Sequence
atgc intronic sequence ATGC exonic sequencegtaagccttttcgcctgcattaattctggcatcgctgcaccgcatcttgctctaatctagccgctaatcttctcttacaaaacctgaacgacagGTTCTGCCCGGCACACTGGTGGTGAATGCTCTGGCAAAGCAGAGGGCGATGCTGGAGAACATCATGAGGGCCTGTGTTGGCCTGGCCCTAGAGAACAACA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G392513_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os03g09250.2 (Oryza sativa), 3'ss of exon 9
gtaagccttttcgcctgcattaattctggcatcgctgcaccgcatcttgctctaatctagccgctaatcttctcttacaaaacctgaacgacagGTTCTGCCCGGCACACTGGTGGTGAATGCTCTGGCAAAGCAGAGGGCGATGCTGGAGAACATCATGAGGGCCTGTGTTGGCCTGGCCCTAGAGAACAACA
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-------gtactgcc--cattaaccgttatgttctttcatgatataccaa-ctgatttacttatgtcacgaaaaattcgtctcctgga--acagGTTCCTCCTGGCACACCAGTGGTGAACGCCCTGGCAAAGCAGAGGGCAATGCTTGAGAACATCATGAGGGCCTGCGTTGGGCTGGCCCCCGAGAACAACA
upper sequence: GRMZM2G392513_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os03g09250.3 (Oryza sativa), 3'ss of exon 8
gtaagccttttcgcctgcattaattctggcatcgctgcaccgcatcttgctctaatctagccgctaatcttctc---ttacaaaa-------cctgaacgacagGTTCTGCCCGGCACACTGGTGGTGAATGCTCTGGCAAAGCAGAGGGCGATGCTGGAGAACATCATGAGGGCCTGTGTTGGCCTGGCCCTAGAGAACAACA
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gtgagtgcataca--tgcatctgtactgcccattaaccgttatgttctttcatgatataccaactgatttacttatgtcacgaaaaattcgtctcctggaacagGTTCCTCCTGGCACACCAGTGGTGAACGCCCTGGCAAAGCAGAGGGCAATGCTTGAGAACATCATGAGGGCCTGCGTTGGGCTGGCCCCCGAGAACAACA
upper sequence: GRMZM2G392513_T02 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA18G02210.3 (Glycine max), 3'ss of exon 9
----------------------------------------------------------------------------------------------------------gtaagccttttcgcctgcattaattctggcatcgctgcaccgcatcttgctctaatctagccgctaatcttctcttacaaaacctgaacgacagGTTCTGCCCGGCACACTGGTGGTGAATGCTCTGGCAAAGCAGAGGGCGATGCTGGAGAACATCATGAGGGCCTGTGTTGGCCTGGCCCTAGAGAACAACA
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gtgagtttaatctaatcttattcaatgttgagtgcatatccttatttttatataggaattaagttgaaagaaatatgagttttagtattgagatacaattgtgaagttaaatcattgttcagtgaatttcccttttttccccttatcatttttttatc-aaaaaagttggcaaggtta-ctcacaacataactcttgcagGTTCCACCGGGTACACCAGTGGTGAATGCATTGTCAAAGCAGCGTGCAATGCTGGAAAACATAATGAGGGCTTGTGTTGGATTGGCCCCAGAGAATAACA
upper sequence: GRMZM2G392513_T02 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA05G31450.4 (Glycine max), 3'ss of exon 6
gtaagccttttcgcctgcattaattctggcatcgctgcaccgcatcttgc-tctaatctagccgctaatcttctcttacaaaacc--tgaacgacagGTTCTGCCCGGCACACTGGTGGTGAATGCTCTGGCAAAGCAGAGGGCGATGCTGGAGAACATCATGAGGGCCTGTGTTGGCCTGGCCCTAGAGAACAACA
||||| || | ||| || | | || || | ||| | | | | ||| |||| | | || | || |||||||| || || |||| ||||||||||| || |||||||| | || |||||||| |||||| ||||||| |||||||| | || | ||||||||||
gtaagtctaatactaccgattcataattgt-tcaatgaattaattctctcatttccccctttaattaaatttctgaaatacaattattaaattacagGTTCCACCGGGTACACCAGTGGTGAATGCGTTGTCAAAGCAGCGAGCTATGCTGGAAAACATCCTGAGGGCTTGTGTTGGATTAGCTCCTGAGAACAACA
upper sequence: GRMZM2G392513_T02 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA05G31450.3 (Glycine max), 3'ss of exon 9
--gtaagccttttcgcctgcattaattc--tggcatcgctgcaccgcatcttgctctaatctagccgctaatcttctcttacaaaacctgaacgacagGTTCTGCCCGGCACACTGGTGGTGAATGCTCTGGCAAAGCAGAGGGCGATGCTGGAGAACATCATGAGGGCCTGTGTTGGCCTGGCCCTAGAGAACAACA
||| || | | ||| || | | | || || |||| | || | | | ||| ||| |||||||| || || |||| ||||||||||| || |||||||| | || |||||||| |||||| ||||||| |||||||| | || | ||||||||||
gtctaatactaccgattcataattgttcaatgaattaattctctcatttccccctttaattaaatttctgaaatacaattattaaatt------acagGTTCCACCGGGTACACCAGTGGTGAATGCGTTGTCAAAGCAGCGAGCTATGCTGGAAAACATCCTGAGGGCTTGTGTTGGATTAGCTCCTGAGAACAACA
upper sequence: GRMZM2G392513_T02 (Zea mays), 3'ss of exon 7
lower sequence: Vv07s0031g00920.t01 (Vitis vinifera), 3'ss of exon 9
-----gtaagccttttcgcct-gcattaattctggcatcgctgcaccgcatcttgctctaatctagccgctaatcttctcttacaaaacctgaacgacagGTTCTGCCCGGCACACTGGTGGTGAATGCTCTGGCAAAGCAGAGGGCGATGCTGGAGAACATCATGAGGGCCTGTGTTGGCCTGGCCCTAGAGAACAACA
||| || | || | | | | || | || | | ||| | || | | | | | | || |||||||| || ||||| | ||||||||||| ||||| |||||| |||| ||||| |||||||| | ||||| |||||||| |||| | ||||||||||
gacatcaaagttttaccttcttgtttggaatatgcgaggaatgtagagttagttgatagcattatgatgttgtaacgttttgttggtgtattaaaaacagGTTCCACCAGGCACTCCAGTGGTGAATGCACTGGCGAAGCAGCGGGCAATGCTCGAGAACATACTAAGGGCTTGTGTTGGATTGGCTCCCGAGAACAACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccgcatcttgctctaatctagccgctaatcttctcttacaaaacctgaacgacagGTTCTGCCCGGCACACTGGTGGTGAATGCTCTGGCAAAGCAGAGGGCGATGCTGGAGAACATCATGAGGGCCTGTGTTGGCCTGGCCCTAGAGAACAACA
ctcttac putative branch site (score: 3)
ttacaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagccttttcgcctgcattaattctggcatcgctgcaccgcatcttgctctaatctagccgctaatcttctcttacaaaacctgaacgacagGTTCTGCCCGGCACACTGGTGGTGAATGCTCTGGCAAAGCAGAGGGCGATGCTGGAGAACATCATGAGGGCCTGTGTTGGCCTGGCCCTAGAGAACAACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA