Sequence
atgc intronic sequence ATGC exonic sequence...cgttaggaaagactagtctctagacacaatccaattgatttgttaattactttgtttgatgcattttaacaatatattgtgtgtttttttgccttattagATATTCAAATGTTAGAGAGATTTGGTTCGATGGAGCAAAGGGTGCCAATGCAAAAAATATGACCTATTACTTTTCAGATTGGTTTTCCATGGTGAAGGAG
Basic information
species | Glycine max |
transcript | GLYMA20G29080.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G29080.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv16s0022g02170.t01 (Vitis vinifera), 3'ss of exon 1
--------------------------cgttagga-aagactagtctctagacaca--atccaat-tgatttg--ttaattactttgtttgatgcattttaacaata-tattgtgtgtttttttgccttat--tagATATTCAAATGTTAGAGAGATTTGGTTCGATGGAGCAAAGGGTGCCAATGCAAAAAATATGACCTATTACTTTTCAGATTGGTTTTCCATGGTGAAGGAG
| | | ||| | | || | | | || ||| ||| | |||| | | | | | || ||| ||||| | || | | |||| |||||| | ||||||||||||||||||||||||||||| ||||| ||||||| | || |||||| ||| |||||| ||||||||||||
gtaagccattaatgtttcttcataattttcaaaataagtgttattcttaaaaataggatagaatatgaactaccttaaaaaagtagggaatcgaaaaaaaaaaattctattgagatttgatctatattatggcagATATGGGGTCATACAAGAGATTTGGTTCGATGGAGCAAAGGGTGAGGATGCAGCAAATATGTCATACTACTTTGAAGAATGGTTTGAAATGGTGAAGGAG
upper sequence: GLYMA20G29080.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv16s0022g02170.t01 (Vitis vinifera), 3'ss of exon 4
cgttaggaaagactagtctctag-acacaatccaattgatttgtta----attactttgt-ttgatgcattttaacaatatattgtg--tgtttttttgccttattagATATTCAAATGTTAGAGAGATTTGGTTCGATGGAGCAAAGGGTGCCAATGCAAAAAATATGACCTATTACTTTTCAGATTGGTTTTCCATGGTGAAGGAG
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-----------gtaagttactgatactcaatcggtttgctttctaagaaaagtactcaaaattattgtacatttgtaatctttttggattggttggttttttttttagATATGGGAATGTGAGAGAGATTTGGTTCGATGGAGCAAAGGGCGCAAATGCGCCAAATATGTCGTATGACTTTGGAGACTGGTTTGCCATGGTGAGGGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attactttgtttgatgcattttaacaatatattgtgtgtttttttgccttattagATATTCAAATGTTAGAGAGATTTGGTTCGATGGAGCAAAGGGTGCCAATGCAAAAAATATGACCTATTACTTTTCAGATTGGTTTTCCATGGTGAAGGAG
ttttaac putative branch site (score: 2)
tttttttgccttatt putative PPT
attttaacaatatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cgttaggaaagactagtctctagacacaatccaattgatttgttaattactttgtttgatgcattttaacaatatattgtgtgtttttttgccttattagATATTCAAATGTTAGAGAGATTTGGTTCGATGGAGCAAAGGGTGCCAATGCAAAAAATATGACCTATTACTTTTCAGATTGGTTTTCCATGGTGAAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - gaaagac
- - - - - - - - - - - - - caatcca
- - - - - - - - - - - - - - - - - -tgatttg
- - - - - - - - - - - - - - - - - - - - - - - - - -ttgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcattt