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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgattctctacagcaaaagcgttatccaacttttgtatcattcatataaattaaactttgattttgaccagtcgcccacacgtgcctgaggagattccgaccaacctttcactacttgggttgtaacgctgtagtgacgattgttcagATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATGCGACTCGCGCATTTGGCTGATCCTGAAGAGATGGAGACCGTCTCATTTG

Basic information

species Physcomitrella patens
transcript PP1S181_117V6.1
intron # 8
splice site 3'
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|37834676|gb|BJ592688.1|BJ592688
EST:     AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAG                         ATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
genomic: AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAGgtgattctct ... gattgttcagATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
EST: gi|162198876|gb|FC372903.1|FC372903
EST:     AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAG                         ATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
genomic: AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAGgtgattctct ... gattgttcagATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
EST: gi|162258112|gb|FC433894.1|FC433894
EST:     AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAG                         ATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
genomic: AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAGgtgattctct ... gattgttcagATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
EST: gi|162177903|gb|FC355153.1|FC355153
EST:     AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAG                         ATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
genomic: AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAGgtgattctct ... gattgttcagATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
EST: gi|162169196|gb|FC345163.1|FC345163
EST:     AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAG                         ATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
genomic: AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAGgtgattctct ... gattgttcagATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
EST: gi|162233878|gb|FC409728.1|FC409728
EST:     AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAG                         ATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
genomic: AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAGgtgattctct ... gattgttcagATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
EST: gi|162162594|gb|FC338688.1|FC338688
EST:     AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAG                         ATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
genomic: AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAGgtgattctct ... gattgttcagATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
EST: gi|162205687|gb|FC380771.1|FC380771
EST:     AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAG                         ATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
genomic: AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAGgtgattctct ... gattgttcagATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
EST: gi|162221407|gb|FC397216.1|FC397216
EST:     AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAG                         ATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
genomic: AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAGgtgattctct ... gattgttcagATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
EST: gi|162157457|gb|FC333520.1|FC333520
EST:     AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAG                         ATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
genomic: AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAGgtgattctct ... gattgttcagATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
EST: gi|67697073|gb|BJ957306.1|BJ957306
EST:     AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAG                         ATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
genomic: AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAGgtgattctct ... gattgttcagATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
EST: gi|162161113|gb|FC336461.1|FC336461
EST:     AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAG                         ATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
genomic: AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAGgtgattctct ... gattgttcagATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
EST: gi|162228256|gb|FC404972.1|FC404972
EST:     AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAG                         ATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
genomic: AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAGgtgattctct ... gattgttcagATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
EST: gi|162198877|gb|FC372904.1|FC372904
EST:     AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAG                         ATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
genomic: AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAGgtgattctct ... gattgttcagATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
EST: gi|162254786|gb|FC430763.1|FC430763
EST:     AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAG                         ATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
genomic: AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAGgtgattctct ... gattgttcagATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
EST: gi|37829068|gb|BJ587080.1|BJ587080
EST:     AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTCTTCAG                         ATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
genomic: AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAGgtgattctct ... gattgttcagATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
EST: gi|162190739|gb|FC367001.1|FC367001
EST:     AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAG                         ATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
genomic: AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAGgtgattctct ... gattgttcagATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
EST: gi|162254787|gb|FC430764.1|FC430764
EST:     AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAG                         ATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
genomic: AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAGgtgattctct ... gattgttcagATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
EST: gi|208352660|gb|DC921394.1|DC921394
EST:     AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAG                         ATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
genomic: AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAGgtgattctct ... gattgttcagATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
EST: gi|37838228|gb|BJ596236.1|BJ596236
EST:     AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAG                         ATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
genomic: AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAGgtgattctct ... gattgttcagATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
EST: gi|18340613|gb|BJ172641.1|BJ172641
EST:     AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAG                         ATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
genomic: AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAGgtgattctct ... gattgttcagATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
EST: gi|162226196|gb|FC401656.1|FC401656
EST:     AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAG                         ATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
genomic: AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAGgtgattctct ... gattgttcagATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
EST: gi|162205686|gb|FC380770.1|FC380770
EST:     AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAG                         ATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
genomic: AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAGgtgattctct ... gattgttcagATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
EST: gi|162163084|gb|FC338474.1|FC338474
EST:     AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAG                         ATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
genomic: AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAGgtgattctct ... gattgttcagATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
EST: gi|162169197|gb|FC345164.1|FC345164
EST:     AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAG                         ATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
genomic: AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAGgtgattctct ... gattgttcagATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
EST: gi|18336588|gb|BJ168610.1|BJ168610
EST:     AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAG                         ATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
genomic: AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAGgtgattctct ... gattgttcagATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
EST: gi|162205220|gb|FC380902.1|FC380902
EST:     AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAG                         ATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
genomic: AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAGgtgattctct ... gattgttcagATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
EST: gi|162158625|gb|FC335525.1|FC335525
EST:     AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAG                         ATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
genomic: AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAGgtgattctct ... gattgttcagATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
EST: gi|162158626|gb|FC335526.1|FC335526
EST:     AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAG                         ATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
genomic: AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAGgtgattctct ... gattgttcagATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
EST: gi|162157456|gb|FC333519.1|FC333519
EST:     AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAG                         ATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
genomic: AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAGgtgattctct ... gattgttcagATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
EST: gi|162162496|gb|FC339214.1|FC339214
EST:     AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAG                         ATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
genomic: AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAGgtgattctct ... gattgttcagATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
EST: gi|162233877|gb|FC409727.1|FC409727
EST:     AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAG                         ATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG
genomic: AAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAGgtgattctct ... gattgttcagATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATG

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: 17 (upstream exon), 25 (downstream exon)
Score: 3

GCATCATTGGATACAGAGGATCCTCTTTACCAACAGAAAAGGGCTATCGTACAAAAGAACAATCGCTTGACTATACAAACTTTTCAGgtgattctct ... gattgttcagATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATGCGACTCGCGCATTTGGCTGATCCTGAAGAGATGGAGACCGTCTCATTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attccgaccaacctttcactacttgggttgtaacgctgtagtgacgattgttcagATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATGCGACTCGCGCATTTGGCTGATCCTGAAGAGATGGAGACCGTCTCATTTG
                           ttgtaac  putative branch site (score: 3)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgattctctacagcaaaagcgttatccaacttttgtatcattcatataaattaaactttgattttgaccagtcgcccacacgtgcctgaggagattccgaccaacctttcactacttgggttgtaacgctgtagtgacgattgttcagATATACAAGGGCAAAGAAATGGAAGCTGTCCTGGACATGTTACCTTACATGCGACTCGCGCATTTGGCTGATCCTGAAGAGATGGAGACCGTCTCATTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA