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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgacccacgcagatctggcgtctttttgataattactcgctgaccatctccgtagccaagattgatgaccttaaatctcccctcgtgcaaacatgagatgtaatgctcatcgttaatggtgcagCTTTTACTGCGTTTGTCGGTATGACGTTCCCCTTCTTTGGAGCTCTTCTTGGTTTCTTCGGAGGATTCGCCTTCGCTCCTACAACATACTTT

Basic information

species Physcomitrella patens
transcript PP1S5_176V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S5_176V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv01s0011g03180.t01 (Vitis vinifera), 3'ss of exon 5
gtgagtgacccacgcagatctggcgtctttttgataattactcgctgaccatctccgtagccaagattgatgaccttaaatctcccctcgtgcaaacatgagatgtaatgctcatcgttaa-tggtgcagCTTTTACTGCGTTTGTCGGTATGACGTTCCCCTTCTTTGGAGCTCTTCTTGGTTTCTTCGGAGGATTCGCCTTCGCTCCTACAACATACTTT
                                                   |     |  |    ||    |  |||      |      |    | |||  ||    || |   | | || |  ||||||||||||    || |||||  | || ||||| |||||||||| ||||||||||||||| ||||||||||  || ||||| ||  |||| |||
--------------------------------------------------gtaagtttgtcttgtataaccgttcttggcatgcagtgaatttccatatggaatcctctgattgccttgaaattttgcagCTTTTACACTCTTCGTCGGAGTCACCTTCCCTTTCTTTGGAGATCTTCTTGGTTTCTTTGGAGGATTCGGTTTTGCTCCCACTTCATATTTT
















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|67726489|gb|BJ976748.1|BJ976748
EST:     GCTTGCTCCCTCCAGGAAGCTACGGCTCGTCACTCGCTCGCTCTACGTCG                         CTTTTACTGCGTTTGTCGGTATGACGTTCCCCTTCTTTGGAGCTCTTCTTG
genomic: GCTTGCTCCCTCCAGGAAGCTACGGCTCGTCACTCGCTCGCTCTACGTCGgtgagtgacc ... aatggtgcagCTTTTACTGCGTTTGTCGGTATGACGTTCCCCTTCTTTGGAGCTCTTCTTG
EST: gi|208400809|gb|DC925089.1|DC925089
EST:     GCTTGCTCCCTCCAGGAAGCTACGGCTCGTCACTCGCTCGCTCTACGTCG                         CTTTTACTGCGTTNGTCGGTATGACGTTCCCCTGCTTTGGAGCTCTTCTTG
genomic: GCTTGCTCCCTCCAGGAAGCTACGGCTCGTCACTCGCTCGCTCTACGTCGgtgagtgacc ... aatggtgcagCTTTTACTGCGTTTGTCGGTATGACGTTCCCCTTCTTTGGAGCTCTTCTTG
EST: gi|37827465|gb|BJ585477.1|BJ585477
EST:     GCTTGCTCCCTCCAGGAAGCTACGGCTCGTCACTCGCTCGCTCTACGTCG                         CTTTTACTGCGTTTGTCGGTATGACGTTCCCCTTCTTTGGAGCTCTTCTTG
genomic: GCTTGCTCCCTCCAGGAAGCTACGGCTCGTCACTCGCTCGCTCTACGTCGgtgagtgacc ... aatggtgcagCTTTTACTGCGTTTGTCGGTATGACGTTCCCCTTCTTTGGAGCTCTTCTTG
EST: gi|162273084|gb|FC447778.1|FC447778
EST:     GCTTGCTCCCTCCAGGAAGCTACGGCTCGTCACTCGCTCGCTCTACGTCG                         CTTTTACTGCGTTTGTCGGTATGACGTTCCCCTTCTTTGGAGCTCTTCTTG
genomic: GCTTGCTCCCTCCAGGAAGCTACGGCTCGTCACTCGCTCGCTCTACGTCGgtgagtgacc ... aatggtgcagCTTTTACTGCGTTTGTCGGTATGACGTTCCCCTTCTTTGGAGCTCTTCTTG
EST: gi|162264617|gb|FC440900.1|FC440900
EST:     GCTTGCTCCCTCCAGGAAGCTACGGCTCGTCACTCGCTCGCTCTACGTCG                         CTTTTACTGCGTTTGTCGGTATGACGTTCCCCTTCTTTGGAGCTCTTCTTG
genomic: GCTTGCTCCCTCCAGGAAGCTACGGCTCGTCACTCGCTCGCTCTACGTCGgtgagtgacc ... aatggtgcagCTTTTACTGCGTTTGTCGGTATGACGTTCCCCTTCTTTGGAGCTCTTCTTG
EST: gi|162151795|gb|FC328652.1|FC328652
EST:     GCTTGCTCCCTCCAGGAAGCTACGGCTCGTCACTCGCTCGCTCTACGTCG                         CTTTTACTGCGTTTGTCGGTATGACGTTCCCCTTCTTTGGAGCTCTTCTTG
genomic: GCTTGCTCCCTCCAGGAAGCTACGGCTCGTCACTCGCTCGCTCTACGTCGgtgagtgacc ... aatggtgcagCTTTTACTGCGTTTGTCGGTATGACGTTCCCCTTCTTTGGAGCTCTTCTTG
EST: gi|162264616|gb|FC440899.1|FC440899
EST:     GCTTGCTCCCTCCAGGAAGCTACGGCTCGTCACTCGCTCGCTCTACGTCG                         CTTTTACTGCGTTTGTCGGTATGACGTTCCCCTTCTTTGGAGCTCTTCTTG
genomic: GCTTGCTCCCTCCAGGAAGCTACGGCTCGTCACTCGCTCGCTCTACGTCGgtgagtgacc ... aatggtgcagCTTTTACTGCGTTTGTCGGTATGACGTTCCCCTTCTTTGGAGCTCTTCTTG
EST: gi|67725436|gb|BJ975695.1|BJ975695
EST:     GCTTGCTCCCTCCAGGAAGCTACGGCTCGTCACTCGCTCGCTCTACGTCG                         CTTTTACTGCGTTTGTCGGTATGACGTTCCCCTTCTTTGGAGCTCTTCTTG
genomic: GCTTGCTCCCTCCAGGAAGCTACGGCTCGTCACTCGCTCGCTCTACGTCGgtgagtgacc ... aatggtgcagCTTTTACTGCGTTTGTCGGTATGACGTTCCCCTTCTTTGGAGCTCTTCTTG
EST: gi|162151883|gb|FC328129.1|FC328129
EST:     GCTTGCTCCCTCCAGGAAGCTACGGCTCGTCACTCGCTCGCTTTACGTCG                         CTTTTACTGCGTTTGTCGGTATGACGTTCCCCTTCTTTGGAGCTCTTCTTG
genomic: GCTTGCTCCCTCCAGGAAGCTACGGCTCGTCACTCGCTCGCTCTACGTCGgtgagtgacc ... aatggtgcagCTTTTACTGCGTTTGTCGGTATGACGTTCCCCTTCTTTGGAGCTCTTCTTG
EST: gi|162273083|gb|FC447777.1|FC447777
EST:     GCTTGCTCCCTCCAGGAAGCTACGGCTCGTCACTCGCTCGCTTTACGTCG                         CTTTTACTGCGTTTGTCGGTATGACGTTCCCCTTCTTTGGAGCTCTTCTTG
genomic: GCTTGCTCCCTCCAGGAAGCTACGGCTCGTCACTCGCTCGCTCTACGTCGgtgagtgacc ... aatggtgcagCTTTTACTGCGTTTGTCGGTATGACGTTCCCCTTCTTTGGAGCTCTTCTTG
EST: gi|162175568|gb|FC351792.1|FC351792
EST:     GCTTGCTCCCTCCAGGAAGCTACGGCTCGTCACTCGCTCGCTCTACGTCG                         CTTTTACTGCGTTTGTCGGTATGACGTTCCCCTTCTTTGGAGCTCTTCTTG
genomic: GCTTGCTCCCTCCAGGAAGCTACGGCTCGTCACTCGCTCGCTCTACGTCGgtgagtgacc ... aatggtgcagCTTTTACTGCGTTTGTCGGTATGACGTTCCCCTTCTTTGGAGCTCTTCTTG
EST: gi|208358586|gb|DC946547.1|DC946547
EST:     GCTTGCTCCCTCCAGGAAGCTACGGCTCGTCACTCGCTCGCTCTACGTCG                         CTTTTACTGCGTTTGTCGGTATGACGTTCCCCTTCTTTGGAGCTCTTCTTG
genomic: GCTTGCTCCCTCCAGGAAGCTACGGCTCGTCACTCGCTCGCTCTACGTCGgtgagtgacc ... aatggtgcagCTTTTACTGCGTTTGTCGGTATGACGTTCCCCTTCTTTGGAGCTCTTCTTG
EST: gi|67726227|gb|BJ976486.1|BJ976486
EST:     GCTTGCTCCCTCCAGGAAGCTACGGCTCGTCACTCGCTCGCTCTACGTCG                         CTTTTACTGCGTTTGTCGGTATGACGTTCCCCTTCTTTGGAGCTCTTCTTG
genomic: GCTTGCTCCCTCCAGGAAGCTACGGCTCGTCACTCGCTCGCTCTACGTCGgtgagtgacc ... aatggtgcagCTTTTACTGCGTTTGTCGGTATGACGTTCCCCTTCTTTGGAGCTCTTCTTG
EST: gi|162175567|gb|FC351791.1|FC351791
EST:     GCTTGCTCCCTCCAGGAAGCTACGGCTCGTCACTCGCTCGCTCTACGTCG                         CTTTTACTGCGTTTGTCGGTATGACGTTCCCCTTCTTTGGAGCTCTTCTTG
genomic: GCTTGCTCCCTCCAGGAAGCTACGGCTCGTCACTCGCTCGCTCTACGTCGgtgagtgacc ... aatggtgcagCTTTTACTGCGTTTGTCGGTATGACGTTCCCCTTCTTTGGAGCTCTTCTTG
EST: gi|162224629|gb|FC400525.1|FC400525
EST:     CGCTCGCTCTACGTCG                         CTTTTACTGCGTTTGTCGGTATGACGTTCCCCTTCTTTGGAGCTCTTCTTG
genomic: CGCTCGCTCTACGTCGgtgagtgacc ... aatggtgcagCTTTTACTGCGTTTGTCGGTATGACGTTCCCCTTCTTTGGAGCTCTTCTTG
EST: gi|162260734|gb|FC435386.1|FC435386
EST:     GCTTGCTCCCTCCAGGAAGCTACGGCTCGTCACTCGCTCGCTTTACGTCG                         CTTTTACTGCGTTTGTCGGTATGACGTTCCCCTTCTTTGGAGCTCTTCTTG
genomic: GCTTGCTCCCTCCAGGAAGCTACGGCTCGTCACTCGCTCGCTCTACGTCGgtgagtgacc ... aatggtgcagCTTTTACTGCGTTTGTCGGTATGACGTTCCCCTTCTTTGGAGCTCTTCTTG
EST: gi|162224628|gb|FC400524.1|FC400524
EST:     CGCTCGCTCTACGTCG                         CTTTTACTGCGTTTGTCGGTATGACGTTCCCCTTCTTTGGAGCTCTTCTTG
genomic: CGCTCGCTCTACGTCGgtgagtgacc ... aatggtgcagCTTTTACTGCGTTTGTCGGTATGACGTTCCCCTTCTTTGGAGCTCTTCTTG

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), 35 (downstream exon)
Score: 13

GCCATGCCTGTTTTTGATATGTTAGAGTCTGTTCTTGTGAAACGCTTCCGGCTTGCTCCCTCCAGGAAGCTACGGCTCGTCACTCGCTCGCTCTACGTCGgtgagtgacc ... aatggtgcagCTTTTACTGCGTTTGTCGGTATGACGTTCCCCTTCTTTGGAGCTCTTCTTGGTTTCTTCGGAGGATTCGCCTTCGCTCCTACAACATACTTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttaaatctcccctcgtgcaaacatgagatgtaatgctcatcgttaatggtgcagCTTTTACTGCGTTTGTCGGTATGACGTTCCCCTTCTTTGGAGCTCTTCTTGGTTTCTTCGGAGGATTCGCCTTCGCTCCTACAACATACTTT
                                         cgttaat  putative branch site (score: 13)
                            atgtaat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgacccacgcagatctggcgtctttttgataattactcgctgaccatctccgtagccaagattgatgaccttaaatctcccctcgtgcaaacatgagatgtaatgctcatcgttaatggtgcagCTTTTACTGCGTTTGTCGGTATGACGTTCCCCTTCTTTGGAGCTCTTCTTGGTTTCTTCGGAGGATTCGCCTTCGCTCCTACAACATACTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT