Sequence
atgc intronic sequence ATGC exonic sequence...accggctataagtttatttggtcatctgtataattgtttgcttgcattgacctttcttgttttccttattcattcactagcaacaatgttaattgtgcagGAAGATTACATAAACACGTCACACCCAAATTTTATTGGTGGCAGCAAGGCTGTTGAGCAAGCACAGCAGCAAGTTAGGTCTGCCAAAATGTCAGCAGCGG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G129155_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os01g69130.1 (Oryza sativa), 3'ss of exon 12
accggctataagtttatttggtcatctgtataattgtttgctt-gcattgacctttcttgttttccttattcat--tcactagcaacaatgttaattgtgcagGAAGATTACATAAACACGTCACACCCAAATTTTATTGGTGGCAGCAAGGCTGTTGAGCAAGCACAGCAGCAAGTTAGGTCTGCCAAAATGTCAGCAGCGG
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--tgatagctgatgttttttttcccctgatttactcttgactttgcatagatatgctataatctttttcattgtcataacctgcaactctattt-tggttcagGCGGATTACATAAACACATCTCATCCAAATTTCATCGGCGGCAGCAAGGCTGTTGAGCAAGCACAGCAGCAAGTTAGGTCTTCTAGACTGGCAGCTGTGG
upper sequence: GRMZM2G129155_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA15G06380.1 (Glycine max), 3'ss of exon 12
accggctataagtttatttg-gtcatctgt-ataattgtttgcttgcattgacctttcttgttttccttattcat----tcactagcaacaatgttaattgtgcagGAAGATTACATAAACACGTCACACCCAAATTTTATTGGTGGCAGCAAGGCTGTTGAGCAAGCACAGCAGCAAGTTAGGTCTGCCAAAATGTCAGCAGCGG
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-----cagtcagcttattcatgtcaattgcgatggtcagtctctatcagagtgaatcatcaatttccatgtccatgatttctttttgaactac-tcaattctgcagATGGACTACATAAACACTTCCCACCCAAATTTTATTGGTGGAAGCAAGGCATTAGAAATAGCTGCACAGCAGACCAAGTCGTCTAGGGTTGCTATACCAG
upper sequence: GRMZM2G129155_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA13G32940.1 (Glycine max), 3'ss of exon 12
accggctataagtttatttg-gtcatctgt-ataatt-gtttgcttgcat---tgacctttcttgttttccttattcattcactagcaacaatgttaattgtgcagGAAGATTACATAAACACGTCACACCCAAATTTTATTGGTGGCAGCAAGGCTGTTGAGCAAGCACAGCAGCAAGTTAGGTCTGCCAAAATGTCAGCAGCGG
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----tcagtcagcttattcatatcaattgtgatggtcagtctattagagtgaataatcaatttcaatgtccatgatttcttatttg-aactac-tcaattatgcagATGGACTACATAAACACTTCCCACCCAAATTTTATTGGTGGAAGCAAGGCATTAGAAATAGCTGCGCAACAGACCAAGTCCTCTAGGGTTGCTATACCAG
upper sequence: GRMZM2G129155_T01 (Zea mays), 3'ss of exon 12
lower sequence: AT4G33650.1 (Arabidopsis thaliana), 3'ss of exon 12
----------------------------------------------------------------------------------------accggctataagtttatttggtcatctg------tataattgtttgcttgcattgacctttcttgttttccttattcattcactagcaacaatgttaattgtgcagGAAGATTACATAAACACGTCACACCCAAATTTTATTGGTGGCAGCAAGGCTGTTGAGCAAGCACAGCAGCAAGTTAGGTCTGCCAAAATGTCAGCAGCGG
||| | ||| || || || | | | |||| || || | |||| || | || | | | | | ||||| || |||| |||||||||||||| ||||| ||||||||||||||||| | |||||| || || ||| ||| ||||| | |||| | | || | | |
gtctgtataatgaattgaaaatcctacgttgagttgagtttctctattgtgtataaagagcccagactaatatgttggttgattagggaccttttttaatcttgagcagtgatttcctcgtttttgattgattagtttctttgaactaaagtattagtgatggtatcataatttcttgaatgtcgttt--gcagATGGATTACATAAACACTTCACATCCAAATTTTATTGGTGGAACCAAGGCCGTGGAAGCTGCAATGCATCAAGTGAAGTCTTCGAGGATTCCCCATCCTG
upper sequence: GRMZM2G129155_T01 (Zea mays), 3'ss of exon 12
lower sequence: Vv03s0038g00970.t01 (Vitis vinifera), 3'ss of exon 13
accggctataagtttatttggtcatctgtataattgtttgc-ttgcattgacctttcttgttttcctta---ttcattcactagcaacaatgttaattgtgcagGAAGATTACATAAACACGTCACACCCAAATTTTATTGGTGGCAGCAAGGCTGTTGAGCAAGCACAGCAGCAAGTTAGGTCTGCCAAAATGTCAGCAGCGG
| | | || | | | |||||| ||| | ||| | || ||||||| | | | ||| | | |||| || || || || || |||||||| || ||||||||||||||||||||||| || || ||||| ||| ||| ||| || ||| ||| | | || | | | | |
-caaaccaaaaaaagaaaaaaaaagtagc--aattgtatgcacttcatcaaagttaagtgttttcttgacaatggtctcagtctaagcaattcta-ttctgtagATGGACTACATAAATACTTCACACCCAAATTTTATTGGTGGAAGTAAAGCTGTGGAGATGGCATTGCAACAGATTAAGTCCTCTAGGCTGCCTGTACCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgacctttcttgttttccttattcattcactagcaacaatgttaattgtgcagGAAGATTACATAAACACGTCACACCCAAATTTTATTGGTGGCAGCAAGGCTGTTGAGCAAGCACAGCAGCAAGTTAGGTCTGCCAAAATGTCAGCAGCGG
tgttaat putative branch site (score: 3)
aatgttaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
accggctataagtttatttggtcatctgtataattgtttgcttgcattgacctttcttgttttccttattcattcactagcaacaatgttaattgtgcagGAAGATTACATAAACACGTCACACCCAAATTTTATTGGTGGCAGCAAGGCTGTTGAGCAAGCACAGCAGCAAGTTAGGTCTGCCAAAATGTCAGCAGCGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG