Sequence
atgc intronic sequence ATGC exonic sequencegtaggggaagaatgcatatatgtgttcattaatcttgatctagtggtttcctttagtctaatagtgtaagtgcctctcagGCTAGAGGGAATGCAATTCTACAGGCGAGTTTGGAAAGAAGAAAACAAGCGCTACATGAACGCAGATTGGCTTTGGAACAGGAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G115975_T01 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os03g24180.1 (Oryza sativa), 3'ss of exon 16
gtaggggaagaatgcatatatgtgttcattaatcttgatctagtggtttcctttagtctaatagtgtaagtgcctctcagGCTAGAGGGAATGCAATTCTACAGGCGAGTTTGGAAAGAAGAAAACAAGCGCTACATGAACGCAGATTGGCTTTGGAACAGGAT
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gtatgtgaagaaaatgcacataag---aatattct--attttatgcttgcc----atctaacaagg--agtggct-tcagGCTAGGGGTAATGCAATTCTACAGGCAAGTTTGGAAAGAAGGAAACAAGCACTGCATGAACGTCGTTTGGCCCTGGAACAGGAT
upper sequence: GRMZM2G115975_T01 (Zea mays), 3'ss of exon 16
lower sequence: PP1S271_62V6.1 (Physcomitrella patens), 3'ss of exon 16
----------gtaggggaagaatgcatatatgtg---ttcattaatcttgatctagtggtttcctttagtctaatagtgtaagtgcctct-------cagGCTAGAGGGAATGCAATTCTACAGGCGAGTTTGGAAAGAAGAAAACAAGCGCTACATGAACGCAGATTGGCTTTGGAACAGGAT
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tccttcaccttcagaccaatctctactacaagttaaccttaatagttatggtgaaaatgttttactcatgtcatacgttcgtggtcttttgattgaacagGCAAAAGGAAATGCAATTTTACAAGCTAGTTTGGAAAGAAGAAAGCAAGCTCTACATGACCGTCGGCTGGCCCTTGAACAAGAT
upper sequence: GRMZM2G115975_T01 (Zea mays), 3'ss of exon 16
lower sequence: PP1S78_26V6.1 (Physcomitrella patens), 3'ss of exon 15
----------------gtaggggaagaatgcatatatgtgttcattaatcttg---atctagtggtttcctt-tagtctaatagtgtaagtgcctctcagGCTAGAGGGAATGCAATTCTACAGGCGAGTTTGGAAAGAAGAAAACAAGCGCTACATGAACGCAGATTGGCTTTGGAACAGGAT
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atcatcctgctccatattcagaagaaactttacccttcgatacaatgcttgtgtaaatgtaatattcacattattatattttggcattatgaataaacagGCGAAAGGGAATGCAATTTTACAAGCTAGCTTGGAAAGAAGAAAGCAAGCTTTACATGACCGTCGTCTGGCCCTTGAACAAGAT
upper sequence: GRMZM2G115975_T01 (Zea mays), 3'ss of exon 16
lower sequence: EFJ23838 (Selaginella moellendorffii), 3'ss of exon 15
gtaggggaagaatgcatatatgtgttcattaatcttgatctagtggtttcctttagtctaatagtg-taagtgcct-ctcagGCTAGAGGGAATGCAATTCTACAGGCGAGTTTGGAAAGAAGAAAACAAGCGCTACATGAACGCAGATTGGCTTTGGAACAGGAT
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------------------------------------gtactcgcgttcttccatgttattgtactgatatgtgcaagcttagGCTAAAGGAAATGCAATTCTTCAAGCGAGTTTGGAAAGACGAAAGCAAGCACTTCACGATCGCCGGCTCGCTCTTGAACAGGAC
upper sequence: GRMZM2G115975_T01 (Zea mays), 3'ss of exon 16
lower sequence: EFJ24423 (Selaginella moellendorffii), 3'ss of exon 15
gtaggggaagaatgcatatatgtgttcattaatcttgatctagtggtttcctttagtctaata-gtgtaagtgcctctcagGCTAGAGGGAATGCAATTCTACAGGCGAGTTTGGAAAGAAGAAAACAAGCGCTACATGAACGCAGATTGGCTTTGGAACAGGAT
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----------------------------gtactcgcgttcttgcatgttattgta--ctgatatgtgcaag-----cttagGCTAAAGGAAATGCAATTCTTCAAGCGAGTTTGGAAAGACGAAAGCAAGCACTTCATGATCGCCGGCTCGCTCTTGAACAAGACMapped 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|60396241|gb|DN229110.1|DN229110EST: AAAGACTAGAGATTGCGAAGAATGATCTGCAAAACAGAATTGCAAAAGAG GCTAGAGGGAATGCAATTCTACAGGCGAGTTTGGAAAGAAGAAAACAAGCG
genomic: AAAGACTAGAGATTGCGAAGAATGATCTGCAAAACAGAATTGCAAAAGAGgtaggggaag ... tgcctctcagGCTAGAGGGAATGCAATTCTACAGGCGAGTTTGGAAAGAAGAAAACAAGCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcattaatcttgatctagtggtttcctttagtctaatagtgtaagtgcctctcagGCTAGAGGGAATGCAATTCTACAGGCGAGTTTGGAAAGAAGAAAACAAGCGCTACATGAACGCAGATTGGCTTTGGAACAGGAT
gtctaat putative branch site (score: 3)
tgcctctc putative PPT
tctaata 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
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gtaggggaagaatgcatatatgtgttcattaatcttgatctagtggtttcctttagtctaatagtgtaagtgcctctcagGCTAGAGGGAATGCAATTCTACAGGCGAGTTTGGAAAGAAGAAAACAAGCGCTACATGAACGCAGATTGGCTTTGGAACAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT