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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCGCCCTATGTACTCCAACCCTCCCTTGCATGGTGCTTTGCTTGTGTCCACCATTTTGGAGGACCCTGAACTTAAGTCCCTCTGGTACAAAGAAGTTAAGgtaagcatttcttcagtttttgagatttcttgtactgttatttatcgcagattttcttgcttattgcacaagcgactctgttagtcatatgcttgtgttt...

Basic information

species Physcomitrella patens
transcript PP1S223_31V6.1
intron # 7
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|37840459|gb|BJ598467.1|BJ598467
EST:     TCTGGTACAAAGAAGTTAAG                         GAAATGGCTGACCGTATCATCGGCATGCGTGAGACACTCCGTACCAATCTT
genomic: TCTGGTACAAAGAAGTTAAGgtaagcattt ... ttcttcgcagGGAATGGCTGACCGTATCATCGGCATGCGTGAGACACTCCGTACCAATCTT
EST: gi|7286670|gb|AW599157.1|AW599157
EST:     CCATTTTGGAGGACCCTGAACTTAAGTCCCTCTGGTACAAAGAAGTTAAG                         GGAATGGCTGACCGTATCATCGGCATGCGTGAGACACTCCGTACCAATCTT
genomic: CCATTTTGGAGGACCCTGAACTTAAGTCCCTCTGGTACAAAGAAGTTAAGgtaagcattt ... ttcttcgcagGGAATGGCTGACCGTATCATCGGCATGCGTGAGACACTCCGTACCAATCTT
EST: gi|162192505|gb|FC371696.1|FC371696
EST:     CCTGAACTTAAGTCCCTCTGGTACAAAGAAGTTAAG                         GGAATGGCTGACCGTATCATCGGCATGCGTGAGACACTCCGTACCAATCTT
genomic: CCTGAACTTAAGTCCCTCTGGTACAAAGAAGTTAAGgtaagcattt ... ttcttcgcagGGAATGGCTGACCGTATCATCGGCATGCGTGAGACACTCCGTACCAATCTT
EST: gi|37845929|gb|BJ603937.1|BJ603937
EST:     CCATTTTGGAGGACCCTGAACTTAAGTCCCTCTGGTACAAAGAAGTTAAG                         GGAATGGCTGACCGTATCATCGGCATGCGTGAGACACTCCGTACCAATCTT
genomic: CCATTTTGGAGGACCCTGAACTTAAGTCCCTCTGGTACAAAGAAGTTAAGgtaagcattt ... ttcttcgcagGGAATGGCTGACCGTATCATCGGCATGCGTGAGACACTCCGTACCAATCTT
EST: gi|208369208|gb|DC955837.1|DC955837
EST:     CCATTTTGGAGGACCCTGAACTTAAGTCCCTCTGGTACAAAGAAGTTAAG                         GGAATGGCTGACCGTATCATCGGCATGCGTGAGACACTCCGTACCAATCTT
genomic: CCATTTTGGAGGACCCTGAACTTAAGTCCCTCTGGTACAAAGAAGTTAAGgtaagcattt ... ttcttcgcagGGAATGGCTGACCGTATCATCGGCATGCGTGAGACACTCCGTACCAATCTT
EST: gi|37822610|gb|BJ580676.1|BJ580676
EST:     CCATTTTGGAGGACCCTGAACTTAAGTCCNTCTGGTACAAAGAAGTTAAG                         GGAATGGCTGACCGTATCATCGGCATGCGTGAGACACTCCGTACCAATCTT
genomic: CCATTTTGGAGGACCCTGAACTTAAGTCCCTCTGGTACAAAGAAGTTAAGgtaagcattt ... ttcttcgcagGGAATGGCTGACCGTATCATCGGCATGCGTGAGACACTCCGTACCAATCTT
EST: gi|37827861|gb|BJ585873.1|BJ585873
EST:     TGGTACAAAGAAGTTAAG                         GGAATGGCTGACCGTATCATCGGCATGCGTGAGACACTCCGTACCAATCTT
genomic: TGGTACAAAGAAGTTAAGgtaagcattt ... ttcttcgcagGGAATGGCTGACCGTATCATCGGCATGCGTGAGACACTCCGTACCAATCTT
EST: gi|162164021|gb|FC339309.1|FC339309
EST:     CCATTTTGGAGGACCCTGAACTTAAGTCCCTCTGGTACAAAGAAGTTAAG                         GGAATGGCTGACCGTATCATCGGCATGCGTGAGACACTCCGTACCAATCTT
genomic: CCATTTTGGAGGACCCTGAACTTAAGTCCCTCTGGTACAAAGAAGTTAAGgtaagcattt ... ttcttcgcagGGAATGGCTGACCGTATCATCGGCATGCGTGAGACACTCCGTACCAATCTT
EST: gi|19789721|gb|BQ041471.1|BQ041471
EST:     CCATTTTGGAGGACCCTGAACTTAAGTCCCTCTGGTACAAAGAAGTTAAG                         GGAATGGCTGACCGTATCATCGGCATGCGTGAGACACTCCGT
genomic: CCATTTTGGAGGACCCTGAACTTAAGTCCCTCTGGTACAAAGAAGTTAAGgtaagcattt ... ttcttcgcagGGAATGGCTGACCGTATCATCGGCATGCGTGAGACACTCCGT
EST: gi|162221031|gb|FC398283.1|FC398283
EST:     CCATTTTGGAGGACCCTGAACTTAAGTCCCTCTGGTACAAAGAAGTTAAG                         GGAATGGCTGACCGTATCATCGGCATGCGTGAGACACTCCGTACCAATCTT
genomic: CCATTTTGGAGGACCCTGAACTTAAGTCCCTCTGGTACAAAGAAGTTAAGgtaagcattt ... ttcttcgcagGGAATGGCTGACCGTATCATCGGCATGCGTGAGACACTCCGTACCAATCTT
EST: gi|162221032|gb|FC398284.1|FC398284
EST:     CCATTTTGGAGGACCCTGAACTTAAGTCCCTCTGGTACAAAGAAGTTAAG                         GGAATGGCTGACCGTATCATCGGCATGCGTGAGACACTCCGTACCAATCTT
genomic: CCATTTTGGAGGACCCTGAACTTAAGTCCCTCTGGTACAAAGAAGTTAAGgtaagcattt ... ttcttcgcagGGAATGGCTGACCGTATCATCGGCATGCGTGAGACACTCCGTACCAATCTT
EST: gi|162198688|gb|FC373469.1|FC373469
EST:     CCATTTTGGAGGACCCTGAACTTAAGTCCCTCTGGTACAAAGAAGTTAAG                         GGAATGGCTGACCGTATCATCGGCATGCGTGAGACACTCCGTACCAATCTT
genomic: CCATTTTGGAGGACCCTGAACTTAAGTCCCTCTGGTACAAAGAAGTTAAGgtaagcattt ... ttcttcgcagGGAATGGCTGACCGTATCATCGGCATGCGTGAGACACTCCGTACCAATCTT
EST: gi|162257989|gb|FC434083.1|FC434083
EST:     CCATTTTGGAGGACCCTGAACTTAAGTCCCTCTGGTACAAAGAAGTTAAG                         GGAATGGCTGACCGTATCATCGGCATGCGTGAGACACTCCGTACCAATCTT
genomic: CCATTTTGGAGGACCCTGAACTTAAGTCCCTCTGGTACAAAGAAGTTAAGgtaagcattt ... ttcttcgcagGGAATGGCTGACCGTATCATCGGCATGCGTGAGACACTCCGTACCAATCTT
EST: gi|7286761|gb|AW599248.1|AW599248
EST:     CCATTTTGGAGGACCCTGAACTTAAGTCCCTCTGGTACAAAGAAGTTAAG                         GGAATGGCTGACCGTATCATCGGCATGCGTGAGACACTCCGTACCAATCTT
genomic: CCATTTTGGAGGACCCTGAACTTAAGTCCCTCTGGTACAAAGAAGTTAAGgtaagcattt ... ttcttcgcagGGAATGGCTGACCGTATCATCGGCATGCGTGAGACACTCCGTACCAATCTT
EST: gi|208348127|gb|DC916937.1|DC916937
EST:     CCATTTTGGAGGACCCTGAACTTAAGTCCCTCTGGTACAAAGAAGTTAAG                         GGAATGGCTGACCGTATCATCGGCATGCGCGAGACACTCCGTACCAATCTT
genomic: CCATTTTGGAGGACCCTGAACTTAAGTCCCTCTGGTACAAAGAAGTTAAGgtaagcattt ... ttcttcgcagGGAATGGCTGACCGTATCATCGGCATGCGTGAGACACTCCGTACCAATCTT
EST: gi|67724754|gb|BJ975013.1|BJ975013
EST:     CCATTTTGGAGGACCCTGAACTTAAGTCCCTCTGGTACAAAGAAGTTAAG                         GGAATGGCTGACCGTATCATCGGCATGCGTGAGACACTCCGTACCAATCTT
genomic: CCATTTTGGAGGACCCTGAACTTAAGTCCCTCTGGTACAAAGAAGTTAAGgtaagcattt ... ttcttcgcagGGAATGGCTGACCGTATCATCGGCATGCGTGAGACACTCCGTACCAATCTT
EST: gi|37852295|gb|BJ610303.1|BJ610303
EST:     CTGGTACAAAGAAGTTAAG                         GGAATGGCTGACCGTATCATCGGCATGCGTGAGACACTCCGTACCAATCTT
genomic: CTGGTACAAAGAAGTTAAGgtaagcattt ... ttcttcgcagGGAATGGCTGACCGTATCATCGGCATGCGTGAGACACTCCGTACCAATCTT
EST: gi|67725499|gb|BJ975758.1|BJ975758
EST:     CCATTTTGGAGGACCCTGAACTTAAGTCCCTCTGGTACAAAGAAGTTAAG                         GGAATGGCTGACCGTATCATCGGCATGCGTGAGACACTCCGTACCAATCTT
genomic: CCATTTTGGAGGACCCTGAACTTAAGTCCCTCTGGTACAAAGAAGTTAAGgtaagcattt ... ttcttcgcagGGAATGGCTGACCGTATCATCGGCATGCGTGAGACACTCCGTACCAATCTT
EST: gi|162256779|gb|FC432673.1|FC432673
EST:     CCATTTTGGAGGACCCTGAACTTAAGTCCCTCTGGTACAAAGAAGTTAAG                         GGAATGGCTGACCGTATCATCGGCATGCGTGAGACACTCCGTACCAATCTT
genomic: CCATTTTGGAGGACCCTGAACTTAAGTCCCTCTGGTACAAAGAAGTTAAGgtaagcattt ... ttcttcgcagGGAATGGCTGACCGTATCATCGGCATGCGTGAGACACTCCGTACCAATCTT
EST: gi|162244629|gb|FC423452.1|FC423452
EST:     CCATTTTGGAGGACCCTGAACTTAAGTCCCTCTGGTACAAAGAAGTTAAG                         GGAATGGCTGACCGTATCATCGGCATGCGTGAGACACTCCGTACCAATCTT
genomic: CCATTTTGGAGGACCCTGAACTTAAGTCCCTCTGGTACAAAGAAGTTAAGgtaagcattt ... ttcttcgcagGGAATGGCTGACCGTATCATCGGCATGCGTGAGACACTCCGTACCAATCTT

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: 34 (upstream exon), 24 (downstream exon)
Score: 4

TCGCCCTATGTACTCCAACCCTCCCTTGCATGGTGCTTTGCTTGTGTCCACCATTTTGGAGGACCCTGAACTTAAGTCCCTCTGGTACAAAGAAGTTAAGgtaagcattt ... ttcttcgcagGGAATGGCTGACCGTATCATCGGCATGCGTGAGACACTCCGTACCAATCTTGAGAAGGCTGGATCTCAGCACAGCTGGAAGCATATCACTGATCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCGCCCTATGTACTCCAACCCTCCCTTGCATGGTGCTTTGCTTGTGTCCACCATTTTGGAGGACCCTGAACTTAAGTCCCTCTGGTACAAAGAAGTTAAGgtaagcatttcttcagtttttgagatttcttgtactgttatttatcgcagattttcttgcttattgcacaagcgactctgttagtcatatgcttgtgttt

- - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT