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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGATGCTCTCAAGGAGGGGATGGGCGGAGGTGGCGGTGGACACAATCCATTCGACATCTTTGAATCGTTCTTCGGTGGTGGTGGAAGTCCATTTGGGGgtaagtgtgtactccgttcccatcatcacgatctggattgggtacagctgttcagtcgaattacttgtctatcccccgagggaacaatacttatgttactaagggcaatcgggtcatttttctctgattggcag

Basic information

species Physcomitrella patens
transcript PP1S100_36V6.1
intron # 2
splice site 5'
intron type U2

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|162173330|gb|FC349501.1|FC349501
EST:     ATTCGACATCTTTGAATCGTTCTTCGGTGGTGGTGGAAGTCCATTTGGGG                         ATTCGTTTGCTGGCGGTAGTGGCAGGGGCGGCGGTAGGCGACAGAGAAGAG
genomic: ATTCGACATCTTTGAATCGTTCTTCGGTGGTGGTGGAAGTCCATTTGGGGgtaagtgtgt ... tgattggcagATTCGTTTGCTGGCGGTAGTGGCAGGGGCGGCGGTAGGCGACAGAGAAGAG
EST: gi|100406346|gb|BY955581.1|BY955581
EST:     ATTCGACATCTTTGAATCGTTCTTCGGTGGTGGTGGAAGTCCATTTGGGG                         ATTCGTTTGCTGGCGGTAGTGGCAGGGGCGGCGGTAGGCGACAGAGAAGAG
genomic: ATTCGACATCTTTGAATCGTTCTTCGGTGGTGGTGGAAGTCCATTTGGGGgtaagtgtgt ... tgattggcagATTCGTTTGCTGGCGGTAGTGGCAGGGGCGGCGGTAGGCGACAGAGAAGAG
EST: gi|162221418|gb|FC397227.1|FC397227
EST:     CGACATCTTTGAATCGTTCTTCGGTGGTGGTGGAAGTCCATTTGGGG                         ATTCGTTTGCTGGCGGTAGTGGCAGGGGCGGCGGTAGGCGACAGAGAAGAG
genomic: CGACATCTTTGAATCGTTCTTCGGTGGTGGTGGAAGTCCATTTGGGGgtaagtgtgt ... tgattggcagATTCGTTTGCTGGCGGTAGTGGCAGGGGCGGCGGTAGGCGACAGAGAAGAG
EST: gi|162152660|gb|FC328327.1|FC328327
EST:     ATTCGACATCTTTGAATCGTTCTTCGGTGGTGGTGGAAGTCCATTTGGGG                         ATTCGTTTGCTGGCGGTAGTGGCAGGGGCGGCCGTAGGCGACAGAGAAGAG
genomic: ATTCGACATCTTTGAATCGTTCTTCGGTGGTGGTGGAAGTCCATTTGGGGgtaagtgtgt ... tgattggcagATTCGTTTGCTGGCGGTAGTGGCAGGGGCGGCGGTAGGCGACAGAGAAGAG
EST: gi|162258184|gb|FC433966.1|FC433966
EST:     TCGACATCTTTGAATCGTTCTTCGGTGGTGGTGGAAGTCCATTTGGGG                         ATTCGTTTGCTGGCGGTAGTGGCAGGGGCGGCGGTAGGCGACAGAGAAGAG
genomic: TCGACATCTTTGAATCGTTCTTCGGTGGTGGTGGAAGTCCATTTGGGGgtaagtgtgt ... tgattggcagATTCGTTTGCTGGCGGTAGTGGCAGGGGCGGCGGTAGGCGACAGAGAAGAG
EST: gi|100384792|gb|BY950782.1|BY950782
EST:     ATTCGACATCTTTGAATCGTTCTTCGGTGGTGGTGGAAGTCCATTTGGGG                         ATTCGTTTTGCTG-CGGTAGTGGCAGGGGCGGCGGTAGGCGACAGAGAAGA
genomic: ATTCGACATCTTTGAATCGTTCTTCGGTGGTGGTGGAAGTCCATTTGGGGgtaagtgtgt ... tgattggcagATTCGTTT-GCTGGCGGTAGTGGCAGGGGCGGCGGTAGGCGACAGAGAAGA
EST: gi|162152283|gb|FC328470.1|FC328470
EST:     ATTCGACATCTTTGAATCGTTCTTCGGTGGTGGTGGAAGTCCATTTGGGG                         ATTCGTTTGCTGGCGGTAGTGGCAGGGGCGGCGGTAGGCGACAGAGAAGAG
genomic: ATTCGACATCTTTGAATCGTTCTTCGGTGGTGGTGGAAGTCCATTTGGGGgtaagtgtgt ... tgattggcagATTCGTTTGCTGGCGGTAGTGGCAGGGGCGGCGGTAGGCGACAGAGAAGAG
EST: gi|208388016|gb|DC933136.1|DC933136
EST:     ATTCGACATCTTTGAATCGTTCTTCGGTGGTGGTGGAAGTCCATTTGGGG                         AT-CNTTTGCTGGCGGTANTGGCANGGGCGGCGGTA
genomic: ATTCGACATCTTTGAATCGTTCTTCGGTGGTGGTGGAAGTCCATTTGGGGgtaagtgtgt ... tgattggcagATTCGTTTGCTGGCGGTAGTGGCAGGGGCGGCGGTA
EST: gi|162158335|gb|FC334754.1|FC334754
EST:     ATTCGACATCTTTGAATCGTTCTTCGGTGGTGGTGGAAGTCCATTTGGGG                         ATTCGTTTGCTGGCGGTAGTGGCAGGGGCGGCGGTAGGCGACAGAGAAGAG
genomic: ATTCGACATCTTTGAATCGTTCTTCGGTGGTGGTGGAAGTCCATTTGGGGgtaagtgtgt ... tgattggcagATTCGTTTGCTGGCGGTAGTGGCAGGGGCGGCGGTAGGCGACAGAGAAGAG
EST: gi|162184181|gb|FC360461.1|FC360461
EST:     ATTCGACATCTTTGAATCGTTCTTCGGTGGTGGTGGAAGTCCATTTGGGG                         ATTCGTTTGCTGGCGGTAGTGGCAGGGGCGGCGGTAGGCGACAGAGAAGAG
genomic: ATTCGACATCTTTGAATCGTTCTTCGGTGGTGGTGGAAGTCCATTTGGGGgtaagtgtgt ... tgattggcagATTCGTTTGCTGGCGGTAGTGGCAGGGGCGGCGGTAGGCGACAGAGAAGAG
EST: gi|162175064|gb|FC351145.1|FC351145
EST:     ATTCGACATCTTTGAATCGTTCTTCGGTGGTGGTGGAAGTCCATTTGGGG                         ATTCGTTTGCTGGCGGTAGTGGCAGGGGCGGCGGTAGGCGACCGAGAAGAG
genomic: ATTCGACATCTTTGAATCGTTCTTCGGTGGTGGTGGAAGTCCATTTGGGGgtaagtgtgt ... tgattggcagATTCGTTTGCTGGCGGTAGTGGCAGGGGCGGCGGTAGGCGACAGAGAAGAG
EST: gi|100410644|gb|BY992199.1|BY992199
EST:     ATTCGACATCTTTGAATCGTTCTTCGGTGGTGGTGGAAGTCCATTTGGGG                         ATTCGTTTGCTGGCGGTAGTGGCAGGNGCGGCGGTAGGCGACAGAGAAGAG
genomic: ATTCGACATCTTTGAATCGTTCTTCGGTGGTGGTGGAAGTCCATTTGGGGgtaagtgtgt ... tgattggcagATTCGTTTGCTGGCGGTAGTGGCAGGGGCGGCGGTAGGCGACAGAGAAGAG
EST: gi|100356515|gb|BY946404.1|BY946404
EST:     ATTCGACATCTTTGAATCGTTCTTCGGTGGTGGTGGAAGTCCATTTGGGG                         ATTCGTTTTGCTG-CGGTAGTGGCAAGGGGCG-CGGTAGGCGACAGAAAAG
genomic: ATTCGACATCTTTGAATCGTTCTTCGGTGGTGGTGGAAGTCCATTTGGGGgtaagtgtgt ... tgattggcagATTCGTTT-GCTGGCGGTAGTGGCA-GGGGCGGCGGTAGGCGACAGAGAAG
EST: gi|162160636|gb|FC336379.1|FC336379
EST:     ATTCGACATCTTTGAATCGTTCTTCGGTGGTGGTGGAAGTCCATTTGGGG                         ATTCGTTTGCTGGCGGTAGTGGCAGGGGCGGCGGTAGGCGACAGAGAAGAG
genomic: ATTCGACATCTTTGAATCGTTCTTCGGTGGTGGTGGAAGTCCATTTGGGGgtaagtgtgt ... tgattggcagATTCGTTTGCTGGCGGTAGTGGCAGGGGCGGCGGTAGGCGACAGAGAAGAG
EST: gi|162163670|gb|FC340282.1|FC340282
EST:     ATTCGACATCTTTGAATCGTTCTTCGGTGGTGGTGGAAGTCCATTTGGGG                         ATTCGTTTGCTGGCGGTAGTGGCAGGGGCGGCGGTAGGCGACAGAGAAGAG
genomic: ATTCGACATCTTTGAATCGTTCTTCGGTGGTGGTGGAAGTCCATTTGGGGgtaagtgtgt ... tgattggcagATTCGTTTGCTGGCGGTAGTGGCAGGGGCGGCGGTAGGCGACAGAGAAGAG

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), 34 (downstream exon)
Score: 27

GAGGATGCTCTCAAGGAGGGGATGGGCGGAGGTGGCGGTGGACACAATCCATTCGACATCTTTGAATCGTTCTTCGGTGGTGGTGGAAGTCCATTTGGGGgtaagtgtgt ... tgattggcagATTCGTTTGCTGGCGGTAGTGGCAGGGGCGGCGGTAGGCGACAGAGAAGAGGAGAAGACGTAGTTCACCCCTTGAAGGTTTCGCTGGAAGACTTGTACAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGGATGCTCTCAAGGAGGGGATGGGCGGAGGTGGCGGTGGACACAATCCATTCGACATCTTTGAATCGTTCTTCGGTGGTGGTGGAAGTCCATTTGGGGgtaagtgtgtactccgttcccatcatcacgatctggattgggtacagctgttcagtcgaattacttgtctatcccccgagggaacaatacttatgttactaagggcaatcgggtcatttttctctgattggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG