Sequence
atgc intronic sequence ATGC exonic sequence...gccgtagttgattacctgcagttctgttagcatacaaataaatgtgacatcaaacgatgactttcatcaagtgttcttcattaagaatattctttcacagGTCGTCATTGGCCCAGCCACTGTAGGAGGTATACAGGCTGGTGCATTCAAAATTGGTGATACTGCAGGCACGTTGGACAATATCATTCACTGCAAGCTTT
Basic information
species | Physcomitrella patens |
transcript | PP1S46_63V6.3 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S46_63V6.3 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os01g19450.1 (Oryza sativa), 3'ss of exon 5
gccgtagttgattacctgcagttctgttagcatacaaata--aatg-tgacatcaaac--gatgactttcatcaagtgttcttcattaagaatattctttcacagGTCGTCATTGGCCCAGCCACTGTAGGAGGTATACAGGCTGGTGCATTCAAAATTGGTGATACTGCAGGCACGTTGGACAATATCATTCACTGCAAGCTTT
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----ttggtgttggcatgctattttattgcctgccaggcactaacgctgacggcggcctgcatgtttctcgtttattttaccaagtaactgttgttgtttc-tagGTAATCATTGGACCAGCAACAGTTGGAGGAATCCAAGCTGGTGCTTTCAAGATTGGTGATACTGCTGGAACCATTGACAACATTATTCAATGCAAGCTTT
upper sequence: PP1S46_63V6.3 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ33298 (Selaginella moellendorffii), 3'ss of exon 4
gccgtagttgattacctgcagttctgttagcatacaaataaatgtgacatcaaacgatgactttcatcaagtgttcttcattaagaatattctttcacagGTCGTCATTGGCCCAGCCACTGTAGGAGGTATACAGGCTGGTGCATTCAAAATTGGTGATACTGCAGGCACGTTGGACAATATCATTCACTGCAAGCTTT
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-----------------------------------gtactcttgagacttggaataa--acttacgagatttgttcttcacttg---------ttcatagGTAGTCATTGGGCCTGCTACTGTAGGTGGTATGCAGGCTGGTGCCTTCAAGATTGGAGATACTGCTGGTACTCTCGATAACATCGTGAGTTGTAAGCTTT
upper sequence: PP1S46_63V6.3 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ15935 (Selaginella moellendorffii), 3'ss of exon 4
gccgtagttgattacctgcagttctgttagcatacaaataaatgtgacatcaaacgatgactttcatcaagtgttcttcattaagaatattctttcacagGTCGTCATTGGCCCAGCCACTGTAGGAGGTATACAGGCTGGTGCATTCAAAATTGGTGATACTGCAGGCACGTTGGACAATATCATTCACTGCAAGCTTT
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--------------------------------------gtactctgagacttggaataaacttacgagatttgttcttcacttg---------ttcatagGTAGTCATTGGGCCTGCTACTGTAGGTGGTATGCAGGCTGGTGCCTTCAAGATTGGAGATACTGCTGGTACTCTCGATAACATCGTGAGTTGTAAGCTTTMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|162150458|gb|FC326106.1|FC326106EST: CTCGTGCAAACAACAAG GTCGTCATTGGCCCAGCCACTGTAGGAGGTATACAGGCTGGTGCATTCAAA
genomic: CTCGTGCAAACAACAAGgtatagggga ... tctttcacagGTCGTCATTGGCCCAGCCACTGTAGGAGGTATACAGGCTGGTGCATTCAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gacatcaaacgatgactttcatcaagtgttcttcattaagaatattctttcacagGTCGTCATTGGCCCAGCCACTGTAGGAGGTATACAGGCTGGTGCATTCAAAATTGGTGATACTGCAGGCACGTTGGACAATATCATTCACTGCAAGCTTT
tattctttc CT-rich tract
attaagaatattcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gccgtagttgattacctgcagttctgttagcatacaaataaatgtgacatcaaacgatgactttcatcaagtgttcttcattaagaatattctttcacagGTCGTCATTGGCCCAGCCACTGTAGGAGGTATACAGGCTGGTGCATTCAAAATTGGTGATACTGCAGGCACGTTGGACAATATCATTCACTGCAAGCTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT