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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTATCTGCGAATCGTAAAATACAAAACTGCATATTATTCATTTTATCTTCCTgtaaggttccttcgctccaagtgttggttttttgaatacttgacaactagtcatgtgtttaaagatgttttctgtggattatctggcaatatatgcaatc...

Basic information

species Physcomitrella patens
transcript PP1S101_225V6.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S101_225V6.1 (Physcomitrella patens), 5'ss of exon 8
lower sequence: EFJ10874 (Selaginella moellendorffii), 5'ss of exon 8
TTATCTGCGAATCGTAAAATACAAAACTGCATATTATTCATTTTATCTTCCTgtaaggttccttcgctccaagtgttggttttttgaatacttgacaactagtcatgtgtttaaagatgttttctgtggattatctggcaatatatgcaatc
 ||| |  |||| ||||||||||| || ||||||||||| || |||||||| |||||  |  |   ||          ||| | |||   ||||||      ||  ||| || |                                      
CTATTTAAGAATTGTAAAATACAAGACAGCATATTATTCTTTCTATCTTCCAgtaagtattgtaacctt---------gttctatgacagcttgactgtgtttctggtgcttcacag-----------------------------------

upper sequence: PP1S101_225V6.1 (Physcomitrella patens), 5'ss of exon 8
lower sequence: EFJ25934 (Selaginella moellendorffii), 5'ss of exon 8
TTATCTGCGAATCGTAAAATACAAAACTGCATATTATTCATTTTATCTTCCTgtaaggttccttcgctccaagtgttggttttttgaatacttgacaactagtcatgtgtttaaagatgttttctgtggattatctggcaatatatgcaatc
 ||| |  |||| ||||||||||| || ||||||||||| || |||||||| |||||          | |||   |  ||| | |||   ||||||      ||  ||| || |                                      
CTATTTAAGAATTGTAAAATACAAGACAGCATATTATTCTTTCTATCTTCCAgtaag-------tattgcaacctt--gttctatgacagcttgactgtgtttctggtgcttcacag-----------------------------------
















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|162152921|gb|FC329223.1|FC329223
EST:     ATCTGCGAATCGTAAAATACAAAACTGCATATTATTCATTTTATCTTCCT                         GTGGCATGTGCCTTGCTTTTAGCTGGGGAGACGAGCGTGGCCAAGTTTGAG
genomic: ATCTGCGAATCGTAAAATACAAAACTGCATATTATTCATTTTATCTTCCTgtaaggttcc ... tgtgttgcagGTGGCATGTGCCTTGCTTTTAGCTGGGGAGACGAGCGTGGCCAAGTTTGAG
EST: gi|162152920|gb|FC329222.1|FC329222
EST:     ATCTGCGAATCGTANAATACAAAACTGCATATTATTCATTTTATCTTCCT                         GTGGCATGTGCCTTGCTTTTAGCTGG
genomic: ATCTGCGAATCGTAAAATACAAAACTGCATATTATTCATTTTATCTTCCTgtaaggttcc ... tgtgttgcagGTGGCATGTGCCTTGCTTTTAGCTGG
EST: gi|100401204|gb|BY990883.1|BY990883
EST:     ATCTGCGAATCGTANAATACAAAACTGCATATAATTCATTTTATCTTCCT                         GTGGCATGTGCCTTGCTTTTAGCTGG
genomic: ATCTGCGAATCGTAAAATACAAAACTGCATATTATTCATTTTATCTTCCTgtaaggttcc ... tgtgttgcagGTGGCATGTGCCTTGCTTTTAGCTGG
EST: gi|100361028|gb|BY946877.1|BY946877
EST:     TCTGCGAATCGTAAAATACAAAACTGCATATAATTCATTTTATCTCCCNT                         GTG-CATGTGCCTTGCTTTTAGCTGGGGAGACGAGCGTGGCCAAGTTTGA
genomic: TCTGCGAATCGTAAAATACAAAACTGCATATTATTCATTTTATCTTCC-Tgtaaggttcc ... tgtgttgcagGTGGCATGTGCCTTGCTTTTAGCTGGGGAGACGAGCGTGGCCAAGTTTGA
EST: gi|162230234|gb|FC406590.1|FC406590
EST:     ATCTGCGAATCGTANAATACAAAACTGCATATTATTCATTTTATCTTCCT                         GTGGCATGTGCCTTGCTTTTAGCTGGNGAGACGAGCGTGGCCCAGTTTGAG
genomic: ATCTGCGAATCGTAAAATACAAAACTGCATATTATTCATTTTATCTTCCTgtaaggttcc ... tgtgttgcagGTGGCATGTGCCTTGCTTTTAGCTGGGGAGACGAGCGTGGCCAAGTTTGAG
EST: gi|100383945|gb|BY987202.1|BY987202
EST:     TCTGCGAATCGTAAAATACAAAAACTGCATATTATTCATTTTATCTTCCT                         GTGGCATGTGCCTTGCTTTTAGCTGGGGAGACGAGCGTGGCCAAGTTTGAG
genomic: TCTGCGAATCGTAAAATACAAAA-CTGCATATTATTCATTTTATCTTCCTgtaaggttcc ... tgtgttgcagGTGGCATGTGCCTTGCTTTTAGCTGGGGAGACGAGCGTGGCCAAGTTTGAG
EST: gi|100402689|gb|BY954960.1|BY954960
EST:     TCTGCGAATCGTAAAATACAAAACTGCATATAATTCATTTTATCT-CCNT                         GTGGAAGGTGCCTTGCTTTTAGCTGGGGAGACGAGCGTG-CCAAAGTTTG
genomic: TCTGCGAATCGTAAAATACAAAACTGCATATTATTCATTTTATCTTCC-Tgtaaggttcc ... tgtgttgcagGTGGCATGTGCCTTGCTTTTAGCTGGGGAGACGAGCGTGGCCAA-GTTTG
EST: gi|100396655|gb|BY990233.1|BY990233
EST:     CTGCGAATCGTAAAATANCAAA-CTGCATATNATTCATTTTTATCT-CCT                         GTGGCATGTGCCTTGCTTTTAGCTGGGGAGACGAG
genomic: CTGCGAATCGTAAAATA-CAAAACTGCATATTATTCATTTT-ATCTTCCTgtaaggttcc ... tgtgttgcagGTGGCATGTGCCTTGCTTTTAGCTGGGGAGACGAG

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: 24 (upstream exon), 15 (downstream exon)
Score: 2

TTATCTGCGAATCGTAAAATACAAAACTGCATATTATTCATTTTATCTTCCTgtaaggttcc ... tgtgttgcagGTGGCATGTGCCTTGCTTTTAGCTGGGGAGACGAGCGTGGCCAAGTTTGAGGCAGCTAAGGAAGTCCTTGTACAGATGGGCACATACTTCCAAGTCCAG




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