Sequence
atgc intronic sequence ATGC exonic sequence...attttcatcaaaatacagtgatttacactaacaaaattcataaaaatccatggttcagtaatctttaagtggtgttattaagtgtttatactttatgcagACATGGATGCCAAAGTAAAAGCAATGATCAAGCTTATTGAAGAGGATGCAGACTCATTTGCAAGGAGGGCAGAGATGTACTATAAGAAGCGGCCAGAACT
Basic information
species | Glycine max |
transcript | GLYMA20G28750.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G28750.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os03g06510.1 (Oryza sativa), 3'ss of exon 4
-attttcatcaaaatacagtgatttacactaacaaaattcataaaaatccatggttcagtaatctttaagtggtgttattaagtgtttatactttatgcagACATGGATGCCAAAGTAAAAGCAATGATCAAGCTTATTGAAGAGGATGCAGACTCATTTGCAAGGAGGGCAGAGATGTACTATAAGAAGCGGCCAGAACT
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tgtctgtatttacctttt-tgatacatcatgtacaaactggctgcatttattggaactgaactaaatgtatggtaactaaatgagttccttttgtgaacagATATGGACGTGATGGTCAAAGCAATGATCAAACTTATCAATGAAGATGCTGACTCTTTTGCAAGAAGAGCGGAAATGTACTATAAGAAACGGCCTGAACT
upper sequence: GLYMA20G28750.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G012030_T01 (Zea mays), 3'ss of exon 1
----attttcatcaaaatacagtgat--ttacactaacaaaatt-cataaaaatccatggttcagtaatctttaagtggtgttattaagtgtttatactttatgcagACATGGATGCCAAAGTAAAAGCAATGATCAAGCTTATTGAAGAGGATGCAGACTCATTTGCAAGGAGGGCAGAGATGTACTATAAGAAGCGGCCAGAACT
|| | |||| | || || || || | | || | | ||| | | | || || | | || | ||| || || | | |||||||||| | || || |||||||||||||| ||||| | || ||||| || || ||||||||||| |||||||||||||| ||||| || ||||| ||
aactatgctagtcaatttgaagatataattgcaatgaaaagactgcatttacaagtgttgtctggt--ccatgaacta-----attgggtcttgttttgtggaacagACATGGACACAAAGGTTAAAGCAATGATCAAACTTATCAATGAAGATGCTGATTCTTTTGCAAGGAGAGCAGAGATGTACTACAAGAAACGTCCAGAGCT
upper sequence: GLYMA20G28750.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G22790.1 (Arabidopsis thaliana), 3'ss of exon 2
attttcatcaaaatacagtgatttacactaacaaaattcataaaaatccatggttcagtaatctttaagtggtgttattaagtgtttatactttatgcagACATGGATGCCAAAGTAAAAGCAATGATCAAGCTTATTGAAGAGGATGCAGACTCATTTGCAAGGAGGGCAGAGATGTACTATAAGAAGCGGCCAGAACT
||| | || | | ||| || | | ||| || || | | || | | ||| ||| ||| ||| |||||| ||||||| || |||||||| || || || ||||| |||||||| || |||||||| |||||||||||||| || ||||| || ||||| ||
-----------------gtgcctctttctctctatgttctaaagtgttaagtgttttgttcctttgtattattgcttacggttatttt--cttgatgtagATATGGATTCCAAAGTGAAGGCAATGATTAAACTCATCGAAGAAGATGCAGATTCTTTTGCAAGAAGGGCAGAGATGTATTACAAGAAACGTCCAGAGCT
upper sequence: GLYMA20G28750.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G14760.1 (Arabidopsis thaliana), 3'ss of exon 2
--------------------------------------------------attttcatcaaaatacagtgatttacactaacaaaattcataaaaatccatggttcagtaatctttaagtggtgttattaagtgtttatactttatgcagACATGGATGCCAAAGTAAAAGCAATGATCAAGCTTATTGAAGAGGATGCAGACTCATTTGCAAGGAGGGCAGAGATGTACTATAAGAAGCGGCCAGAACT
| | | | || | || ||| | | | || | | | | | | | | | | | | || ||||| | || | ||||||||||| ||||||| || ||||||| ||||| || |||| |||||||| || |||||||| |||||||| ||||||| ||||| || ||||| ||
gtattctataatctttcttgacttctccttggtgttttttatgagtcttgaaaattgtggcattataatgcttttgatttgtatgtttaaagatattttgtttcttttggaagtcaatttaaaggaaatatttgtttgtg-ttgaaacagACATGGATTCCAAAGTCAAGACAATGATAAAGCTCATCGAAGCTGATGCAGATTCGTTTGCAAGAAGGGCAGACATGTACTTCAAGAAACGTCCAGAGCT
upper sequence: GLYMA20G28750.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv05s0020g03890.t01 (Vitis vinifera), 3'ss of exon 4
-attttcatcaaaatacagtgatttacactaacaaaattcataaaaatccatggttcagtaatct-ttaagtggtgttattaagtgtttatactttatgcagACATGGATGCCAAAGTAAAAGCAATGATCAAGCTTATTGAAGAGGATGCAGACTCATTTGCAAGGAGGGCAGAGATGTACTATAAGAAGCGGCCAGAACT
||| | | | | |||| | | | | | | | | | | | || | || | ||| | || || |||| ||| ||||||| |||||| ||||||||||||||||| |||||||| |||||||| || |||||| |||||||||| |||||||| |||||||| ||||||||
aattgttttggttgtttattgatc-agattgattttttcctcttttttttttcaacagccactgtattcactgatcctat-atgtattatctctttgaatagATATGGATGTCAAAGTGAAAGCAATGATCAAGCTCATTGAAGAAGATGCAGATTCCTTTGCACGGAGGGCAGAAATGTACTACAAGAAGCGTCCAGAACT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atccatggttcagtaatctttaagtggtgttattaagtgtttatactttatgcagACATGGATGCCAAAGTAAAAGCAATGATCAAGCTTATTGAAGAGGATGCAGACTCATTTGCAAGGAGGGCAGAGATGTACTATAAGAAGCGGCCAGAACT
ttattaagtgtttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attttcatcaaaatacagtgatttacactaacaaaattcataaaaatccatggttcagtaatctttaagtggtgttattaagtgtttatactttatgcagACATGGATGCCAAAGTAAAAGCAATGATCAAGCTTATTGAAGAGGATGCAGACTCATTTGCAAGGAGGGCAGAGATGTACTATAAGAAGCGGCCAGAACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - -tacagtg
- - - - - - - - - - - - -cactaac
- - - - - - - - - - - - - - - - - - - -ataaaaa
- - - - - - - - - - - - - - - - - - - - - - - -ccatggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agtggtg