Sequence
atgc intronic sequence ATGC exonic sequence...atcagatctgattattcatctctttctgtacttacatttaatgttataaattcttcaaattttaatattccatattttaataatttgacatctgtaacagGTTTTGTTTTTGATGTATCATTACTTTGCTGCATCTGAAATCTACAATGCAATCCGTTTGTTCATTGCTGCATATGTATGGATGACTGGATTTGGGAACT
Basic information
species | Glycine max |
transcript | GLYMA17G04070.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G04070.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g19970.1 (Oryza sativa), 3'ss of exon 6
atcagatctgattattcatctctttctgtacttacatttaatgttataaat-tcttcaaattttaatattccatattttaataat-ttgacatctgtaa--cagGTTTTGTTTTTGATGTATCATTACTTTGCTGCATCTGAAATCTACAATGCAATCCGTTTGTTCATTGCTGCATATGTATGGATGACTGGATTTGGGAACT
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ctcaatgcc--tcaatagcatacatgtgtggttag--taagtttttcatctatgttcaagtgcatgcatatcacttgttttcagcattgatttccctcattcagGTGCTGTTTTTGATGTACCACTACTTCAATGCTAAAGAGATATACAATGCAATTCGTGTGTTCATTGCTGCATATGTCTGGATGACTGGATTTGGTAACT
upper sequence: GLYMA17G04070.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G020721_T01 (Zea mays), 3'ss of exon 6
atcagatctgattattcatctctttctgtacttacatttaatgttataaattcttcaaattttaatattccata--ttttaataatttgacatctg--taacagGTTTTGTTTTTGATGTATCATTACTTTGCTGCATCTGAAATCTACAATGCAATCCGTTTGTTCATTGCTGCATATGTATGGATGACTGGATTTGGGAACT
|| | || | | | | |||| || || | | || | | | | | | | | || | || | |||| | ||||| | || |||||||| |||||||| ||| ||||||||||||||||||||| ||||||| ||||||||||| ||||||||||||||||| || |
ggagaatttccttttatagactgtaatatactgg-gttcaacttct---gtcctcctactagcagcctgcaacagtcttcagtattactttatctaatttccagGTGCTATTCTTGATGTACCATTACTTCAATGCTAAAGAAATCTACAATGCAATCCGTGTGTTCATCGCTGCATATGTCTGGATGACTGGATTTGGCAATT
upper sequence: GLYMA17G04070.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G06550.3 (Arabidopsis thaliana), 3'ss of exon 6
atcagatctgattattcatctctttctgtacttacatttaatgttataaattcttcaaattttaatattccatattttaataatttgacatctgtaacagGTTTTGTTTTTGATGTATCATTACTTTGCTGCATCTGAAATCTACAATGCAATCCGTTTGTTCATTGCTGCATATGTATGGATGACTGGATTTGGGAACT
| || | | || | | | ||| || | | |||| | || ||| || | || | ||| |||| | || |||||||| || ||||||||||| | || ||| ||||| |||||| | ||||||||| |||||||||||||||||||||||||| |
---------gtttgtcatttaacttttatgttagtgttttatct----gccttttcatttgccgctacctcatcattgttttcttattctggtgttgtagGTCCTTTTCTTGATGTACCACTACTTTGCTGCTGCAGAGTACTATAATGCGATCCGTGTTTTCATTGCTTGCTATGTATGGATGACTGGATTTGGGAATT
upper sequence: GLYMA17G04070.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv05s0077g00620.t01 (Vitis vinifera), 3'ss of exon 6
atcagatctgattattc-atctctttctgtacttacatttaatgttataaattcttcaaattttaatattccatattttaataatttgacatctgta--acagGTTTTGTTTTTGATGTATCATTACTTTGCTGCATCTGAAATCTACAATGCAATCCGTTTGTTCATTGCTGCATATGTATGGATGACTGGATTTGGGAACT
|| | | ||| | | || ||| | || || || | | | | || || || || | | | | | | | ||| | |||||| || ||||||||||||||||||||||| ||| | |||||||| ||||| ||||| | || |||||||||||||| |||||||||||||||||||| |
atatgtaggaactatcctagacacttttgttgcca-gctttatattctg--ctttctagatgttcatcatcggtggtctcactctctttcttctatcctacagGTATTATTTTTGATGTATCATTACTTTGCGGCAACAGAAATCTATAATGCCATCCGCCTTTTTATTGCTGCATATGTGTGGATGACTGGATTTGGGAATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataaattcttcaaattttaatattccatattttaataatttgacatctgtaacagGTTTTGTTTTTGATGTATCATTACTTTGCTGCATCTGAAATCTACAATGCAATCCGTTTGTTCATTGCTGCATATGTATGGATGACTGGATTTGGGAACT
ttcttcaaattttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atcagatctgattattcatctctttctgtacttacatttaatgttataaattcttcaaattttaatattccatattttaataatttgacatctgtaacagGTTTTGTTTTTGATGTATCATTACTTTGCTGCATCTGAAATCTACAATGCAATCCGTTTGTTCATTGCTGCATATGTATGGATGACTGGATTTGGGAACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - -ctttctg