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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggatatctatacatatcgacatgggttttgctaacgctttttttttgttatgattctaattatgaactatgtgaaggctagggtttaagttttattctttacaaagggattagactctgtttactcaacggactgccttggtcactcttgactttctcttgtgattctcatcctctttcctaatgtgcagGTGCTGAGAAAGGATCTACCGATCCGCAAAAGGTGAAGGTCGGAAAGGTCACCATCGATCAACTCAAGACTATTGCACAAGAGAAGCTTCCTGATCTGAA

Basic information

species Physcomitrella patens
transcript PP1S46_69V6.1
intron # 3
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|100410606|gb|BY992182.1|BY992182
EST:     TTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTCCTGAAAGCAGCAG                         GTGCTGAGAAAGGATCTACCGATCCGCAAAAGGTGAAGGTCGGAAAGGTCA
genomic: TTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTCCTGAAAGCAGCAGgtaggatatc ... taatgtgcagGTGCTGAGAAAGGATCTACCGATCCGCAAAAGGTGAAGGTCGGAAAGGTCA
EST: gi|162277905|gb|FC453828.1|FC453828
EST:     TTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTCCTGAAAGCAGCAG                         GTGCTGAGAAAGGATCTACCGATCCGCAAAAGGTGAAGGTCGGAAAGGTCA
genomic: TTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTCCTGAAAGCAGCAGgtaggatatc ... taatgtgcagGTGCTGAGAAAGGATCTACCGATCCGCAAAAGGTGAAGGTCGGAAAGGTCA
EST: gi|162228458|gb|FC405252.1|FC405252
EST:     TTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTCCTGAAAGCAGCAG                         GTGCTGAGAAAGGATCTACCGATCCGCAAAAGGTGAAGGTCGGAAAGGTCA
genomic: TTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTCCTGAAAGCAGCAGgtaggatatc ... taatgtgcagGTGCTGAGAAAGGATCTACCGATCCGCAAAAGGTGAAGGTCGGAAAGGTCA
EST: gi|100411876|gb|BY992384.1|BY992384
EST:     TTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTCCTGAAAGCAGCAG                         GTGCTGAGAAAGGATCTACCGATCCGCANAAGGTGAAGGTCGGAAAGGTCA
genomic: TTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTCCTGAAAGCAGCAGgtaggatatc ... taatgtgcagGTGCTGAGAAAGGATCTACCGATCCGCAAAAGGTGAAGGTCGGAAAGGTCA
EST: gi|162234054|gb|FC410320.1|FC410320
EST:     TTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTCCTGAAAGCAGCAG                         GTGCTGAGAAAGGATCTACCGATCCGCAAAAGGTGAAGGTCGGAAAGGTCA
genomic: TTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTCCTGAAAGCAGCAGgtaggatatc ... taatgtgcagGTGCTGAGAAAGGATCTACCGATCCGCAAAAGGTGAAGGTCGGAAAGGTCA
EST: gi|7147874|gb|AW509796.1|AW509796
EST:     TTCATCTTGGAA-ACACCCACTGCCTCTGTCCTTCTCCTGAGAGCAGCAG                         GTGCTGAGAAAGGATCT
genomic: TTCATCTTG-AAGACACCCCCTGCCTCTGTCCTTCTCCTGAAAGCAGCAGgtaggatatc ... taatgtgcagGTGCTGAGAAAGGATCT
EST: gi|162260840|gb|FC438196.1|FC438196
EST:     TTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTCCTGAAAGCAGCAG                         GTGCTGAGAAAGGATCTACCGATCCGCAAAAGGTGAAGGTCGGAAAGGTCA
genomic: TTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTCCTGAAAGCAGCAGgtaggatatc ... taatgtgcagGTGCTGAGAAAGGATCTACCGATCCGCAAAAGGTGAAGGTCGGAAAGGTCA
EST: gi|19776753|gb|BQ039104.1|BQ039104
EST:     TTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTCCTGAAAGCAGCAG                         GTGCTGAGAAAGGATCTACCGAT
genomic: TTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTCCTGAAAGCAGCAGgtaggatatc ... taatgtgcagGTGCTGAGAAAGGATCTACCGAT
EST: gi|162277904|gb|FC453827.1|FC453827
EST:     TTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTCCTGAAAGCAGCAG                         GTGCTGAGAAAGGATCTACCGATCCGCAAAAGGTGAAGGTCGGAAAGGTCA
genomic: TTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTCCTGAAAGCAGCAGgtaggatatc ... taatgtgcagGTGCTGAGAAAGGATCTACCGATCCGCAAAAGGTGAAGGTCGGAAAGGTCA
EST: gi|208356326|gb|DC957360.1|DC957360
EST:     TTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTCCTGAAAGCAGCAG                         GTGCTGAGAAAGGATCTACCGATCCGCAAAAGGTGAAGGTCGGAAAGGTCA
genomic: TTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTCCTGAAAGCAGCAGgtaggatatc ... taatgtgcagGTGCTGAGAAAGGATCTACCGATCCGCAAAAGGTGAAGGTCGGAAAGGTCA
EST: gi|162260841|gb|FC438197.1|FC438197
EST:     TTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTCCTGAAAGCAGCAG                         GTGCTGAGAAAGGATCTACCGATCCGCAAAAGGTGAAGGTCGGAAAGGTCA
genomic: TTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTCCTGAAAGCAGCAGgtaggatatc ... taatgtgcagGTGCTGAGAAAGGATCTACCGATCCGCAAAAGGTGAAGGTCGGAAAGGTCA
EST: gi|162234055|gb|FC410321.1|FC410321
EST:     TTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTCCTGAAAGCAGCAG                         GTGCTGAGAAAGGATCTACCGATCCGCANAAGGTGAAGGTCGGAAAGGTCA
genomic: TTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTCCTGAAAGCAGCAGgtaggatatc ... taatgtgcagGTGCTGAGAAAGGATCTACCGATCCGCAAAAGGTGAAGGTCGGAAAGGTCA
EST: gi|208386417|gb|DC937084.1|DC937084
EST:     TTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTCCTGAAAGCAGCAG                         GTGCTGAGAAAGGATCTACCGATCCGCAAAAGGTGAAGGTCGGAAAGGTCA
genomic: TTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTCCTGAAAGCAGCAGgtaggatatc ... taatgtgcagGTGCTGAGAAAGGATCTACCGATCCGCAAAAGGTGAAGGTCGGAAAGGTCA
EST: gi|19782770|gb|BQ039911.1|BQ039911
EST:     TTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTCCTGAAAGCAGCAG                         GTGCTGAGAAAGGATCT
genomic: TTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTCCTGAAAGCAGCAGgtaggatatc ... taatgtgcagGTGCTGAGAAAGGATCT

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), 29 (downstream exon)
Score: 8

GATAGGAGTTTCACTTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTCCTGAAAGCAGCAGgtaggatatc ... taatgtgcagGTGCTGAGAAAGGATCTACCGATCCGCAAAAGGTGAAGGTCGGAAAGGTCACCATCGATCAACTCAAGACTATTGCACAAGAGAAGCTTCCTGATCTGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttggtcactcttgactttctcttgtgattctcatcctctttcctaatgtgcagGTGCTGAGAAAGGATCTACCGATCCGCAAAAGGTGAAGGTCGGAAAGGTCACCATCGATCAACTCAAGACTATTGCACAAGAGAAGCTTCCTGATCTGAA
                                          tcctaat  putative branch site (score: 8)
                ctttctcttgtgattc  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggatatctatacatatcgacatgggttttgctaacgctttttttttgttatgattctaattatgaactatgtgaaggctagggtttaagttttattctttacaaagggattagactctgtttactcaacggactgccttggtcactcttgactttctcttgtgattctcatcctctttcctaatgtgcagGTGCTGAGAAAGGATCTACCGATCCGCAAAAGGTGAAGGTCGGAAAGGTCACCATCGATCAACTCAAGACTATTGCACAAGAGAAGCTTCCTGATCTGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC