Sequence
atgc intronic sequence ATGC exonic sequence...aatcaagtctattgcactgtcactcacactcatgcaggtttatgtgctccctgactgattactgtttccgtttctattattaattgaatattactttcagGGTAATGGGTGCTGCTGCACTCCAGAAGTACATAGGTAGCTTAGGTGGGATAGGTGCATCAGGTGTTGGCTCAAGCTCTTCCTATGCGCCTAAAGAGTTA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv16s0050g02630.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g43150.1 (Oryza sativa), 3'ss of exon 4
aatcaagtcta--ttgcactgtcactcacactcatgcaggtttatgtgctccctgactgattactgtttccgtttctattattaattgaatattacttt-cagGGTAATGGGTGCTGCTGCACTCCAGAAGTACATAGGTAGCTTAGGTGGGATAGGTGCATCAGGTGTTGGCTCAAGCTCTTCCTATGCGCCTAAAGAGTTA
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--tcttgccgaaatatcattttcagtgcttcttgcatgggttttttt-tggattagttacttattgagataatttctttgttttggtgcttcatattttgcagGGTAATGGGTGCTGCTGCTCTTCAAAAGTATATTGGTAGCTTAGGTGGAATAGGGGCATCTGGTGTTGGTTCCAGTTCATCATATTCTCCTAAAGAATTG
upper sequence: Vv16s0050g02630.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G156069_T01 (Zea mays), 3'ss of exon 4
--aatcaagtctattgcactgtcactcacactcatgcaggtttatgtgctccctgactgattactgtttccgtttctattattaattgaatattactttcagGGTAATGGGTGCTGCTGCACTCCAGAAGTACATAGGTAGCTTAGGTGGGATAGGTGCATCAGGTGTTGGCTCAAGCTCTTCCTATGCGCCTAAAGAGTTA
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aggagaaccactatcaaagactacctggtttcgttgcaaccataaacaccatttacccaaaatgttttttcgatgct--cactgcataatattttgttccagGGTGATGGGTGCTGCTGCACTTCAAAAGTATATTGGGAGCTTAGGTGGAATTGGGGCATCTGGTGTTGGTTCTAGCTCATCATATTCTCCAAAAGAGATG
upper sequence: Vv16s0050g02630.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G004040_T01 (Zea mays), 3'ss of exon 4
aatcaagtctattgcactgtcactcacactcatgcaggtttatgtgctccctgactgattact--gtttccgtttctattattaattgaatattacttt----cagGGTAATGGGTGCTGCTGCACTCCAGAAGTACATAGGTAGCTTAGGTGGGATAGGTGCATCAGGTGTTGGCTCAAGCTCTTCCTATGCGCCTAAAGAGTTA
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--tgaaatgaataattttcttaat-atgttaatt---gtttgggccaaacttggtatatgtttaaatttgctttgtggatgctcactgcataatatcttgttccagGGTGATGGGTGCTGCTGCACTTCAAAAATATATTGGGAGCTTAGGTGGAATTGGGGCATCTGGTGCTGGTTCTAGCTCATCATATTCTCCAAAAGAGATG
upper sequence: Vv16s0050g02630.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA13G08160.1 (Glycine max), 3'ss of exon 4
aatcaagtct---attgcactgtcactcacactcatgcaggtttatgtgctccctgactgattactgtttccgtttctattattaattgaatattactttcagGGTAATGGGTGCTGCTGCACTCCAGAAGTACATAGGTAGCTTAGGTGGGATAGGTGCATCAGGTGTTGGCTCAAGCTCTTCCTATGCGCCTAAAGAGTTA
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gtatgggtctttagtttccctttctccctctctttttcatgtataagcatccactctttgattttaatatac--ttgtattgcta-ctacacatc-ctttcagGTTTATGGGTGCTGCTGCACTTCAAAAATACATTGGAAGCTTGGGTGGGATTGGACCTTCAGGAGTTGGATCAAGTTCTTCCTATGCCCCAAAGGAGCTA
upper sequence: Vv16s0050g02630.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA14G29780.1 (Glycine max), 3'ss of exon 4
aatcaagtct---attgcactgtcactcacactcatgcaggtttatgtgctccctgactgattactgtttccgtttctattattaattgaatattactttcagGGTAATGGGTGCTGCTGCACTCCAGAAGTACATAGGTAGCTTAGGTGGGATAGGTGCATCAGGTGTTGGCTCAAGCTCTTCCTATGCGCCTAAAGAGTTA
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gtatgagtctttagtttccctttctccctcactttctcttgtataagcatccactctttgatttttatatac--ttgtattgcta-ctacacgtc-cattcagGTTTATGGGTGCTGCTGCACTTCAAAAATACATTGGAAGCTTGGGTGGGATTGGACCTTCAGGAGTTGGATCAAGTTCTTCCTATGCCCCAAAGGAGCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctccctgactgattactgtttccgtttctattattaattgaatattactttcagGGTAATGGGTGCTGCTGCACTCCAGAAGTACATAGGTAGCTTAGGTGGGATAGGTGCATCAGGTGTTGGCTCAAGCTCTTCCTATGCGCCTAAAGAGTTA
tattaat putative branch site (score: 2)
ttactttc putative PPT
tttctattattaattg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatcaagtctattgcactgtcactcacactcatgcaggtttatgtgctccctgactgattactgtttccgtttctattattaattgaatattactttcagGGTAATGGGTGCTGCTGCACTCCAGAAGTACATAGGTAGCTTAGGTGGGATAGGTGCATCAGGTGTTGGCTCAAGCTCTTCCTATGCGCCTAAAGAGTTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- tcaagtc
- - - - - - - - ctgtcac
- - - - - - - - - - - - cacactc
- - - - - - - - - - - - - - - - tgcaggt
- - - - - - - - - - - - - - - - - - - - tatgtgc
- - - - - - - - - - - - - - - - - - - - - - - - ccctgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aattgaa