Sequence
atgc intronic sequence ATGC exonic sequenceGTTGACCGGAAAGCCACTTTTCCCTGGGAAGAATGTTGTTCATCAGCTGGATCTTATGACAGACATGCTTGGAAGTCCATCTTCAGAAACCGTTCAAAGGgtaagagcacagtcctgaaatactttaacttggtgaggctcaatgcaagtgaaagaatcctatggagagttttaagcggcataaattcctgattctgtct...
Basic information
species | Physcomitrella patens |
transcript | PP1S87_157V6.2 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S87_157V6.2 (Physcomitrella patens), 5'ss of exon 5
lower sequence: LOC_Os05g05160.1 (Oryza sativa), 5'ss of exon 5
GTTGACCGGAAAGCCACTTTTCCCTGGGAAGAATGTTGTTCATCAGCTGGATCTTATGACAGACATGCTTGGAAGTCCATCTTCAGAAACCGTTCAAAGGgtaagagcaca--gtcctgaaatactttaacttggtgaggctcaatgcaagtgaaagaatcctatggagagttttaagcggcataaattcctgattctgtct
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TTTAACCGGAAAACCTCTTTTCCCTGGGAAGAATGTGGTTCATCAACTTGATATAATTACAGATCTACTAGGAACACCTTCTCCAGAAACAATATCTAGGgtcagtatggattgacttcaaaaaatt--gcttatta---cttagttccaataaaa---tcctat--aatgcttatatctacattcacttatgcaacag---
upper sequence: PP1S87_157V6.2 (Physcomitrella patens), 5'ss of exon 5
lower sequence: LOC_Os01g45620.1 (Oryza sativa), 5'ss of exon 4
GTTGACCGGAAAGCCACTTTTCCCTGGGAAGAATGTTGTTCATCAGCTGGATCTTATGACAGACATGCTTGGAAGTCCATCTTCAGAAACCGTTCAAAGGgtaagagcacagtcctgaaatactttaacttggtgaggctcaatgcaagtgaaagaatcctatggagagttttaagcggcataaattc--ctgattctgtct---
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GCTTATGGGAAAGCCACTTTTTCCTGGAAAGAATGTGGTACATCAATTGGATCTCATGACCGACTTACTTGGCTCTCCTTCAGGAGAAACTATTTCCAGGgtggg-gttcactttcccagtctc----cctgcaaatctgcaattagttggagcctgtcttctatgcaatttcatttaacctttttcctactgatggtcattatc
upper sequence: PP1S87_157V6.2 (Physcomitrella patens), 5'ss of exon 5
lower sequence: GRMZM2G062761_T02 (Zea mays), 5'ss of exon 5
GTTGACCGGAAAGCCACTTTTCCCTGGGAAGAATGTTGTTCATCAGCTGGATCTTATGACAGACATGCTTGGAAGTCCATCTTCAGAAACCGTTCAAAGGgtaagagcacagtcctgaaatactttaacttggtgaggctcaatgcaagtgaaagaatcctatggagagttttaagcggca-taaattcctgattctgtct---
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GCTCACAGGGAAGCCACTCTTTCCAGGGAAGAATGTTGTGCATCAGTTGGATCTTATGACTGATCTACTTGGTACACCTTCAGCAGAGTCTATCTCCAAGgtatgctcactagttactaatgag--accttaatctcactagttactaacga--gtctcattttctgtattccaggcagtactctgtttcagatttttaggtac
upper sequence: PP1S87_157V6.2 (Physcomitrella patens), 5'ss of exon 5
lower sequence: GLYMA15G10940.4 (Glycine max), 5'ss of exon 5
GTTGACCGGAAAGCCACTTTTCCCTGGGAAGAATGTTGTTCATCAGCTGGATCTTATGACAGACATGCTTGGAAGTCCATCTTCAGAAACCGTTCAAAGGgtaaga-gcacagtcctgaaatacttta---acttggtgaggctcaat--gcaagtgaaagaatcctatggagagttttaagcggcataaattcctgattctgtct
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TTTGACCGGAAAACCTCTTTTCCCTGGGAAGAATGTTGTTCATCAACTAGACCTTATGACTGATCTTCTTGGAACTCCATCTCTTGAAGCCATTGCTAGGgtctgttgttcagtttcccttccttttagcaattttgtttgttctattttgttacttaatgaaacct-tggtatatactaatag----------------------
upper sequence: PP1S87_157V6.2 (Physcomitrella patens), 5'ss of exon 5
lower sequence: GLYMA13G28120.1 (Glycine max), 5'ss of exon 5
GTTGACCGGAAAGCCACTTTTCCCTGGGAAGAATGTTGTTCATCAGCTGGATCTTATGACAGACATGCTTGGAAGTCCATCTTCAGAAACCGTTCAAAGGgtaaga-gcacagtcctgaaatacttt---aacttggtgaggctcaa--tgcaagtgaaagaatcctatggagagttttaagcggcataaattcctgattctgtct
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TTTGACGGGAAAACCTCTTTTCCCTGGGAAGAATGTTGTCCATCAACTAGACCTTATGACTGATCTTCTTGGAACTCCATCTCTTGAAGCCATTGCTAGGgtctgttgttcagtttcccttccttttggcaattttgtttgttctattttgttactcaatgcaaccttggtattacactaaaag----------------------Mapped 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|18366249|gb|BJ198327.1|BJ198327EST: ATCTTATGACAGACATGCTTGGAAGTCCATCTTCAGAAACCGTTCAAAGG GTGCGAAATGAGAAAGCAAGGAGATACCTTAGCACCATGCGAAAGAAACTC
genomic: ATCTTATGACAGACATGCTTGGAAGTCCATCTTCAGAAACCGTTCAAAGGgtaagagcac ... tttgttacagGTGCGAAATGAGAAAGCAAGGAGATACCTTAGCACCATGCGAAAGAAACTC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTTGACCGGAAAGCCACTTTTCCCTGGGAAGAATGTTGTTCATCAGCTGGATCTTATGACAGACATGCTTGGAAGTCCATCTTCAGAAACCGTTCAAAGGgtaagagcacagtcctgaaatactttaacttggtgaggctcaatgcaagtgaaagaatcctatggagagttttaagcggcataaattcctgattctgtct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG