Sequence
atgc intronic sequence ATGC exonic sequencegtgattcttgagaactcttgttcctgtgttattcaaatgaaatcgttttctcttaccgtcctatttgtttattgcagATCTTGAAAGGTGATGATGTGGACTTAATGATCATTGCCAGAGGAACACCCGGATTCTCCGGTGCAGACCTTGCTAACTTGGTAAATGTTGCTGCACTTA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G096764_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g39250.1 (Oryza sativa), 3'ss of exon 6
gtgattcttgagaactcttgttcctgtgttattc-------aaatgaaatcgttttctcttaccgtcctatttgttt-attgcagATCTTGAAAGGTGATGATGTGGACTTAATGATCATTGCCAGAGGAACACCCGGATTCTCCGGTGCAGACCTTGCTAACTTGGTAAATGTTGCTGCACTTA
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gtaattcttgagaacttttggtatcatgtttgtccaggctaaaatggaatgtcttatagttatccttatacacatatgattacagGTCTTGAAGAGTGATGATGTGGATTTGATGATCATTGCCAGGGGAACACCTGGATTCTCAGGTGCAGACCTTGCTAACTTGGTAAATGTGGCTGCTCTTA
upper sequence: GRMZM2G096764_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g39260.1 (Oryza sativa), 3'ss of exon 6
gtgattcttgagaactcttgttcctgtgtt-------attcaaatgaaatcgttttctcttaccgtcctatttgttta-ttgcagATCTTGAAAGGTGATGATGTGGACTTAATGATCATTGCCAGAGGAACACCCGGATTCTCCGGTGCAGACCTTGCTAACTTGGTAAATGTTGCTGCACTTA
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gtaattcttgagaacttttggtatcatgtttgtccagactaagatggaatgtcttatatttatccttatacacatatggttacagGTCTTGAAGAGTGATGATGTGGATTTGATGATCATTGCCAGGGGAACACCTGGATTCTCAGGTGCAGACCTTGCTAACTTGGTTAATGTGGCTGCTCTTA
upper sequence: GRMZM2G096764_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA17G34610.1 (Glycine max), 3'ss of exon 4
------------------gtgattcttgagaactctt---gttcctgtgttattcaaatgaaatcgttttctcttaccgtcc--tatttgtttattgcagATCTTGAAAGGTGATGATGTGGACTTAATGATCATTGCCAGAGGAACACCCGGATTCTCCGGTGCAGACCTTGCTAACTTGGTAAATGTTGCTGCACTTA
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tccattaaatgtatatatatgatcttagaaaattgtgtgagcttcttgatcagtgttacctacttgtttatgctggatttttgttgccaatcaagtacagGTTCTGAAGGCTGATGATGTTGATCTAATGATCATTGCCAGAGGAACACCTGGGTTCTCTGGTGCTGACCTTGCAAACTTGATTAACATTGCTGCTATCA
upper sequence: GRMZM2G096764_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA14G10950.1 (Glycine max), 3'ss of exon 6
-------------------gtgattcttgagaactcttgttcctgtgttattcaaatgaaatcgttttctcttaccg---tcctattt---gtttattgcagATCTTGAAAGGTGATGATGTGGACTTAATGATCATTGCCAGAGGAACACCCGGATTCTCCGGTGCAGACCTTGCTAACTTGGTAAATGTTGCTGCACTTA
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atccattaaatgtataactatgatcttagatgattgt-gtgagcttcttgatcagg-gttacctatttcttatgctggatttttgtttcccatcaaatacagGTTCTGAAGGCTGATGATGTTGATCTAATGATCATTGCCCGAGGAACACCGGGGTTCTCTGGTGCTGACCTTGCAAACTTGATTAACATTGCTGCTATCA
upper sequence: GRMZM2G096764_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA14G10960.1 (Glycine max), 3'ss of exon 4
-------------------gtgattcttgagaactcttgttcctgtgttattcaaatgaaatcgttttctcttaccg---tcctattt---gtttattgcagATCTTGAAAGGTGATGATGTGGACTTAATGATCATTGCCAGAGGAACACCCGGATTCTCCGGTGCAGACCTTGCTAACTTGGTAAATGTTGCTGCACTTA
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atccattaaatgtataactatgatcttagatgattgt-gtgagcttcttgatcag-tgttacctttttgttatgctggatttttgtttccaatcaaatacagGTTCTGAAGGCTGATGATGTTGATCTAATGATCATTGCCCGAGTAACACCTGGGTTCTCTGGTGCTGACCTTGCAAACTTGATTAACATTGCTGCTATCAMapped 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|213183957|gb|FM195937.1|FM195937EST: GTCGACGTC-AATCCTAGAATCCCATATGTCAAAG ATCTTGAAAGGTGATGATGTGGACTTAATGATCATTGCCAGAGGAACACCC
genomic: GTCGACGTCAAATCCTAGAATCCCATATGTCAAAGgtgattcttg ... tttattgcagATCTTGAAAGGTGATGATGTGGACTTAATGATCATTGCCAGAGGAACACCC
EST:
gi|149080326|gb|EE169346.2|EE169346EST: ACCCAGATGTTGAAGGTCGACGTCAAATCCTAGAATCCCATATGTCAAAG ATCTTGAAAGGTGATGATGTGGACTTAATGATCATTGCCAGAGGAACACCC
genomic: ACCCAGATGTTGAAGGTCGACGTCAAATCCTAGAATCCCATATGTCAAAGgtgattcttg ... tttattgcagATCTTGAAAGGTGATGATGTGGACTTAATGATCATTGCCAGAGGAACACCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctgtgttattcaaatgaaatcgttttctcttaccgtcctatttgtttattgcagATCTTGAAAGGTGATGATGTGGACTTAATGATCATTGCCAGAGGAACACCCGGATTCTCCGGTGCAGACCTTGCTAACTTGGTAAATGTTGCTGCACTTA
ctcttac putative branch site (score: 3)
tttgttt putative PPT
ttattcaaatgaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgattcttgagaactcttgttcctgtgttattcaaatgaaatcgttttctcttaccgtcctatttgtttattgcagATCTTGAAAGGTGATGATGTGGACTTAATGATCATTGCCAGAGGAACACCCGGATTCTCCGGTGCAGACCTTGCTAACTTGGTAAATGTTGCTGCACTTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC