Sequence
atgc intronic sequence ATGC exonic sequencegtaaggatttgttacatttgaggtgtgagattgttgtggctgaggattggactatgaaaaagtttggatttgatccagGAAACGGCACTTAATCATGTGAAGACCGCTGGGCTGCTAGGTGATGGATTCGGCTCCACACCAGAGATGAGTAAACGGAACTTATTCTGGGTGGTTAGCC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G079308_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os06g39520.2 (Oryza sativa), 3'ss of exon 2
gtaaggatttgttacatttgaggtgtgagattgttgtggctgaggattggactatgaaaaagttt--ggatttgatccagGAAACGGCACTTAATCATGTGAAGACCGCTGGGCTGCTAGGTGATGGATTCGGCTCCACACCAGAGATGAGTAAACGGAACTTATTCTGGGTGGTTAGCC
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gtgaaatattgtgaattttcaggcgtcggattgctcgggctgggcatcagaacattgaaatgtttttggttttgatgcagGAAACCGCACTGAATCATGTGAAGAGCGCTGGGCTGCTAGGAGATGGTTTTGGCTCAACGCCAGAGATGAGTAAACGAGACTTGTTCTGGGTTGTCAGCC
upper sequence: GRMZM2G079308_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA04G21910.1 (Glycine max), 3'ss of exon 2
----------------gtaaggatttgttacatttgaggtgtgagattgttgtggctgaggattggactatg------aaaaagtttggatttgatccagGAAACGGCACTTAATCATGTGAAGACCGCTGGGCTGCTAGGTGATGGATTCGGCTCCACACCAGAGATGAGTAAACGGAACTTATTCTGGGTGGTTAGCC
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atcaaagaacaatgccaaaaacacctatggaatctaagttttgtgcaattgcttattgatgattttattttattgcctaaattgtctgttttccaaacagGAGACTGCACTTAATCATGTTAAGACTGCTGGGCTTCTTGGTGATGGATTTGGTTCCACGCCTGAAATGTGCAAAAAGAACCTGATATGGGTGGTGACTA
upper sequence: GRMZM2G079308_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA17G12940.2 (Glycine max), 3'ss of exon 2
------------------------------------------------------------------------------------------gtaa--ggatttgttacatttgaggtgtgagattgttgtggctg---aggattggactatgaaaaagtttggatttgatccagGAAACGGCACTTAATCATGTGAAGACCGCTGGGCTGCTAGGTGATGGATTCGGCTCCACACCAGAGATGAGTAAACGGAACTTATTCTGGGTGGTTAGCC
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gtaagttcgtcctcatacaagtgaatctttatgagcttcagagatgagtatgttttgactaggacagggctgtatatttagttacactgcataattgaatttcatgtatagataatatcatcctgttgttacttttcatacttgatttatatcaactatttgcttaacaacagGAAACTGCACTTAATCATGTTAAAAGTGCTGGGCTTCTTGGTGATGGCTTCGGTTCCACGCCAGAAATGTGCAAAAAGAACTTGATATGGGTAGTTACTC
upper sequence: GRMZM2G079308_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA06G23560.1 (Glycine max), 3'ss of exon 2
----------------------gtaaggatttgttacatttgaggtgtgagattgttgtggctgag-gattggactatgaaaaagtttggatttg-atccagGAAACGGCACTTAATCATGTGAAGACCGCTGGGCTGCTAGGTGATGGATTCGGCTCCACACCAGAGATGAGTAAACGGAACTTATTCTGGGTGGTTAGCC
| | ||||| ||| ||| | | || || | | | | ||| | | | ||| | | ||||| || |||||||||||||| |||||||||||||| |||||||||||||| || ||||| || || ||| |||| |||| | | |||||||| |
aatgggaaaaacacctatggaaactaagttttgt-acaattgca-tattgatttattttattttattgtttgaattgtttgtttatttaaaaaaacaaacagGAGACTGCACTTAATCATGTTAAGACCGCTGGGCTTCTAGGTGATGGATTTGGTTCCACGCCTGAAATGTGTAAGAAGAACCTGATATGGGTGGTGACTA
upper sequence: GRMZM2G079308_T01 (Zea mays), 3'ss of exon 9
lower sequence: AT1G08510.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaaggatttgttacatttgaggtgtgagattgttgtggctgaggattggac-tatgaaaaagtttggat--ttgatccagGAAACGGCACTTAATCATGTGAAGACCGCTGGGCTGCTAGGTGATGGATTCGGCTCCACACCAGAGATGAGTAAACGGAACTTATTCTGGGTGGTTAGCC
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gtaccatttgattatgattacggttacctgttgtcactggtttaattgatatgtatgaacaagctcttatgctcatgacagGAAACGGCGCTTAATCATGTTAAGACTGCTGGATTGCTTGGAGATGGGTTTGGCTCTACACCTGAGATGTTTAAGAAGAACTTGATATGGGTTGTCACTCMapped 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|211076640|gb|FL394059.1|FL394059EST: TAGAGACAATGATGAACCATTTGCAG GAAACGGCACTTAATCATGTGAAGACCGCTGGGCTGCTAGGTGATGGATTC
genomic: TAGAGACAATGATGAACCATTTGCAGgtaaggattt ... tttgatccagGAAACGGCACTTAATCATGTGAAGACCGCTGGGCTGCTAGGTGATGGATTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtgagattgttgtggctgaggattggactatgaaaaagtttggatttgatccagGAAACGGCACTTAATCATGTGAAGACCGCTGGGCTGCTAGGTGATGGATTCGGCTCCACACCAGAGATGAGTAAACGGAACTTATTCTGGGTGGTTAGCC
atttgat putative branch site (score: 5)
tatgaaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaggatttgttacatttgaggtgtgagattgttgtggctgaggattggactatgaaaaagtttggatttgatccagGAAACGGCACTTAATCATGTGAAGACCGCTGGGCTGCTAGGTGATGGATTCGGCTCCACACCAGAGATGAGTAAACGGAACTTATTCTGGGTGGTTAGCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG