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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATCGCAGTTTCTCACGACCGGTACTTCTTGAGGCAGATAGTGAACCGTGTGGTGGAAGTGACCGATAACAAGCTCAGAGACTACAGTGGCGATTACAACgtatgcttctgtgttcatgttttcacttttgctgtacaaatctcttgtttaggtgcttgtatctgatattacgtttcagtcagtttcacatattcagtat...

Basic information

species Physcomitrella patens
transcript PP1S495_14V6.1
intron # 5
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|37833592|gb|BJ591604.1|BJ591604
EST:     AAGCTCAGAGACTACAGTGGCGATTACAAC                         TATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
genomic: AAGCTCAGAGACTACAGTGGCGATTACAACgtatgcttct ... tcctttgcagTATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
EST: gi|162194076|gb|FC370251.1|FC370251
EST:     TGGTGGAAGTGACCGATAACAAGCTCAGAGACTACAGTGGCAATTACAAC                         TATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
genomic: TGGTGGAAGTGACCGATAACAAGCTCAGAGACTACAGTGGCGATTACAACgtatgcttct ... tcctttgcagTATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
EST: gi|162168211|gb|FC344941.1|FC344941
EST:     TGGTGGAAGTGACCGATAACAAGCTCAGAGACTACAGTGGCAATTACAAC                         TATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
genomic: TGGTGGAAGTGACCGATAACAAGCTCAGAGACTACAGTGGCGATTACAACgtatgcttct ... tcctttgcagTATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
EST: gi|162269948|gb|FC445946.1|FC445946
EST:     TGGTGGAAGTGACCGATAACAAGCTCAGAGACTACAGTGGCGATTACAAC                         TATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
genomic: TGGTGGAAGTGACCGATAACAAGCTCAGAGACTACAGTGGCGATTACAACgtatgcttct ... tcctttgcagTATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
EST: gi|162194862|gb|FC370526.1|FC370526
EST:     TGGTGGAAGTGACCGATAACAAGCTCAGAGACTACAGTGGCAATTACAAC                         TATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
genomic: TGGTGGAAGTGACCGATAACAAGCTCAGAGACTACAGTGGCGATTACAACgtatgcttct ... tcctttgcagTATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
EST: gi|162269947|gb|FC445945.1|FC445945
EST:     TGGTGGAAGTGACCGATAACAAGCTCAGAGACTACAGTGGCGATTACAAC                         TATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
genomic: TGGTGGAAGTGACCGATAACAAGCTCAGAGACTACAGTGGCGATTACAACgtatgcttct ... tcctttgcagTATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
EST: gi|162173200|gb|FC349254.1|FC349254
EST:     TGGTGGAAGTGACCGATAACAAGCTCAGAGACTACAGTGGCAATTACAAC                         TATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
genomic: TGGTGGAAGTGACCGATAACAAGCTCAGAGACTACAGTGGCGATTACAACgtatgcttct ... tcctttgcagTATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
EST: gi|162197640|gb|FC374474.1|FC374474
EST:     TGGTGGAAGTGACCGATAACAAGCTCAGAGACTACAGTGGCAATTACAAC                         TATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
genomic: TGGTGGAAGTGACCGATAACAAGCTCAGAGACTACAGTGGCGATTACAACgtatgcttct ... tcctttgcagTATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
EST: gi|162194077|gb|FC370252.1|FC370252
EST:     TGGTGGAAGTGACCGATAACAAGCTCAGAGACTACAGTGGCAATTACAAC                         TATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
genomic: TGGTGGAAGTGACCGATAACAAGCTCAGAGACTACAGTGGCGATTACAACgtatgcttct ... tcctttgcagTATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
EST: gi|162255731|gb|FC431391.1|FC431391
EST:     TGGTGGAAGTGACCGATAACAAGCTCAGAGACTACAGTGGCGATTACAAC                         TATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
genomic: TGGTGGAAGTGACCGATAACAAGCTCAGAGACTACAGTGGCGATTACAACgtatgcttct ... tcctttgcagTATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
EST: gi|162168210|gb|FC344940.1|FC344940
EST:     CAGAGACTACAGTGGCAATTACAAC                         TATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
genomic: CAGAGACTACAGTGGCGATTACAACgtatgcttct ... tcctttgcagTATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
EST: gi|37850178|gb|BJ608186.1|BJ608186
EST:     TGGTGGAAGTGACCGATAACAAGCTCAGAGACTACAGTGGCGATTACAAC                         TATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
genomic: TGGTGGAAGTGACCGATAACAAGCTCAGAGACTACAGTGGCGATTACAACgtatgcttct ... tcctttgcagTATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
EST: gi|162222621|gb|FC397433.1|FC397433
EST:     CCGATAACAAGCTCAGAGACTACAGTGGCAATTACAAC                         TATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
genomic: CCGATAACAAGCTCAGAGACTACAGTGGCGATTACAACgtatgcttct ... tcctttgcagTATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
EST: gi|162166021|gb|FC340417.1|FC340417
EST:     TGGTGGAAGTGACCGATAACGAGCTCAGAGACTACAGTGGCAATTACAAC                         TATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
genomic: TGGTGGAAGTGACCGATAACAAGCTCAGAGACTACAGTGGCGATTACAACgtatgcttct ... tcctttgcagTATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
EST: gi|162150677|gb|FC327573.1|FC327573
EST:     TGGTGGAAGTGACCGATAACAAGCTCAGAGACTACAGTGGCAATTACAAC                         TATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
genomic: TGGTGGAAGTGACCGATAACAAGCTCAGAGACTACAGTGGCGATTACAACgtatgcttct ... tcctttgcagTATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
EST: gi|162246026|gb|FC421889.1|FC421889
EST:     TGGTGGAAGTGACCGATAACAAGCTCAGAGACTACAGTGGCAATTACAAC                         TATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
genomic: TGGTGGAAGTGACCGATAACAAGCTCAGAGACTACAGTGGCGATTACAACgtatgcttct ... tcctttgcagTATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
EST: gi|162164376|gb|FC341021.1|FC341021
EST:     TGGTGGAAGTGACCGATAACAAGCTCAGAGACTACAGTGGCAATTACAAC                         TATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
genomic: TGGTGGAAGTGACCGATAACAAGCTCAGAGACTACAGTGGCGATTACAACgtatgcttct ... tcctttgcagTATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
EST: gi|162279602|gb|FC455354.1|FC455354
EST:     GCGATTAC-AC                         TATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
genomic: GCGATTACAACgtatgcttct ... tcctttgcagTATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
EST: gi|162192497|gb|FC369127.1|FC369127
EST:     TGGTGGAAGTGACCGATAACAAGCTCAGAGACTACAGTGGCAATTACAAC                         TATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
genomic: TGGTGGAAGTGACCGATAACAAGCTCAGAGACTACAGTGGCGATTACAACgtatgcttct ... tcctttgcagTATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
EST: gi|162173199|gb|FC349253.1|FC349253
EST:     AGTGACCGATAACAAGCTCAGAGACTACAGTGGCAATTACAAC                         TATTACTTGGAGCAAAACTT-GAAGCCCGACAGAGGGAGCTAGACCGTGAG
genomic: AGTGACCGATAACAAGCTCAGAGACTACAGTGGCGATTACAACgtatgcttct ... tcctttgcagTATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
EST: gi|162169804|gb|FC346160.1|FC346160
EST:     TGGTGGAAGTGACCGATAACAAGCTCAGAGACTACAGTGGCAATTACAAC                         TATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
genomic: TGGTGGAAGTGACCGATAACAAGCTCAGAGACTACAGTGGCGATTACAACgtatgcttct ... tcctttgcagTATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
EST: gi|162179616|gb|FC355258.1|FC355258
EST:     TGGTGGAAGTGACCGATAACAAGCTCAGAGACTACAGTGGCAATTACAAC                         TATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
genomic: TGGTGGAAGTGACCGATAACAAGCTCAGAGACTACAGTGGCGATTACAACgtatgcttct ... tcctttgcagTATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
EST: gi|162194863|gb|FC370527.1|FC370527
EST:     TGGTGGAAGTGACCGATAACAAGCTCAGAGACTACAGTGGCAATTACAAC                         TATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
genomic: TGGTGGAAGTGACCGATAACAAGCTCAGAGACTACAGTGGCGATTACAACgtatgcttct ... tcctttgcagTATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
EST: gi|162222622|gb|FC397434.1|FC397434
EST:     CCGATAACAAGCTCAGAGACTACAGTGGCAATTACAAC                         TATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
genomic: CCGATAACAAGCTCAGAGACTACAGTGGCGATTACAACgtatgcttct ... tcctttgcagTATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
EST: gi|162165977|gb|FC340976.1|FC340976
EST:     TGGTGGAAGTGACCGATAACAAGCTCAGAGACTACAGTGGCAATTACAAC                         TATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
genomic: TGGTGGAAGTGACCGATAACAAGCTCAGAGACTACAGTGGCGATTACAACgtatgcttct ... tcctttgcagTATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
EST: gi|162150678|gb|FC327574.1|FC327574
EST:     TGGTGGAAGTGACCGATAACAAGCTCAGAGACTACAGTGGCAATTACAAC                         TATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
genomic: TGGTGGAAGTGACCGATAACAAGCTCAGAGACTACAGTGGCGATTACAACgtatgcttct ... tcctttgcagTATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
EST: gi|162163638|gb|FC340263.1|FC340263
EST:     TGGTGGAAGTGACCGATAACAAGCTCAGAGACTACAGTGGCAATTACAAC                         TATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
genomic: TGGTGGAAGTGACCGATAACAAGCTCAGAGACTACAGTGGCGATTACAACgtatgcttct ... tcctttgcagTATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
EST: gi|162170426|gb|FC346805.1|FC346805
EST:     TGGTGGAAGTGACCGATAACAAGCTCAGAGACTACAGTGGCAATTACAAC                         TATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
genomic: TGGTGGAAGTGACCGATAACAAGCTCAGAGACTACAGTGGCGATTACAACgtatgcttct ... tcctttgcagTATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
EST: gi|162279601|gb|FC455353.1|FC455353
EST:     GCGATTACAAC                         TATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG
genomic: GCGATTACAACgtatgcttct ... tcctttgcagTATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAG

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: 35 (upstream exon), 35 (downstream exon)
Score: 79

CATCGCAGTTTCTCACGACCGGTACTTCTTGAGGCAGATAGTGAACCGTGTGGTGGAAGTGACCGATAACAAGCTCAGAGACTACAGTGGCGATTACAACgtatgcttct ... tcctttgcagTATTACTTGGAGCAAAACTTGGAAGCCCGACAGAGGGAGCTAGACCGTGAGGAGGAGCTTGAAATGAAGGGTCCAACAGTGAAGGCCAAGTCCAAGATGT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATCGCAGTTTCTCACGACCGGTACTTCTTGAGGCAGATAGTGAACCGTGTGGTGGAAGTGACCGATAACAAGCTCAGAGACTACAGTGGCGATTACAACgtatgcttctgtgttcatgttttcacttttgctgtacaaatctcttgtttaggtgcttgtatctgatattacgtttcagtcagtttcacatattcagtat

- - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA