Sequence
atgc intronic sequence ATGC exonic sequencegtaaggataagcataagctcaattgcctcacaactcacacttgatctatgttggttagctctgttttttttttgttcgtttgttttcaacctaccaacatgtttttttgcccatctgttttcaacttacgaatagGTTTGTGCTGGACTTTCATCCTGCCTCCAAGAGTATAAGTCTAAAAATGCACAGCTGGAGGAACTTCTTGTTCAAGAGGTCTAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM5G870802_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g54119.1 (Oryza sativa), 3'ss of exon 5
gtaaggataagcataagctcaattgcctcacaactcacacttgatctatgttggttagctctgttttttttttgttcgtttgttttcaacctaccaacatgtttttttgcccatctgttttcaacttacgaatagGTTTGTGCTGGACTTTCATCCTGCCTCCAAGAGTATAAGTCTAAAAATGCACAGCTGGAGGAACTTCTTGTTCAAGAGGTCTAG
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-------------------------------------------gtaagagcagtataagtttgaccctgcctgttatctatgttgt-ggctagttcatatgctgacttgtagatttatttgttact-accaatagGTCTGCGCTGGACTTTCATCCCGCCTCCAGGAGTATAAATCTGAGAATGCACAGCTGGAGGAACTTCTTGTTCAGGAG------
upper sequence: GRMZM5G870802_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA16G08430.1 (Glycine max), 3'ss of exon 5
gtaaggataagcataagctcaattgcctcacaactcacacttgatctatgttggttagctctgttttttttttgttcgtttgttttcaacctaccaacatgtttttttgcccatctgttttcaacttacgaatagGTTTGTGCTGGACTTTCATCCTGCCTCCAAGAGTATAAGTCTAAAAATGCACAGCTGGAGGAACTTCTTGTTCAAGAGGTCTAG
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-----------------------------------------------------gtaagggtgttgcttaaaccaataaaatctttctaattgcttattatagatgcctgattat-tatttcctaatgatgctcagGTCTGTGCTGGATTGTCATCCCGTCTTCAAGAATACAAATCTGAAAATGCACAGTTGGAGGAACTTCTCACTTCAGAG------
upper sequence: GRMZM5G870802_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA01G01230.1 (Glycine max), 3'ss of exon 7
gtaaggataagcataagctcaattgcctcacaactcacacttgatctatgttggttagctctgttttttttttgttcgtttgttttcaacctaccaacatgtttttttgcccatctgttttcaacttacgaatagGTTTGTGCTGGACTTTCATCCTGCCTCCAAGAGTATAAGTCTAAAAATGCACAGCTGGAGGAACTTCTTGTTCAAGAGGTCTAG
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-----------------------------------------------------gtaagggtgtttcttaaaccaataaaatcttcctaattgcttattatagatgcctgattaa-tatttcctaatgatgctcagGTCTGTGCTGGATTGTCATCCCGTCTTCAAGAATACAAATCTGAAAATGCACAGTTGGAGGAACTTCTCACTTCAGAG------ atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttttcaacctaccaacatgtttttttgcccatctgttttcaacttacgaatagGTTTGTGCTGGACTTTCATCCTGCCTCCAAGAGTATAAGTCTAAAAATGCACAGCTGGAGGAACTTCTTGTTCAAGAGGTCTAG
aacttac putative branch site (score: 2)
atgttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaggataagcataagctcaattgcctcacaactcacacttgatctatgttggttagctctgttttttttttgttcgtttgttttcaacctaccaacatgtttttttgcccatctgttttcaacttacgaatagGTTTGTGCTGGACTTTCATCCTGCCTCCAAGAGTATAAGTCTAAAAATGCACAGCTGGAGGAACTTCTTGTTCAAGAGGTCTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG