Sequence
atgc intronic sequence ATGC exonic sequencegtgattcagtgacatctggatattttactcaactgtattttctaagtcatggcattgatattattattgttttttatcttctagGTAGGCAAAAACCTTCATGTTCTAGGCCAGATTGACGGCGTTGACCTTGATATGTACAAAGAAACTGTTCTTCCAAGGATATTAGAGCAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM5G844195_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os03g58700.1 (Oryza sativa), 3'ss of exon 6
gtgattcagtgacatctggatattttactcaactgtattttctaagtcatggcattgatattattattgttttttatctt--ctagGTAGGCAAAAACCTTCATGTTCTAGGCCAGATTGACGGCGTTGACCTTGATATGTACAAAGAAACTGTTCTTCCAAGGATATTAGAGCAG
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gtaatcatcaattacatgtattccctacactacatgttctttggtgtcatttcaatgacattgctactgttctttcttttttctagGTAGGCAAAAACCTTCACGTTCTAAGCCAGATTGAGGGTGTTGACCTTGACATGTACAAAGAAACTGTCCTTCCAAGGATATTAGAACAG
upper sequence: GRMZM5G844195_T02 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA17G37870.1 (Glycine max), 3'ss of exon 7
gtgattcagtgacatctggatatttt---actcaactgtattttctaagtcatggcattgatattatt--attgttttttat----cttctagGTAGGCAAAAACCTTCATGTTCTAGGCCAGATTGACGGCGTTGACCTTGATATGTACAAAGAAACTGTTCTTCCAAGGATATTAGAGCAG
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gtaatataaaaatatgatactatctcctgatgaagcaatgtgttacacattttgatagataagttatgtgatttccttttctgaaattattagGTAGGGAAAAATCTACATGTTCTGAGTCAGATAGAGGGCGTGGACCTTGAGATGTACAAAGACACCGTCCTTCCTAGTGTCTTAGAGCAG
upper sequence: GRMZM5G844195_T02 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA11G08390.1 (Glycine max), 3'ss of exon 6
gtgat-tcagtgacatctggatattttactcaactgta------ttttctaagtcatggcattgatat-------tattattg-ttttttatcttc----------tagGTAGGCAAAAACCTTCATGTTCTAGGCCAGATTGACGGCGTTGACCTTGATATGTACAAAGAAACTGTTCTTCCAAGGATATTAGAGCAG
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gtaatacctgaagcttgttactggtttgcttctctgcaatggggttgtataaatgatgaaatgcttatagaaggcttttcttgcttttttgtccttgatacataattagGTTGGCAAGAATCTTCATGTTCTCAGTCAGATAGAGGGTGTTGACCTAGATATGTACAAAGATGTTGTGCTTCCCAGAGTACTGGAGCAG
upper sequence: GRMZM5G844195_T02 (Zea mays), 3'ss of exon 7
lower sequence: AT1G75850.1 (Arabidopsis thaliana), 3'ss of exon 6
gtgattcagtgacatctggatattttactcaactgtattttctaagtcatggcattgatattattattgttttttatcttctagGTAGGCAAAAACCTTCATGTTCTAGGCCAGATTGACGGCGTTGACCTTGATATGTACAAAGAAACTGTTCTTCCAAGGATATTAGAGCAG
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gtaacatcgataccactacttgaattagtatcctatttttgctatgtactgcccactaagttgtatttaatgttttcctctcagGTTGGAAAAAATCTGCATGTTCTAGGACAGATAGAAGGTGTTGACCTTGAGATGTACAAAGAGACTGTTCTTCCTAGGGTCTTAGAGCAG
upper sequence: GRMZM5G844195_T02 (Zea mays), 3'ss of exon 7
lower sequence: Vv18s0001g14680.t01 (Vitis vinifera), 3'ss of exon 6
--gtgattcagtgacatctggatattttactcaactgtattttctaagtcatggcattgatattat--tattgttttttatcttct----agGTAGGCAAAAACCTTCATGTTCTAGGCCAGATTGACGGCGTTGACCTTGATATGTACAAAGAAACTGTTCTTCCAAGGATATTAGAGCAG
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gtaagatcagataatctgggtctatgtaataccacta-gttggagcagtgtctatagagaagttatggtgctgtcctgtattttctttgtagGTTGGGAAGAATCTACATGTTCTCAGTCAGATTGAGGGTATTGACCTTGAAATGTATAAAGATACTGTTCTTCCCAGGGTCTTAGAGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caactgtattttctaagtcatggcattgatattattattgttttttatcttctagGTAGGCAAAAACCTTCATGTTCTAGGCCAGATTGACGGCGTTGACCTTGATATGTACAAAGAAACTGTTCTTCCAAGGATATTAGAGCAG
cattgat putative branch site (score: 4)
ttgttttttatcttct putative PPT
attgatattattattg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgattcagtgacatctggatattttactcaactgtattttctaagtcatggcattgatattattattgttttttatcttctagGTAGGCAAAAACCTTCATGTTCTAGGCCAGATTGACGGCGTTGACCTTGATATGTACAAAGAAACTGTTCTTCCAAGGATATTAGAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG