Sequence
atgc intronic sequence ATGC exonic sequence...ttttctttgtgtattaatccaaaaaatgaatattctttattggttactcaaatatgatctttgtattcatattgttttctgttcattctgttgtggtcagGAACTGTAGTTCCAATGCTTTTGGCTGTAATGGCTGTTGTGCCAGCGGAGAAGCTTGCTGTCCACTTCCATGACACTTACGGGCAATCCCTTGCAAATAT
Basic information
species | Glycine max |
transcript | GLYMA07G36340.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G36340.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g16350.1 (Oryza sativa), 3'ss of exon 6
ttttctttgtgtattaatccaaaaaatgaatattctttattggttactcaaatatgatctttgtattcatattgttttctgttcattctgt---tgtggtcagGAACTGTAGTTCCAATGCTTTTGGCTGTAATGGCTGTTGTGCCAGCGGAGAAGCTTGCTGTCCACTTCCATGACACTTACGGGCAATCCCTTGCAAATAT
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-agtttttgtctactagctttggt--ttattacccttcttctccagcttcatgatcccattactagccaggttttaaacagtttacttcctccatctatccagGCACCGTTGTTCCAATGCTTGAGGCTGTTATGTTCTTTGTTCCAAAGGAGAAGCTTGCTGTCCATTTCCACGATACCTACGGCCAATCGCTTTCAAATAT
upper sequence: GLYMA07G36340.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G175071_T01 (Zea mays), 3'ss of exon 6
----ttttctttgtgtattaatccaaaaaatgaatattctttattggttactcaaatatgatctttgtattcatattgttttctgttcattctgttgtggtcagGAACTGTAGTTCCAATGCTTTTGGCTGTAATGGCTGTTGTGCCAGCGGAGAAGCTTGCTGTCCACTTCCATGACACTTACGGGCAATCCCTTGCAAATAT
||||| ||| | || | | | || | || || || | | | | | |||| | |||| | | |||| ||| |||| || || ||||| |||||| ||| | || | || || || | ||||||||| |||||||||||||| ||||| ||||| || ||||| | || ||
gtcattttccttgatttctatttcccagc-tgcacatgct--atctgcagccttgtggtcctgtgaagattctgaacagtttcagctt-ttctcatgtatgcagGCACCGTGGTTCCGATGCTTGAGGCAGCTATCTCCGTCGTTCCCGTGGAGAAGCTCGCTGTCCACTTCCACGACACCTACGGCCAGTCCCTCTCGAACAT
upper sequence: GLYMA07G36340.1 (Glycine max), 3'ss of exon 6
lower sequence: AT2G26800.2 (Arabidopsis thaliana), 3'ss of exon 7
ttttctttgtgtattaatccaaaaaa-tgaatattctttattggttactcaaatatgatctttgtattcatattgttt-tctgttcattctgttgtg---gtcagGAACTGTAGTTCCAATGCTTTTGGCTGTAATGGCTGTTGTGCCAGCGGAGAAGCTTGCTGTCCACTTCCATGACACTTACGGGCAATCCCTTGCAAATAT
|| | | | || | || || | | | | | | ||| | ||| || || |||||| | ||| ||||| |||| |||||||||||| || || ||||| |||||||||||||| ||||| ||||| ||||||||||| || || |||||| | |||||||| ||
-----ttagagagtagatagggagggctggatttatgcgcattttcgttgagagttgagtctctcattaatcaagtccctctgtttggtgaattgaacaaatcagGTTCTGTGGTTCCAATGCTTGAAGCCGTGATGGCAGTTGTGCCAGCGGACAAGCTGGCTGTTCACTTCCATGATACCTATGGGCAAGCTCTTGCAAACAT
upper sequence: GLYMA07G36340.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv06s0009g02640.t01 (Vitis vinifera), 3'ss of exon 6
ttttctttgtgtatt-aatccaaaaaatgaatattctttattggttactcaaatatgatctttgtattcatattgttttctgttcattctgttgtg-gtcagGAACTGTAGTTCCAATGCTTTTGGCTGTAATGGCTGTTGTGCCAGCGGAGAAGCTTGCTGTCCACTTCCATGACACTTACGGGCAATCCCTTGCAAATAT
||| |||||| || | |||| | | | | ||| | | ||| | | | | |||||| || || ||||| | | ||||| |||||| ||||||||||||||||| || | |||||||||||||||||||||||||||||||| ||||| || ||| |||||||
--agcttaatgtatttgatagtttgtgtcaataattagttaaatgcagtagaattaagaaagagaaaccatcatctataatcttcatttatttatgtatcagGCGCCATTGTTCCTATGCTTGAAGCTGTAATGGCTGTTGTTCCTGTTGAGAAGCTTGCTGTCCACTTCCATGACACTTATGGGCAGTCTCTTCCAAATAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actcaaatatgatctttgtattcatattgttttctgttcattctgttgtggtcagGAACTGTAGTTCCAATGCTTTTGGCTGTAATGGCTGTTGTGCCAGCGGAGAAGCTTGCTGTCCACTTCCATGACACTTACGGGCAATCCCTTGCAAATAT
ttctgtt CT-rich tract
tattcatattgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttctttgtgtattaatccaaaaaatgaatattctttattggttactcaaatatgatctttgtattcatattgttttctgttcattctgttgtggtcagGAACTGTAGTTCCAATGCTTTTGGCTGTAATGGCTGTTGTGCCAGCGGAGAAGCTTGCTGTCCACTTCCATGACACTTACGGGCAATCCCTTGCAAATAT
- - ctttgtg
- - - - - - - - - - aaaaaat
- - - - - - - - - - - - - - - - - - - - - - -actcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtattc