Sequence
atgc intronic sequence ATGC exonic sequenceGTGGGCTATTACCTTCCCATGAGGGTCACCGCCCGCAAGGTCGAACTCGACCTTATCCGCGACCTGGACCTGTACAAGCTAGAGCCATGGGATCTTCAAGgtatgcaacaattcatttcagagtattcgtagcatttttcatgttgagggatgtcaatagatttgggacccggaacatagccttaagaactggattgaaaaccacaccacctgatgtgatatttgactccatacttcatcacctaaaattcgggtgttaaatcatgcaacag
Basic information
species | Physcomitrella patens |
transcript | PP1S223_12V6.2 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S223_12V6.2 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G091490_T01 (Zea mays), 5'ss of exon 1
GTGGGCTATTACCTTCCCATGAGGGTCACCGCCCGCAAGGTCGAACTCGACCTTATCCGCGACCTGGACCTGTACAAGCTAGAGCCATGGGATCTTCAAGgtatgcaacaattcatttcagagtattcgtagcatttttcatgttgagggatgtcaatagatttgggacccg-gaacatagc-cttaagaactggat--tgaaaaccacaccacctgatgtgatatttgactccatacttcatcacctaaaattcgggtgttaaatcatgcaacag
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CTGACCTACTACCTGAAGAAGAAGGTGGCGTCGGAGCGCATCGACCTGGACGTCATCCGCGACGTGGACCTCAACAAGCTGGAGCCATGGGACATCCAAGgtatgcatccatgcatatagtaggatctgt-gtacgagacacatgcatgatcatcgtctatctcattgcttgcgcatgcaatgcatgaaacttacatggcgacgaccggactgacccctgcag-----------------------------------------------------
upper sequence: PP1S223_12V6.2 (Physcomitrella patens), 5'ss of exon 2
lower sequence: Vv16s0022g00690.t01 (Vitis vinifera), 5'ss of exon 1
GTGGGCTATTACCTTCCCATGAGGGTCACCGCCCGCAAGGTCGAACTCGACCTTATCCGCGACCTGGACCTGTACAAGCTAGAGCCATGGGATCTTCAAGgtatgcaacaattcatttcagagtattcgtagcatttttcatgttgagggatgtcaatagatttgggacccggaacatagccttaagaactggattgaaaaccacaccacctgatgtgatatttgactccatacttcatcacctaaaattcgggtgttaaatcatgcaacag
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GTAGATTACTACCTCAGAAAAAAGGTTACTTCAAGAAGAATTGACCTAGATGTCATTAAGGATGTTGATCTCTATAAAATAGAGCCATGGGATCTTCAAGgtattccatgatt---ttacaatcattcccatcaat----agaatgaactctatccttagaattaaactacccaaa------ttaacaaatgtattgttaaccgaacta---agttgactttgtaaatttgaacag------------------------------------
upper sequence: PP1S223_12V6.2 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ37712 (Selaginella moellendorffii), 5'ss of exon 1
GTGGGCTATTACCTTCCCATGAGGGTCACCGCCCGCAAGGTCGAACTCGACCTTATCCGCGACCTGGACCTGTACAAGCTAGAGCCATGGGATCTTCAAGgtatgcaacaattcatttcagagtattcgtagcatttttcatgttgagggatgtcaatagatttgggacccggaacatagccttaagaactggattgaaaaccacaccacctgatgtgatatttgactccatacttcatcacctaaaattcgggtgttaaatcatgcaacag
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GTGGGTTACTACTTGGCCAAGAAAGTAGCCGCGAGCAAAATTGATTTGGATGTCATCCGCGAGATCGACTTGTACAAGCTGGAGCCATGGGATCTTCAAGgtaag--acggtc-----------atccctcaagcttctcatttcgggaaa----aaaaaaaccgttctttggaa---gtctttgcgttctaaat-----gtctcttctctcactgccatcgatgaattgcgtttgccacacacag--------------------------
upper sequence: PP1S223_12V6.2 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ32131 (Selaginella moellendorffii), 5'ss of exon 1
GTGGGCTATTACCTTCCCATGAGGGTCACCGCCCGCAAGGTCGAACTCGACCTTATCCGCGACCTGGACCTGTACAAGCTAGAGCCATGGGATCTTCAAGgtatgcaacaattcatttcagagtattcgtagcatttttcatgttgagggatgtcaatagatttgggacccggaacatagccttaagaactggattgaaaaccacaccacctgatgtgatatttgactccatacttcatcacctaaaattcgggtgttaaatcatgcaacag
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GTGGGTTACTACTTGGCCAAGAAAGTGGCCGCGAGCAAAATTGATTTGGATGTCATCCGCGAGATCGACTTGTACAAGCTGGAGCCATGGGATCTTCAAGgtaag--acggtc-----------atccctcaagcttctcatttcggaaaaaaaaaaccgttct-----ttggaa---gtctttgcgttctaaat-----gtctcttctctcactgccatcgatgaattgcgtttgccacacacag--------------------------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|18367000|gb|BJ199080.1|BJ199080EST: CCTTATCCGCGACCTGGACCTGTACAAGCTAGAGCCATGGGATCTTCAAG ATCTTTGCAAAATCCAGGCCGACTCAAATGAGAAGCAAACCGATTACTACT
genomic: CCTTATCCGCGACCTGGACCTGTACAAGCTAGAGCCATGGGATCTTCAAGgtatgcaaca ... catgcaacagATCTTTGCAAAATCCAGGCCGACTCAAATGAGAAGCAAACCGATTACTACT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTGGGCTATTACCTTCCCATGAGGGTCACCGCCCGCAAGGTCGAACTCGACCTTATCCGCGACCTGGACCTGTACAAGCTAGAGCCATGGGATCTTCAAGgtatgcaacaattcatttcagagtattcgtagcatttttcatgttgagggatgtcaatagatttgggacccggaacatagccttaagaactggattgaaaaccacaccacctgatgtgatatttgactccatacttcatcacctaaaattcgggtgttaaatcatgcaacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT