Sequence
atgc intronic sequence ATGC exonic sequence...agtgattaattgtccgagtaaccgactaggggtcgactagtcgcctggtcttcgaccaggcgacttgaaatcattggttctgatcatctatttgccccagCCATGTAAAGGGATATTGCTTTTTGGTCCACCTGGCACCGGTAAGACCATGCTTGCCAAAGCTGTTGCAACAGAGGCTGGTGCTAATTTTATCAACATAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G157621_T03 (Zea mays), 3'ss of exon 21
lower sequence: LOC_Os07g47530.2 (Oryza sativa), 3'ss of exon 21
-agtg-attaattgtccgagtaaccgactaggggtcgactagtcgcctggtcttcgaccaggcgacttgaaatcattggttctgatcatc-tatttgccccagCCATGTAAAGGGATATTGCTTTTTGGTCCACCTGGCACCGGTAAGACCATGCTTGCCAAAGCTGTTGCAACAGAGGCTGGTGCTAATTTTATCAACATAT
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tagcatgctaattatcatggtctgttttttttatttggtctcttgtttctttttt--ccacttgtttcacaaacat-agttctgatcaccatttattcaccagCCATGTAAGGGAATATTGCTTTTTGGCCCACCTGGTACGGGGAAGACCATGCTTGCTAAAGCTGTTGCAACAGAGGCTGGCGCCAATTTTATCAACATAT
upper sequence: GRMZM2G157621_T03 (Zea mays), 3'ss of exon 21
lower sequence: GLYMA10G02410.1 (Glycine max), 3'ss of exon 17
agtgattaattgtccgagtaaccgactagg-ggtcgactagtcgcctggtct--tcgaccaggcgacttga--aatcattggttctgatcatctatttgccccagCCATGTAAAGGGATATTGCTTTTTGGTCCACCTGGCACCGGTAAGACCATGCTTGCCAAAGCTGTTGCAACAGAGGCTGGTGCTAATTTTATCAACATAT
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-gtgaaagattttcattttagttgtttaaatgacttgtgaaagaaattgttgagtagatcatgccatgtgtgtagcacctaattgtaattact--ttgggtatagCCTTGCAAAGGAATATTGCTTTTTGGCCCTCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTTATTAACATTT
upper sequence: GRMZM2G157621_T03 (Zea mays), 3'ss of exon 21
lower sequence: GLYMA10G02400.1 (Glycine max), 3'ss of exon 20
agtgattaattgtccgagtaaccgactaggggtcgactagtcgcctg-gtcttcgaccaggcgac-ttgaaatcattggt------tctgatcat--ctattt--gccccagCCATGTAAAGGGATATTGCTTTTTGGTCCACCTGGCACCGGTAAGACCATGCTTGCCAAAGCTGTTGCAACAGAGGCTGGTGCTAATTTTATCAACATAT
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gttggtagattttctttttagttgctttaaa--tgacaagtggaacacattttttagtagatgatattcatatcatgtgtgtagcacctcattgtaattactttggatatagCCTTGCAAGGGAATATTGCTTTTTGGGCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTCATTAACATTT
upper sequence: GRMZM2G157621_T03 (Zea mays), 3'ss of exon 21
lower sequence: GLYMA02G17400.1 (Glycine max), 3'ss of exon 17
agtgattaattgtccgagt--aaccgactagg-ggtcgactagtcgcctggtct--tcgaccaggcga--cttgaaatcattggttctgatcatctatttgccccagCCATGTAAAGGGATATTGCTTTTTGGTCCACCTGGCACCGGTAAGACCATGCTTGCCAAAGCTGTTGCAACAGAGGCTGGTGCTAATTTTATCAACATAT
|||| ||| | | | | | || | | | | || | || || || | | || | | || | || | || | |||| || || || |||||||||||||| || |||||||| || || || |||||||| || ||||| ||||| || ||||| || |||||||| ||||| |
-gtgaaaaatattttcattttagttgtttaaatgacttgtgaaagacattgttaagtagatcatgccatgcgtgtagcacctaattgtaattact--ttgggtatagCCTTGCAAGGGAATATTGCTTTTTGGCCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTGGCAACTGAAGCTGGAGCAAATTTTATTAACATTT
upper sequence: GRMZM2G157621_T03 (Zea mays), 3'ss of exon 21
lower sequence: GLYMA02G17410.1 (Glycine max), 3'ss of exon 16
agtgattaattgtccgagtaaccgactaggggtcgactagtcg--cctggtcttcgaccaggcgacttgaaatcattggt------tctgatcat--ctattt--gccccagCCATGTAAAGGGATATTGCTTTTTGGTCCACCTGGCACCGGTAAGACCATGCTTGCCAAAGCTGTTGCAACAGAGGCTGGTGCTAATTTTATCAACATAT
|||| ||| || || | | |||| || | | | || | || |||||| || || || | || || | |||| || || || |||||||||||||| || |||||||| || || || |||||||| || ||||| ||||| || ||||| || ||||| || ||||| |
gttgatagattttctttttagttgctttaaa--tgacttgtggaacacattttttagtagatcatattcgaatcatgtgtgtagcacctcattgtaattactttggatatagCCTTGCAAGGGAATATTGCTTTTTGGGCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTCATTAACATTT
upper sequence: GRMZM2G157621_T03 (Zea mays), 3'ss of exon 21
lower sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 20
--------------------------------------------------agtgattaattgtccgagtaacc-----gactaggggtcgactagtcgcctggtcttcgaccaggcgacttgaaatcattggttctgatcatctatttgccccagCCATGTAAAGGGATATTGCTTTTTGGTCCACCTGGCACCGGTAAGACCATGCTTGCCAAAGCTGTTGCAACAGAGGCTGGTGCTAATTTTATCAACATAT
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gttaggtgtttcacatgttttatttctttattgtgtatgtatatatatatattgtgtatctggtggaattttcttttgaattatggaagtaagttttatctaattcatgccttgtatgtctatcatc--tgaatgaggtta-ctattt--ttcagCCTTGCAAGGGAATTCTTCTATTTGGGCCTCCTGGGACTGGAAAAACAATGCTTGCGAAGGCGGTTGCAACTGAGGCAGGTGCAAATTTTATCAACATAT
upper sequence: GRMZM2G157621_T03 (Zea mays), 3'ss of exon 21
lower sequence: EFJ31084 (Selaginella moellendorffii), 3'ss of exon 8
agtgattaattgtccgagtaaccgactaggggtcgactagtcgcctggtcttcgaccaggcgacttgaaatcattggttctg-atcatctatttgccccagCCATGTAAAGGGATATTGCTTTTTGGTCCACCTGGCACCGGTAAGACCATGCTTGCCAAAGCTGTTGCAACAGAGGCTGGTGCTAATTTTATCAACATAT
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-----------------------------------------------gtctgtgtgtttgttatttgctttttttctttgtctaacgaatttatatggcagCCTTGTAGGGGCCTACTCTTATTTGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTT
upper sequence: GRMZM2G157621_T03 (Zea mays), 3'ss of exon 21
lower sequence: EFJ34631 (Selaginella moellendorffii), 3'ss of exon 10
agtgattaattgtccgagtaaccgactaggggtcgactagtcgcctggtcttcgaccaggcgacttgaaatcattggttctgatcatctatttgccccagCCATGTAAAGGGATATTGCTTTTTGGTCCACCTGGCACCGGTAAGACCATGCTTGCCAAAGCTGTTGCAACAGAGGCTGGTGCTAATTTTATCAACATAT
| ||| | | | || | || || |||||| || | |||| |||| || || | | |||||||| || || || ||||||||||||||||| || || ||||| |||||||||||||| ||||| ||||| || |
------------------------------------------gtctgtgtgtttgttatttgcttttt--ttctttgtctaacgaatctatatggc--agCCTTGTAGGGGCCTACTCTTATTTGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggtcttcgaccaggcgacttgaaatcattggttctgatcatctatttgccccagCCATGTAAAGGGATATTGCTTTTTGGTCCACCTGGCACCGGTAAGACCATGCTTGCCAAAGCTGTTGCAACAGAGGCTGGTGCTAATTTTATCAACATAT
ttctgat putative branch site (score: 3)
tttgcccc putative PPT
aaatcatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agtgattaattgtccgagtaaccgactaggggtcgactagtcgcctggtcttcgaccaggcgacttgaaatcattggttctgatcatctatttgccccagCCATGTAAAGGGATATTGCTTTTTGGTCCACCTGGCACCGGTAAGACCATGCTTGCCAAAGCTGTTGCAACAGAGGCTGGTGCTAATTTTATCAACATAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT