Sequence
atgc intronic sequence ATGC exonic sequencegtagagtttttgttgatcacatggtgcttgtgtgatttttattttaagttttacttgatccgctctcttgtttcagGAACCCCTGCTCTTACTTCTAGAGGATTTGTTGAAGAGGATTTTGTTAAAGTAGCAGAATACTTTGACGTTGCTGTGACCGTGGCAGTGAAGATCAAGGC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv00s0211g00090.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G135283_T02 (Zea mays), 3'ss of exon 12
gtagagtttttgttgatcacatggt-gcttgtgtgatttttattttaagttttacttga--tccgctctcttgt--ttcagGAACCCCTGCTCTTACTTCTAGAGGATTTGTTGAAGAGGATTTTGTTAAAGTAGCAGAATACTTTGACGTTGCTGTGACCGTGGCAGTGAAGATCAAGGC
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gtacgatattttgtcatagaatgtttgtatactttattcttaattttgcaaattcttaatattagctctcccgtcatgcagGAACCCCAGCCCTTACGTCGAGAGGATTTGTTGAAGAAGATTTCGCTAAAGTTGCTGACTTCTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGC
upper sequence: Vv00s0211g00090.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA18G27710.1 (Glycine max), 3'ss of exon 14
--gtagagtttttgttgatcacatggtgcttgtgtgatttttattttaagttttacttgatccgctctcttgt-ttcagGAACCCCTGCTCTTACTTCTAGAGGATTTGTTGAAGAGGATTTTGTTAAAGTAGCAGAATACTTTGACGTTGCTGTGACCGTGGCAGTGAAGATCAAGGC
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gtacaagctctttgttgcttctattataatttt-tatgttttaattca---cttacatgatttctcttgtggaattcagGAACCCCTGCTCTTACTTCTAGAGGATTTGTTGAGGAGGATTTTGTTAAGGTAGCAGAGTTCTTTGATGCAGCAGTGAAGTTGGCTGTGAAGATTAAGGG
upper sequence: Vv00s0211g00090.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA08G37270.1 (Glycine max), 3'ss of exon 13
--gtagagtttttgttgatcacatggtgcttgtgtgatttttattttaagtt--ttacttgatccgctctcttgt-ttcagGAACCCCTGCTCTTACTTCTAGAGGATTTGTTGAAGAGGATTTTGTTAAAGTAGCAGAATACTTTGACGTTGCTGTGACCGTGGCAGTGAAGATCAAGGC
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gtacaggctctttgttgcttctgttaccatt------tttatgtcttcagtcagttacatgatttctcttgtggaattcagGAACCCCTGCTCTTACTTCTAGAGGATTTGTTGAGGAGGATTTTGTCAAGGTAGCAGAGTTTTTTGATGCAGCAGTGAAGATAGCTGTGAAGATTAAGGG
upper sequence: Vv00s0211g00090.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA09G33480.1 (Glycine max), 3'ss of exon 13
--gtagagtttttgttgatc-acatggtgcttgtgtgatttttattt-taagttttacttgatccgctctcttg--tttcagGAACCCCTGCTCTTACTTCTAGAGGATTTGTTGAAGAGGATTTTGTTAAAGTAGCAGAATACTTTGACGTTGCTGTGACCGTGGCAGTGAAGATCAAGGC
||| || || |||| | | || || || || | ||||| | || | | | | ||| || |||||||||| ||||||||||||||||| ||||||| ||| ||||||||||||| || ||||| | ||||| | ||||| | | || |||||||||||| |
gtatagggtcttcgttgttttatattttgattttggtgtcattattcatttacttgatcttaatagttctagtggatttcagGAACTCCTGCTCTTACTTCTAGGGGATTTGCTGAGGAGGATTTTGTTATGGTGGCAGAGTTTTTTGATGCAGCTGTAAATTTAGCTGTGAAGATCAAGTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggtgcttgtgtgatttttattttaagttttacttgatccgctctcttgtttcagGAACCCCTGCTCTTACTTCTAGAGGATTTGTTGAAGAGGATTTTGTTAAAGTAGCAGAATACTTTGACGTTGCTGTGACCGTGGCAGTGAAGATCAAGGC
acttgat putative branch site (score: 5)
tccgctctcttgtttc CT-rich tract
tgatttttattttaag 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagagtttttgttgatcacatggtgcttgtgtgatttttattttaagttttacttgatccgctctcttgtttcagGAACCCCTGCTCTTACTTCTAGAGGATTTGTTGAAGAGGATTTTGTTAAAGTAGCAGAATACTTTGACGTTGCTGTGACCGTGGCAGTGAAGATCAAGGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA