctgtatgcttctgtatatccttctcagttcttgtgggt---attttctcttgcagAGGTTAGCAATCAAATGTTGGAACTCTATGAGCAGAA------TAGACTTCCACCAGCACAGGGAAGTGAAGTAGAAGGAAGTGCTGGAGGAACAAGAGCTGCTTC
|| | | | | || || | || || |||| | || | || | | || | ||| || | || ||| ||||||||||||| || ||||||||||| |||||||| || | || |||||| |||| || | ||| ||||| ||| ||| | |
-tcttcacttttgaca-tatttctgctttgaaagatcatttttatgaattatac-catcaaagctacatgcttatgccttatgtttttggttactcctttcagAGGTTAGCAACCAGATGTTGGAACTGTATGAGCAAAACCGTGTTCAACCACCACCATCACAAGGCAATGATACTGAAGGCAGTTCTGCAAGTGTTGCGAA------
upper sequence: GLYMA20G02860.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv00s0125g00270.t01 (Vitis vinifera), 3'ss of exon 5
cagtttattgctatgagtagtttaacaatggg-ctgtccttttgtgtgtctgt---atgcttctgtatatccttctcagttcttgtgggtattttctcttgcagAGGTTAGCAATCAAATGTTGGAACTCTATGAGCAGAATAGACTTCCACCAGCACAGGGAAGTGAAGTAGAAGGAAGTGCTGGAGGAACAAGAGCTGCTTC
|| | || | || | ||||| ||||||||||| || | | || || | | ||| | || ||| ||||| |||||||||| |||||||||||||||||||||| |||||||| || ||| | || ||| | || || |||||| | |||| | || | || | | |
---gccatgggcattgctgtttcattcatggggctgtccttttgcgtcttcttcgggtgaacctttttggatttccctaacattatggttatttg-tcttgcagAGATTAGCAATCAAATGTTGGAACTGTATGAGCAAAACAGAGTGCCTCCACCTCAAGGGAGTGAAATGGAAGTTAACGCCAGTGGTGGACTAAACCATAG
upper sequence: GLYMA20G02860.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S86_187V6.1 (Physcomitrella patens), 3'ss of exon 6
cagtttattgctatgagtagtttaacaatgggctgtccttttgtgtgtctgtatgcttctgtatatccttctcagttcttgtgggtattttctcttg-----cagAGGTTAGCAATCAAATGTTGGAACTCTATGAGCAGAATAGACTTC-CACCAGCACAGGGAAGTGAAGTAGAAGGAAGTGCTGGAGGAACAAGAGCTGCTTC
|| || | | ||| | | || | ||| | | || | | | || ||| | ||| ||| | || | | ||| |||| ||||||||||| ||||||||||| || |||||||||||| | | | ||||| || || || | | || | |
---cttgttttaaccgatgttttccaagtagg--atacttgactcttattgcgttgatatttagatcgggcacagatctcataagtgtcagtttttggttttcagAAGTTAGCAATCAGATGTTGGAACTTTACGAGCAGAATAGAAATAACGGCGCAACAGGCTCACTGGCTAACGACCCAAGCCCCAGTGAAATGAACCGGGG-
upper sequence: GLYMA20G02860.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ27727 (Selaginella moellendorffii), 3'ss of exon 5
---cagtttattg-ctatgagtagtttaacaatgggctgtccttttgtgtgtctgtatgcttctgtatatccttctcagttcttgtgggtatt---ttctcttgcagAGGTTAGCAATCAAATGTTGGAACTCTATGAGCAGAATAGACTTCCACCAGCACAGGGAAGTGAAGTAGAAGGAAGTGCTGGAGGAACAAGAGCTGCTTC
| | | | | || ||| | | | ||| ||||| ||| || || | || | | | || || | || | ||||||| || |||||||||||| |||||||||| ||||||||
gtacgttctctggactttgatagactctagtttccattgttcttttttgtttc---attttcatggtcgtattgagaaagggatgcacgtctcctatttttttgcagAAGTCAGCAATCAAATGCTGGAACTCTACGAGCAGAAC-------------------------------------------------------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtctgtatgcttctgtatatccttctcagttcttgtgggtattttctcttgcagAGGTTAGCAATCAAATGTTGGAACTCTATGAGCAGAATAGACTTCCACCAGCACAGGGAAGTGAAGTAGAAGGAAGTGCTGGAGGAACAAGAGCTGCTTC
tattttctctt CT-rich tract
tattttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cagtttattgctatgagtagtttaacaatgggctgtccttttgtgtgtctgtatgcttctgtatatccttctcagttcttgtgggtattttctcttgcagAGGTTAGCAATCAAATGTTGGAACTCTATGAGCAGAATAGACTTCCACCAGCACAGGGAAGTGAAGTAGAAGGAAGTGCTGGAGGAACAAGAGCTGCTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT