Sequence
atgc intronic sequence ATGC exonic sequence...aataatgtgtttgtatttctttaaaaatgcattaactcatctttcatatttacattctgatggcctacaatgctgggaattttactatttatttcatcagGTACAAAAGAGAAGAATATATGACATCACCAATGTGTTAGAAGGGATTGGGTTAATTGAGAAGAAGCTGAAAAACCGGATTAGATGGAA
Basic information
species | Physcomitrella patens |
transcript | PP1S97_96V6.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S97_96V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA10G09410.1 (Glycine max), 3'ss of exon 4
aataatgtgtttgtatttctttaaaaatgcattaactcatctttcatatttacattctgatggcctacaatgctgggaattttactatttatttcatca--gGTACAAAAGAGAAGAATATATGACATCACCAATGTGTTAGAAGGGATTGGGTTAATTGAGAAGAAGCTGAAAAACCGGATTAGATGGAA
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gtccctcttttttcttttttcaaaaaatgttatgaccaaaatatctgatatttattct--tcctctattatatatgtatttaaatttttttcttttttatagGTGCAAAAGAGGAGAATATATGACATAACTAATGTTTTGGAAGGCATTGGTCTCATTGAAAAGAAGCTCAAGAACAGAATACATTGGAA
upper sequence: PP1S97_96V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: AT5G22220.2 (Arabidopsis thaliana), 3'ss of exon 4
aataatgtgtttgtatttctttaaaaatgcattaactc--atctttcatatttacattctgatggcctacaatgctgg--gaattttactatttatttcatcagGTACAAAAGAGAAGAATATATGACATCACCAATGTGTTAGAAGGGATTGGGTTAATTGAGAAGAAGCTGAAAAACCGGATTAGATGGAA
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---------------------gtgacatatttgaactctagactcccatattgatgtattactttctgtcaaacttagctgtatgttcctgttgatg----cagGTACAAAAGAGAAGGATATATGATATAACCAATGTGTTAGAAGGAATAGGTTTGATAGAGAAGACGCTTAAGAACAGGATTCAGTGGAA
upper sequence: PP1S97_96V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ05155 (Selaginella moellendorffii), 3'ss of exon 3
aataatgtgtttgtatttctttaaaaatgcattaactcatctttcatatttacattctgatggcctacaatgctgggaattttactatttatttcatcagGTACAAAAGAGAAGAATATATGACATCACCAATGTGTTAGAAGGGATTGGGTTAATTGAGAAGAAGCTGAAAAACCGGATTAGATGGAA
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----------------------gtaagtgcat-gctgcattcagtgtgtgt-ctctttcgcaacctgc--ttcagagaggctttcttctgcctt--tcagGTGCAAAAGCGAAGGATCTATGACATCACCAATGTGTTGGAAGGAATTGGCTTAATAGAAAAGAAGTTGAAAAACAGGATAAGATGGAA
upper sequence: PP1S97_96V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ05692 (Selaginella moellendorffii), 3'ss of exon 3
aataatgtgtttgtatttctttaaaaatgcattaactcatctttcatatttacattctgatggcctacaatgctgggaattttactatttatttcatcagGTACAAAAGAGAAGAATATATGACATCACCAATGTGTTAGAAGGGATTGGGTTAATTGAGAAGAAGCTGAAAAACCGGATTAGATGGAA
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----------------------gtaagtgcat-gctgcattcagtgtctgtctctttcgcaagc---tgcttcagagaggctttcttctgcctt--tcagGTGCAAAAGCGAAGGATCTATGACATCACCAATGTGTTGGAAGGAATTGGCTTAATAGAAAAGAAGTTGAAAAACAGAATAAGATGGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatttacattctgatggcctacaatgctgggaattttactatttatttcatcagGTACAAAAGAGAAGAATATATGACATCACCAATGTGTTAGAAGGGATTGGGTTAATTGAGAAGAAGCTGAAAAACCGGATTAGATGGAA
ttctgat putative branch site (score: 3)
tttatttc putative PPT
aattttactatttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aataatgtgtttgtatttctttaaaaatgcattaactcatctttcatatttacattctgatggcctacaatgctgggaattttactatttatttcatcagGTACAAAAGAGAAGAATATATGACATCACCAATGTGTTAGAAGGGATTGGGTTAATTGAGAAGAAGCTGAAAAACCGGATTAGATGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA