Sequence
atgc intronic sequence ATGC exonic sequenceAGTTCAGTACAAGAACGTCGAGTTTACAGTGTGGGATGTTGGAGGTCAAGAGAAATTGCGGCCTCTGTGGCGGCATTATTTCAACAACACTGATGGTTTGgtaaattatcttcattggatatcatctctcaagtaatcatcattgtatggatattaattttactatagattgttgtgagcacaattctaacgctagatta...
Basic information
species | Physcomitrella patens |
transcript | PP1S47_298V6.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S47_298V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: LOC_Os02g47110.1 (Oryza sativa), 5'ss of exon 3
AGTTCAGTACAAGAACGTCGAGTTTACAGTGTGGGATGTTGGAGGTCAAGAGAAATTGCGGCCTCTGTGGCGGCATTATTTCAACAACACTGATGGTTTGgtaaattat-cttcattggatatcatctctcaagtaat-catcattgtatggatattaattttactatagattgttgtgagcacaattctaacgctagatta
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AGTACAGTACAAGAACGTGATGTTTACAGTATGGGATGTCGGTGGCCAAGAGAAGTTGAGGCCTCTGTGGAGGCATTACTTCAATAATACGGATGGTTTGgtatgttttgtttcctttgtggttatctttttgggaatacgtgaaagatttgtgcatcgttgcattaaagaaggaaagaagtggttatttgattttgaca--
upper sequence: PP1S47_298V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G113995_T01 (Zea mays), 5'ss of exon 3
AGTTCAGTACAAGAACGTCGAGTTTACAGTGTGGGATGTTGGAGGTCAAGAGAAATTGCGGCCTCTGTGGCGGCATTATTTCAACAACACTGATGGTTTGgtaaattatcttcattggatatcatctctcaagtaatcatcattgtatggatattaattttactatagattgttgtgagcacaattctaacgctagatta-----
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AGTTCAATACAAGAATGTGATGTTTACTGTGTGGGATGTTGGTGGCCAAGAAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTGgtatgttttattgctaaaatgatattgatct-gtactctactttgtaattgttctgcttg----atgagttgggttacttatgtttgtcttggtgagtttatggg
upper sequence: PP1S47_298V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G106795_T03 (Zea mays), 5'ss of exon 3
AGTTCAGTACAAGAACGTCGAGTTTACAGTGTGGGATGTTGGAGGTCAAGAGAAATTGCGGCCTCTGTGGCGGCATTATTTCAACAACACTGATGGTTTGgtaaatt-atcttcattggatatcatctctcaagtaatcatcattgtatggatattaattttact--atagattgttgtgagcacaattctaacgctagatta
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AGTTCAATACAAGAATGTGATGTTTACTGTTTGGGATGTTGGTGGCCAAGAAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTGgtatgtttattattcttttaagacctttatgaaatgatatcgattgtttg--taattgttctgcttgacgggttgggttatttattcttcacttcttgagtt-
upper sequence: PP1S47_298V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G011518_T01 (Zea mays), 5'ss of exon 3
AGTTCAGTACAAGAACGTCGAGTTTACAGTGTGGGATGTTGGAGGTCAAGAGAAATTGCGGCCTCTGTGGCGGCATTATTTCAACAACACTGATGGTTTGgtaaattatcttcattggatatcatctctcaagtaatcatcattgtatggatatt---aattttactatagattgttgtgagcacaattctaacgctagatta
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GGTTCAATACAAGAATGTAGTGTTCACCGTGTGGGATGTTGGTGGCCAGGAGAAGCTCAGGCCCCTGTGGAGGCACTACTTCAACAACACTGATGCTCTGgtcattactctcgtttctgtttcacaagtgaagcggcataaattctattcaaagttgaaattttacatagaagtgtttatgctgtaatgtttcttccact---
upper sequence: PP1S47_298V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA12G02110.1 (Glycine max), 5'ss of exon 3
AGTTCAGTACAAGAACGTCGAGTTTACAGTGTGGGATGTTGGAGGTCAAGAGAAATTGCGGCCTCTGTGGCGGCATTATTTCAACAACACTGATGGTTTGgtaa--atta-tcttcattggatatcatctctcaagtaatcatcattgtatggatattaattt--tactatagattgttgtgagcacaattctaacgc-tagatta-----------------------------------------------------
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GGTTCAGTATAAGAATGTTGTTTTCACGGTTTGGGATGTTGGAGGGCAAGAGAAATTAAGGGCACTTTGGAGGCACTATTTTAACAACACTGATGGTTTGgtaagaatgagtttccattatttgttgtgttttatcttaatgaaaacacaacttctgcaatttggtatcttgtaaagttttccgtctattacaaaatcattcatcacatgttacagatctatagttgccaggttgatacatatgtgcatatttatgcag
upper sequence: PP1S47_298V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA11G09790.3 (Glycine max), 5'ss of exon 2
AGTTCAGTACAAGAACGTCGAGTTTACAGTGTGGGATGTTGGAGGTCAAGAGAAATTGCGGCCTCTGTGGCGGCATTATTTCAACAACACTGATGGTTTGgtaa--attatcttcattggatatcatctctcaagtaatcatcattgtatggatattaattttactatagattgttgtgagca----caattctaacgctagatta--------------------------------------------------------------------------------
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GGTTCAGTATAAGAATGTTGTTTTCACGGTTTGGGATGTTGGAGGGCAAGAGAAATTAAGGGCACTTTGGAGGCACTATTTTAACAATACTGATGGTTTGgtaagaattagtttc------cattatttattgggtt-ttatcttaatgaaaacacaacttctgcaattcggtatcttgtggagttttccttctattacaaaatcattcatctgtccaatagaactgaaaagacatgatacagatctgtagttgccaggttgatacatatgtgcatatttatgcag
upper sequence: PP1S47_298V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA11G01380.2 (Glycine max), 5'ss of exon 4
AGTTCAGTACAAGAACGTCGAGTTTACAGTGTGGGATGTTGGAGGTCAAGAGAAATTGCGGCCTCTGTGGCGGCATTATTTCAACAACACTGATGGTTTGgtaa--attatcttcattggatatcatctc--tcaagtaatcatcattgtatggatattaattttactatagattgttgtgagcacaattctaacgctagatta--------------------------------------------------------------------------
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AGTTCAGTATAAAAATGTTATTTTCACAGTTTGGGATGTTGGAGGACAAGAGAAACTAAGGCCACTTTGGAGGCACTATTTTAACAACACAGATGGCCTGgtgagaattagttttcatgccttttatctcggtgaaagaaaagttatgctgagcttgttgtttttcgaaaagttccttctttctccatatcattaatcagtccagtaggctggaaagaaaggtctacaggcacaaggtagcaaggttgatatatttgttgatgtgtgcatttatgcag
upper sequence: PP1S47_298V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: AT5G17060.1 (Arabidopsis thaliana), 5'ss of exon 3
AGTTCAGTACAAGAACGTCGAGTTTACAGTGTGGGATGTTGGAGGTCAAGAGAAATTGCGGCCTCTGTGGCGGCATTATTTCAACAACACTGATGGTTTGgtaaat------tatcttcattggatatcatctc---tcaagtaatcatcattgtatgg------atattaattttactatagattgttgtgagcacaattctaacgctagatta----------------------------------------------------------------------------------
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AGTTCAGTACAAGAATGTGATGTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAACTGAGACCTCTTTGGAGGCATTACTTCAATAATACTGATGGACTTgtacgtatatagtttttttttcgatttttgctttcagtcagatacttaactttcaaggtttttccatctctatgttggcatatgttatcctatatttggttatgatgttgcagtatcatatgttgcttggccaatctttagatctttttccatctttatcgaccatggtataagactactctatgatgctcttgcagMapped 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|208352067|gb|DC925876.1|DC925876EST: AGAAATTGCGGCCTCTGTGGCGGCATTATTTCAACAACACTGATGGTTTG ATCTATGTTGTTGATTCATGTGATAGAGAACGAATTGGCAAGGCAGCGACT
genomic: AGAAATTGCGGCCTCTGTGGCGGCATTATTTCAACAACACTGATGGTTTGgtaaattatc ... gttttcccagATCTATGTTGTTGATTCATGTGATAGAGAACGAATTGGCAAGGCAGCGACT
EST:
gi|162208431|gb|FC384186.1|FC384186EST: GCGGCATTATTTCAACAACACTGATGGTTTG ATCTATGTTGTTGATTCATGTGATAGAGAACGAATTGGCAAGGCAGCGACT
genomic: GCGGCATTATTTCAACAACACTGATGGTTTGgtaaattatc ... gttttcccagATCTATGTTGTTGATTCATGTGATAGAGAACGAATTGGCAAGGCAGCGACT
EST:
gi|67575986|gb|BJ948810.1|BJ948810EST: AGAAATTGCGGCCTCTGTGGCGGCATTATTTCAACAACACTGATGGTTTG ATCTATGTTGTTGATTCATGTGATAGAGAACGAATTGGCAAGGCAGCGACT
genomic: AGAAATTGCGGCCTCTGTGGCGGCATTATTTCAACAACACTGATGGTTTGgtaaattatc ... gttttcccagATCTATGTTGTTGATTCATGTGATAGAGAACGAATTGGCAAGGCAGCGACT
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
31 (upstream exon),
35 (downstream exon)
Score:
11AGTTCAGTACAAGAACGTCGAGTTTACAGTGTGGGATGTTGGAGGTCAAGAGAAATTGCGGCCTCTGTGGCGGCATTATTTCAACAACACTGATGGTTTGgtaaattatc ... gttttcccagATCTATGTTGTTGATTCATGTGATAGAGAACGAATTGGCAAGGCAGCGACTGAATTTCAG
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