Sequence
atgc intronic sequence ATGC exonic sequencegtaaaggcgttcagacgtccatattgcatgacaattgagtttatttgcaccagtaaatcagttattctcttccttgcagggcaatttaagttgctgtttgtctttgttgtctgctttacattacaagtatcggtttagaaaccgtcgcgtttgatttatcagaatttggacgtgttgcgcagGGACACTGCTGGACAGGAGAGGTTTAGGAGTTTGATTCCCAGCTACATCCGGGATTCGTCCGTGGCAGTGGTTGTCTATGATGTTTCCA
Basic information
species | Physcomitrella patens |
transcript | PP1S39_147V6.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S39_147V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os03g09140.1 (Oryza sativa), 3'ss of exon 2
gtaaaggcgttcagacgtccatattgcatgacaattgagtttatttgcaccagtaaatcagttattctcttccttgcagggcaatttaagttgctgtttgtctttgttgtctgctttacattacaagtatcggtttagaaaccgtcgcgtttgatttatcagaatttggacgtgttgcgcagGGACACTGCTGGACAGGAGAGGTTTAGGAGTTTGATTCCCAGCTACATCCGGGATTCGTCCGTGGCAGTGGTTGTCTATGATGTTTCCA
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--------------------------------------------------------------------------tgaactgaaatcacgcgcacaagacaattcagcta---gtgaaaactgggaggttttcagctagtaaaaaccgggagagttttatggtgatg-----ataatgtgcagGGATACAGCTGGGCAGGAGAGGTTCCGGAGCTTGATCCCAAGTTACATCAGGGATTCTTCTGTGGCAGTGATTGTTTACGATGTGACTG
upper sequence: PP1S39_147V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G128771_T01 (Zea mays), 3'ss of exon 2
gtaaaggcgttcagacgtccatattgcatgacaattgagtttatttgcaccagtaaatcagttattctcttccttgcagggcaatttaagttgctgtttgtctttgttgtctgctttacattacaagtatcggtttagaaaccgtcgcgtttgatttatcagaatttggacgtgttgcgcagGGACACTGCTGGACAGGAGAGGTTTAGGAGTTTGATTCCCAGCTACATCCGGGATTCGTCCGTGGCAGTGGTTGTCTATGATGTTTCCA
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-------------------------------------------------------------------nnnnnnnnnnnnnnnnnnncacattactatttgagttt--tggtagctttg--tta-gttcattttcttggaga-----acagttagcatttca----ttgttcttgctgt-cagGGATACTGCAGGACAGGAGAGGTTTAGGAGTCTTATTCCAAGCTACATCAGGGACTCTTCTGTTGCGGTGGTTGTTTATGATGTATCCA
upper sequence: PP1S39_147V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ30542 (Selaginella moellendorffii), 3'ss of exon 2
gtaaaggcgttcagacgtccatattgcatgacaattgagtttatttgcaccagtaaatcagttattctcttccttgcagggcaatttaagttgctgtttgtctttgttgtctgctttacattacaagtatcggtttagaaaccgtcgcgtttgatttatcagaatttggacgtgttgcgcagGGACACTGCTGGACAGGAGAGGTTTAGGAGTTTGATTCCCAGCTACATCCGGGATTCGTCCGTGGCAGTGGTTGTCTATGATGTTTCCA
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----------------------------------------------------------------------------------------------------------------------------gtatgctggttct--agcttcaaaggatggttttttacgagtctatttttacgtccagGGATACTGCTGGCCAGGAGCGCTTCCGGAGTTTGATTCCCAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGAMapped 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|208346149|gb|DC917102.1|DC917102EST: CTCTCCAAGACCATGTATCNTGAGGATCGCACTGTTAGACTACAGCTCTG GGACACTGCTGGACAGGAGAGGTTTAGGAGTTTGATTCCCAGCTACATCCG
genomic: CTCTCCAAGACCATGTATCTTGAGGATCGCACTGTTAGACTACAGCTCTGgtaaaggcgt ... tgttgcgcagGGACACTGCTGGACAGGAGAGGTTTAGGAGTTTGATTCCCAGCTACATCCG
EST:
gi|208390126|gb|DC941947.1|DC941947EST: CTCTCCAAGACCATGTATCTTGAGGATCGCACTGTTAGACTACAGCTCTG GGACACTGCTGGACAGGAGAGGTTTAGGAGTTTGATTCCCAGCTACATCCG
genomic: CTCTCCAAGACCATGTATCTTGAGGATCGCACTGTTAGACTACAGCTCTGgtaaaggcgt ... tgttgcgcagGGACACTGCTGGACAGGAGAGGTTTAGGAGTTTGATTCCCAGCTACATCCG
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:
33 (upstream exon),
15 (downstream exon)
Score:
2GCAACTATTGGTATTGATTTTCTCTCCAAGACCATGTATCTTGAGGATCGCACTGTTAGACTACAGCTCTGgtaaaggcgt ... tgttgcgcagGGACACTGCTGGACAGGAGAGGTTTAGGAGTTTGATTCCCAGCTACATCCGGGATTCGTCCGTGGCAGTGGTTGTCTATGATGTTTCCA
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatcggtttagaaaccgtcgcgtttgatttatcagaatttggacgtgttgcgcagGGACACTGCTGGACAGGAGAGGTTTAGGAGTTTGATTCCCAGCTACATCCGGGATTCGTCCGTGGCAGTGGTTGTCTATGATGTTTCCA
gtttgat putative branch site (score: 2)
atttatcagaattt TA-rich tract