Sequence
atgc intronic sequence ATGC exonic sequencegtagtaaaaaaaacccaatcagcttagtctgacttttcactgggatttcgcgtggattggcggcgcttaaccatgaagtgtctactgtcttgcagCTGGATGACTGGGTGCTGTGCCGGATCTACAACAAGAAGGGTGTTATCGAGCGGTACGACACAGTGGACGACGACGACGGCGACGGCGCCGTGGCCGAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G123667_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os11g08210.1 (Oryza sativa), 3'ss of exon 2
gtagtaaaaaaaacccaatcagcttagtctg---acttttcactgggatttcgcgtggattggcgg------cgcttaaccatgaagtgtctactgtcttgcagCTGGATGACTGGGTGCTGTGCCGGATCTACAACAAGAAGGGTGTTATCGAGCGGTACGACACAGTGGACGACGACGACGGCGACGGCGCCGTGGCCGAAG
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----ccaaaaactttttaccaccaccactcgcatgcattccacatcaatcttgatcactttgctaataatttcagttttttttttggttaatttttttttgcagTTGGATGATTGGGTGTTGTGCCGAATCTACAACAAGAAGGGAGTGATCGAGAGGTACGACACGGTGGACGCCGGCGAGGACGTGAAGCCGGCGGCGGCGG
upper sequence: GRMZM2G123667_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA02G26480.1 (Glycine max), 3'ss of exon 2
-gtagtaaaaaaaacccaatcagcttagtctgacttttcactgggatttcgcgtggattggcgg--cgcttaaccatga--agtgtctactgtcttgcagCTGGATGACTGGGTGCTGTGCCGGATCTACAACAAGAAGGGTGTTATCGAGCGGTACGACACAGTGGACGACGACGACG-GCGACGGCGCCGTGGCCGAAG
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ggaaattattcgttctttcttatctctattgaagttagggatatgagaaattgaaaattaaaaaaatgtttgcacatgattgttgtttctgattatgcagCTGGATGACTGGGTGCTGTGTCGAATTTACAACAAGAAAGGTGCAATTGAGAAGCAGCAACCAGCAC-CGCCACCACCGAGTGGTGTCCACAAAATTGAAT
upper sequence: GRMZM2G123667_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA14G24220.1 (Glycine max), 3'ss of exon 2
---------gtagtaaaaaaaacccaatcagcttagtctgacttttcactgggatttcgcgtggattggcggcgcttaaccatgaagtgtctactgtcttgcagCTGGATGACTGGGTGCTGTGCCGGATCTACAACAAGAAGGGTGTTATCGAGCGGTACGACACAGTGGACGACGACGACGGCGACGGCGCCGTGGCCGAAG------
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ttcgttcttatcttagggatatcggaaattaaa-aattgaagattaaaatatgtgtgcacatg-attgctgac--ttaattttgatgatttctgatttttgcagCTGGATGACTGGGTGCTGTGCCGAATTTACAACAAGAAAGGTGCAATTGAAAAGCA----ACAACTACCACCACCGA--GTGGGGTCCGCAAAATTGAATGTTCCG
upper sequence: GRMZM2G123667_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA06G11970.1 (Glycine max), 3'ss of exon 2
----gtagtaaaaaaaacccaatcagcttagtctgacttttcactgggatttcgcg--tggattggcggcgcttaaccatgaagtgtctactgtcttgcagCTGGATGACTGGGTGCTGTGCCGGATCTACAACAAGAAGGGTGTTATCGAGCGGTACGACACAGTGGACGACGACGACGGCGACGGCGCCGTGGCCGAAG---
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tatctctctcacctgcctccgattgcaatacttataataataaatgaaaatgaagaaataatcttacggtggttg-tgatttttttttttttttgtcgcagTTGGATGATTGGGTGCTTTGCCGTATTTACAACAAGAAGGGCACGATCGAG--AAACTGCA-ACCAAGCAGCGATGTTGCTCATAGCCGAAATATCGAATCCT
upper sequence: GRMZM2G123667_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S140_93V6.1 (Physcomitrella patens), 3'ss of exon 2
-----gtagtaaaaaaaacccaatcagcttagtctgacttttcactgggatttcgcgtggattg---gcggcgcttaaccatgaagtgtctactgtct-tgcagCTGGATGACTGGGTGCTGTGCCGGATCTACAACAAGAAGGGTGTTATCGAGCGGTACGACACAGTGGACGACGACGACGGCGACGGCGCCGTGGCCGAAG
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ggatggtgctgtcactaattctgt--gcacattcc-acacgtcaatcgtatctgaaggcgattgttcatggtgctta-tgattttgtttacattctgtgcgcagTTGGATGATTGGGTGTTGTGCCGGATCTACAAAAAGAGTACAAATGCACAGCGTACTGGCAAGGAGCGTGATAGCTCTTCTTGCGTCGAAGAG-------
upper sequence: GRMZM2G123667_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ36823 (Selaginella moellendorffii), 3'ss of exon 1
----------------------------------------------------gtagtaaaaaaaacccaatcagcttagtctga-cttttcactgggatttcgcgtggattggcggcgcttaaccatgaagtgtctactgtcttgcagCTGGATGACTGGGTGCTGTGCCGGATCTACAACAAGAAGGGTGTTATCGAGCGGTACGACACAGTGGACGACGACGACGGCGACGGCGCCGTGGCCGAAG
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gtaagtttcaattcctccaagtagttgcataagtcctgcatattggggaaaaaaacaaaaaaaaaaaaaaaaaagagagctcgagctcatgagtggtattaaaaaccgatggct--tactttggcaagctgttcttctttcgttgcagCTGGACGACTGGGTGCTGTGCCGGATCTACAGAAAGAAGACA----------------------------------------------------------
upper sequence: GRMZM2G123667_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ27849 (Selaginella moellendorffii), 3'ss of exon 1
-------------------------------------------------------------gtagtaaaaaaaacccaatcagcttagtctga--cttttcactgggatttcgcgtggattggcggcgcttaaccatgaagtgtctactgtcttgcagCTGGATGACTGGGTGCTGTGCCGGATCTACAACAAGAAGGGTGTTATCGAGCGGTACGACACAGTGGACGACGACGACGGCGACGGCGCCGTGGCCGAAG
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gtaagtttcaattcctccaagtagttgcatccagtcctgcatattggggaaaaaaacaaaaaaaacaaaaaaaaaaaaaaaagaaagagcgagagctcgtgagtggtattaaaaaccgatggct--tactttggcaagctgttcttctttcgttgcagCTGGACGACTGGGTGCTGTGCCGGATCTACAGAAAGAAGACA----------------------------------------------------------
upper sequence: GRMZM2G123667_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ31748 (Selaginella moellendorffii), 3'ss of exon 1
gtagtaaaaaaaacccaatcagcttagtctgacttttcactgggatttcgcgtggattggcggcgcttaaccatga--agtgtctactgtcttgcagCTGGATGACTGGGTGCTGTGCCGGATCTACAACAAGAAGGGTGTTATCGAGCGGTACGACACAGTGGACGACGACGACGGCGACGGCGCCGTGGCCGAAG
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---------------------------------gtttgaaagccgctgactagatattgactgtttttgactatgtttgacttccatgttttttcagCTGGACGACTGGGTGCTGTGCCGAATTTACAAAAAGAAG------------------------------------------------------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgggatttcgcgtggattggcggcgcttaaccatgaagtgtctactgtcttgcagCTGGATGACTGGGTGCTGTGCCGGATCTACAACAAGAAGGGTGTTATCGAGCGGTACGACACAGTGGACGACGACGACGGCGACGGCGCCGTGGCCGAAG
gcttaac putative branch site (score: 3)
ctgtctt putative PPT
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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gtagtaaaaaaaacccaatcagcttagtctgacttttcactgggatttcgcgtggattggcggcgcttaaccatgaagtgtctactgtcttgcagCTGGATGACTGGGTGCTGTGCCGGATCTACAACAAGAAGGGTGTTATCGAGCGGTACGACACAGTGGACGACGACGACGGCGACGGCGCCGTGGCCGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA