Sequence
atgc intronic sequence ATGC exonic sequence...tctatgttaaaccgcttctttcggttgtgttgatggtaagagaggccgcttagcccatcagtatactcatcacaagaatactattctgatatccatgcagGTGTCCACATAAATAAAGGTCTTTTAGCCCTTGGAAATGTGATCAGTGCCCTTGGTGATGATAAGAAGCGGAAGGAAGGAGGGCATGTCCCGTACCGTGA
Basic information
species | Physcomitrella patens |
transcript | PP1S74_30V6.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S74_30V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA17G35780.1 (Glycine max), 3'ss of exon 5
tctatgttaaac-cgcttctttcggttgtgttgatggtaagagaggccgcttagcccatcagtatactcatcacaagaatactattctgatatccatgcagGTGTCCACATAAATAAAGGTCTTTTAGCCCTTGGAAATGTGATCAGTGCCCTTGGTGATGATAAGAAGCGGAAGGAAGGAGGGCATGTCCCGTACCGTGA
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-----gttaggcacgacaattttcact-tgtttcttctaaac----ttgctt--ttgatcattatgaattctctaataatttt-ttct----ttcaatcagGAGTCCACATTAACAAAGGCCTTCTAGCGCTTGGTAATGTTATTAGTGCGCTTGGTGATGAAAAGAAGAGAAAAGAAGGTGTTCATGTTCCTTATAGGGA
upper sequence: PP1S74_30V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA04G04380.1 (Glycine max), 3'ss of exon 5
tctatgttaaaccgcttctttcggttgtgttgatggtaagagaggccgcttagcccatcagtatactcat-cacaagaatactattctgatatccatgcagGTGTCCACATAAATAAAGGTCTTTTAGCCCTTGGAAATGTGATCAGTGCCCTTGGTGATGATAAGAAGCGGAAGGAAGGAGGGCATGTCCCGTACCGTGA
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-----gttagtttgggacattttttcacctttatcgttcaagcatgcttttg-------agaacacatattcactagtaatttaatct----ttcaaacagGAGTTCACATTAACAAAGGCCTCCTAGCACTTGGTAATGTTATTAGTGCACTTGGTGATGAAAAGAAGCGAAAGGAAGGTGTTCATGTTCCATATAGGGA
upper sequence: PP1S74_30V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: AT5G60930.1 (Arabidopsis thaliana), 3'ss of exon 5
----tctatgttaaaccgcttctttcggt-tgtgttgatggtaagagaggccgcttagcccatcagtatactc-atcacaagaatac------tattctg---atatccatgcagGTGTCCACATAAATAAAGGTCTTTTAGCCCTTGGAAATGTGATCAGTGCCCTTGGTGATGATAAGAAGCGGAAGGAAGGAGGGCATGTCCCGTACCGTGA
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gttatctatctcatgtttatctttatgatgtataaagttgtataaatattctttctggtttcttaaaagagactatgactaaactataaggtttatttcatcaatatttacacagGTATTCACATCAACAAAGGTCTATTAGCTCTTGGAAATGTTATAAGTGCACTTGGAGATGAGAAAAAGAGAAAGGAAGGAGGTCACGTTCCTTACCGTGA
upper sequence: PP1S74_30V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ26093 (Selaginella moellendorffii), 3'ss of exon 5
tctatgttaaaccgcttctttcggttgtgttgatggtaagagaggccgcttagcccatcagtatactcatcacaagaatactattctgatatccatgcagGTGTCCACATAAATAAAGGTCTTTTAGCCCTTGGAAATGTGATCAGTGCCCTTGGTGATGATAAGAAGCGGAAGGAAGGAGGGCATGTCCCGTACCGTGA
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-----------------------------------------------gttggttttattagtggtttcacgtcaggtttaactttctgtt-----tgcagGTGTTCATATCAATAAGGGACTTTTAGCTCTTGGAAATGTCATCAGTGCTTTGGGAGATGATAAAAAACGTAAAGAAGGAGGGCATGTTCCTTATAGGGA
upper sequence: PP1S74_30V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ10856 (Selaginella moellendorffii), 3'ss of exon 5
tctatgttaaaccgcttctttcggttgtgttgatggtaagagaggccgcttagcccatcagtatactcatcacaagaatactattctgatatccatgcagGTGTCCACATAAATAAAGGTCTTTTAGCCCTTGGAAATGTGATCAGTGCCCTTGGTGATGATAAGAAGCGGAAGGAAGGAGGGCATGTCCCGTACCGTGA
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--------------------------------------------gttggttttattagttgcagaggtttcacgtaaggtttaactttctgtt--tgcagGTGTTCATATCAATAAGGGACTTTTAGCTCTTGGAAATGTCATCAGTGCTTTGGGAGATGATAAAAAACGTAAAGAAGGAGGGCATGTTCCTTATAGGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccgcttagcccatcagtatactcatcacaagaatactattctgatatccatgcagGTGTCCACATAAATAAAGGTCTTTTAGCCCTTGGAAATGTGATCAGTGCCCTTGGTGATGATAAGAAGCGGAAGGAAGGAGGGCATGTCCCGTACCGTGA
ttctgat putative branch site (score: 3)
aatactatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctatgttaaaccgcttctttcggttgtgttgatggtaagagaggccgcttagcccatcagtatactcatcacaagaatactattctgatatccatgcagGTGTCCACATAAATAAAGGTCTTTTAGCCCTTGGAAATGTGATCAGTGCCCTTGGTGATGATAAGAAGCGGAAGGAAGGAGGGCATGTCCCGTACCGTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG