Sequence
atgc intronic sequence ATGC exonic sequence...taaagctacaaaatcctgaatcaccactaaattgagtgacatgtcctgaatgattcccctggatctgacagtttgtctgacaccttgagctggtctgtagAGCTGGGAAAAAACAATGGACTGCCATAGTCCAGGTCAAGGTTTAATGCCCGCCAGCTTCAAAGTGCGGACAATTCCACTTGATGGTGATGAGGATGCAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G040843_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g32730.1 (Oryza sativa), 3'ss of exon 2
taaagct----acaaa-atcctgaatcaccactaaattgagtgacatgtcctgaatgattc-ccctggatctgaca-gtttgtctgacaccttgagctggtctgtagAGCTGGGAAAAAACAATGGACTGCCATAGTCCAGGTCAAGGTTTAATGCCCGCCAGCTTCAAAGTGCGGACAATTCCACTTGATGGTGATGAGGATGCAA
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--aagttcttggcaaatatctcttctagttaccgtagcaacaaaatgaatttgtatgccctatccaaggtgtaacaagttctgctgtcattttgt-----tatgtagAGCTGGGAGAAGACAATGGACTGCCATAGTCCAGGACAGGGCTTAATGCCTGCTAGCTTCAAGGTGCGAACAATTCCACTCGATGGAGATGAAGATGCAA
upper sequence: GRMZM2G040843_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA08G15220.1 (Glycine max), 3'ss of exon 2
taaagctacaaaatcctgaatcaccactaaatt-gagtgacatgtcctg-aatgattcccctggatctgacagtttgtctgacaccttgag--ctggtctgtagAGCTGGGAAAAAACAATGGACTGCCATAGTCCAGGTCAAGGTTTAATGCCCGCCAGCTTCAAAGTGCGGACAATTCCACTTGATGGTGATGAGGATGCAA
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---catta-gtaatttttttttaccacttcttttgccttaactgtattataattactttcttgtttctgatatactgtcttgaacccacacatccatatttcagAGCTGGGAGAAAACAATGGATTGTCATAGTCCAGGACAAGGTTTGATGCCTGCTAGTTTTAAGGTTAGGACAGTTCCTTTGGACGGTGATGATTCTGCAA
upper sequence: GRMZM2G040843_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA05G31920.1 (Glycine max), 3'ss of exon 1
taaagctacaaaatcctgaatcaccactaaatt-gagtgacatgtcctg-aatgattcccctggatctgacagtttgtctgacaccttgag--ctggtctgtagAGCTGGGAAAAAACAATGGACTGCCATAGTCCAGGTCAAGGTTTAATGCCCGCCAGCTTCAAAGTGCGGACAATTCCACTTGATGGTGATGAGGATGCAA
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---catta-gtaatctttttttagcacttcttttgccttaactgtattataattactttgttgtttctgatatattgtcttgaatccacacatccatatttcagAGCTGGGAGAAAACTATGGATTGTCATAGTCCAGGACAAGGTTTGATGCCTGCTAGTTTTAAGGTTAGGACAGTTCCTTTGGATGGTGATGATTCTGCAA
upper sequence: GRMZM2G040843_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT5G22510.1 (Arabidopsis thaliana), 3'ss of exon 2
-----------------------------------------------------------------------------------taaagctacaaaatcctgaatcaccactaaattgagtgaca--tgtcctgaatgattcccctggatctgaca---gtttgtctgacaccttgagctggtctgtagAGCTGGGAAAAAACAATGGACTGCCATAGTCCAGGTCAAGGTTTAATGCCCGCCAGCTTCAAAGTGCGGACAATTCCACTTGATGGTGATGAGGATGCAA
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gtaatagagtctttctttgataagtgcagatggaagcaatagtatgatgttgtcaaatgtttttgtggttaaggaaatatgattgtagtagtaacctctttttgttgcaccgagttcagtgtagattgatacgtagcagttatttggttttgttatgagctgatatgatgcttattcctgacc---agAGTTGGGAGAAAACCATGGATTGCCATAGTCCAGGTCAAGGTTTGATGCCTTGTAGTTTCAAGGTGAAAACTGTTCCTCTCGATGGCGATGATTCAATGA
upper sequence: GRMZM2G040843_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv06s0061g01520.t01 (Vitis vinifera), 3'ss of exon 3
--taaagctaca----aaatcctgaatcaccactaaattgagtgacatgtcctgaatgattcccctggatctgacagtttgtctgacaccttgagctggtctgtagAGCTGGGAAAAAACAATGGACTGCCATAGTCCAGGTCAAGGTTTAATGCCCGCCAGCTTCAAAGTGCGGACAATTCCACTTGATGGTGATGAGGATGCAA
|| ||| | || |||||| || ||| | || | | | | || ||| | | || | | | |||||||||| ||||| ||||| ||||||||||| || ||||| | ||||| ||||| ||||| ||||| || ||||||||||||||||||| |||||
cggaaggctcctctttgaagtgtgaatcttacttatcttgtgaaactttattcttttaagttttttgt-tct-----tccattcagtgaattccatttatttacagAGCTGGGAGAAAACCATGGATTGCCATAGTCCTGGACAAGGACTGATGCCTGCCAGTTTCAAGGTGCGCACTGTTCCACTTGATGGTGATGATTCTGCAA
upper sequence: GRMZM2G040843_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv13s0074g00720.t01 (Vitis vinifera), 3'ss of exon 3
taaagctacaaaat-cctgaatcaccactaaattgagtgacatgtcctgaatgattcccctggatctgacagtttgtctgacaccttgagctggtctgtagAGCTGGGAAAAAACAATGGACTGCCATAGTCCAGGTCAAGGTTTAATGCCCGCCAGCTTCAAAGTGCGGACAATTCCACTTGATGGTGATGAGGATGCAA
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gatgattaattattaccctaactatttatcatttactttacttccttttaaacatggagttt-atttgcccatttgggcacgtttgtggctcatcctgcagAGCTGGGAGAAGACAATGGACTGTCATAGTCCTGGTCAAGGGTTGATGCCTGCAAGTTTCAAGGTGCGCACAGTTCCCCTGGATGGTGATGACTCTGCAAMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|148983072|gb|EE028984.2|EE028984EST: GGGAATATGAAATTGTGCGTAATTTCATTCTACACACACTTCAGCTTCAG AGCTGGGNNNNNNNCA-TGGACTGCCATAGTCCAGGTCAAGGTTTAATGCC
genomic: GGGAATATGAAATTGTGCGTAATTTCATTCTACACACACTTCAGCTTCAGgtactggtct ... tggtctgtagAGCTGGGAAAAAA-CAATGGACTGCCATAGTCCAGGTCAAGGTTTAATGCC
EST:
gi|71774054|gb|DR971940.1|DR971940EST: GGGAATATGAAATTGTGCGTAATTTCATTCTACACACACTTCAGCTTCAG AGCTGGGAAAAAACAATGGACTGCCATAGTCCAGGTCA
genomic: GGGAATATGAAATTGTGCGTAATTTCATTCTACACACACTTCAGCTTCAGgtactggtct ... tggtctgtagAGCTGGGAAAAAACAATGGACTGCCATAGTCCAGGTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgaatgattcccctggatctgacagtttgtctgacaccttgagctggtctgtagAGCTGGGAAAAAACAATGGACTGCCATAGTCCAGGTCAAGGTTTAATGCCCGCCAGCTTCAAAGTGCGGACAATTCCACTTGATGGTGATGAGGATGCAA
gtctgac putative branch site (score: 3)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taaagctacaaaatcctgaatcaccactaaattgagtgacatgtcctgaatgattcccctggatctgacagtttgtctgacaccttgagctggtctgtagAGCTGGGAAAAAACAATGGACTGCCATAGTCCAGGTCAAGGTTTAATGCCCGCCAGCTTCAAAGTGCGGACAATTCCACTTGATGGTGATGAGGATGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG