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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcgtgttgcaatgccattgctattctccttatgggtacctgagctcccttgtttcagaagttattatgcagtatttatctctgtgtgttgaaatcgtaggatatatctgttgtttttgtcttgtggtatgcagGTGCTTATGGGTATGGGACCTAGATATAGTTCAGCCTTGGAGTTGGTTTCTTTTCACACAGTGTCAAAGGGCTTCCTTGGAGAATGTGGACAGCGTGGTG

Basic information

species Physcomitrella patens
transcript PP1S64_220V6.1
intron # 7
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|162155391|gb|FC332005.1|FC332005
EST:     ACCAGCAAAACGTATATCAAGATGAGCGGCCCTTCATCAGCGCGAGAAAG                         GTGCTTATGGGTATGGGACCTAGATATAGTTCAGCCTTGGAGTTGGTTTCT
genomic: ACCAGCAAAACGTATATCAAGATGAGCGGCCCTTCATCAGCGCGAGAAAGgtatcgtgtt ... tggtatgcagGTGCTTATGGGTATGGGACCTAGATATAGTTCAGCCTTGGAGTTGGTTTCT
EST: gi|162160782|gb|FC336681.1|FC336681
EST:     ACCAGCAAAACGTATATCAAGATGAGCGGCCCTTCATCAGCGCGAGAAAG                         GTGCTTATGGGTATGGGACCTAGATATAGTTCAGCCTTGG
genomic: ACCAGCAAAACGTATATCAAGATGAGCGGCCCTTCATCAGCGCGAGAAAGgtatcgtgtt ... tggtatgcagGTGCTTATGGGTATGGGACCTAGATATAGTTCAGCCTTGG
EST: gi|162252058|gb|FC428297.1|FC428297
EST:     ACCAGCAAAACGTATATCAAGATGAGCGGCCCTTCATCAGCGCGAGAAAG                         GTGCTTATGGGTATGGGACCTAGATATAGTTC
genomic: ACCAGCAAAACGTATATCAAGATGAGCGGCCCTTCATCAGCGCGAGAAAGgtatcgtgtt ... tggtatgcagGTGCTTATGGGTATGGGACCTAGATATAGTTC
EST: gi|162156210|gb|FC332585.1|FC332585
EST:     ACCAGCAAAACGTATATCAAGATGAGCGGCCCTTCATCAGCGCGAGAAAG                         GTGCTTATGGGTATGGGACCTAGATATAGTTCAGCCTTGGAGTTGGTTTCT
genomic: ACCAGCAAAACGTATATCAAGATGAGCGGCCCTTCATCAGCGCGAGAAAGgtatcgtgtt ... tggtatgcagGTGCTTATGGGTATGGGACCTAGATATAGTTCAGCCTTGGAGTTGGTTTCT
EST: gi|162153784|gb|FC329915.1|FC329915
EST:     ACCAGCAAAACGTATATCAAGATGAGCGGCCCTTCATCAGCGCGAGAAAG                         GTGCTTATGGGTATGGGACCTAGATATAGTTCAGCCTTGGAGTTGGTTTCT
genomic: ACCAGCAAAACGTATATCAAGATGAGCGGCCCTTCATCAGCGCGAGAAAGgtatcgtgtt ... tggtatgcagGTGCTTATGGGTATGGGACCTAGATATAGTTCAGCCTTGGAGTTGGTTTCT
EST: gi|162165158|gb|FC341153.1|FC341153
EST:     AAACGTATATCAAGATGAGCGGCCCTTCATCAGCGCGAGAAAG                         GTGCTTATGGGTATGGGACCTAGATATAGTTCAGCCTTGGAGTTGGTTTCT
genomic: AAACGTATATCAAGATGAGCGGCCCTTCATCAGCGCGAGAAAGgtatcgtgtt ... tggtatgcagGTGCTTATGGGTATGGGACCTAGATATAGTTCAGCCTTGGAGTTGGTTTCT
EST: gi|162170441|gb|FC347626.1|FC347626
EST:     ACCAGCAAAACGTATATCAAGATGAGCGGCCCTTCATCAGCGCGAGAAAG                         GTGCTTATGGGTATGGGACCTAGATATAGTTCAGCCTTGGAGTTGGTTTCT
genomic: ACCAGCAAAACGTATATCAAGATGAGCGGCCCTTCATCAGCGCGAGAAAGgtatcgtgtt ... tggtatgcagGTGCTTATGGGTATGGGACCTAGATATAGTTCAGCCTTGGAGTTGGTTTCT
EST: gi|6227378|gb|AW155977.1|AW155977
EST:     ACCAGCAAAACGTATATCAAGATGAGCGGCCCTTCATCAGCGCGAGAAAG                         GTGCTTTTGGGTATGGGACCTAGATATAGTTCAGCCTTGGAGTTGGTATTC
genomic: ACCAGCAAAACGTATATCAAGATGAGCGGCCCTTCATCAGCGCGAGAAAGgtatcgtgtt ... tggtatgcagGTGCTTATGGGTATGGGACCTAGATATAGTTCAGCCTTGGAGTTGGT-TTC
EST: gi|162191349|gb|FC368145.1|FC368145
EST:     ACCAGCAAAACGTATATCAAGATGAGCGGCCCTTCATCAGCGCGAGAAAG                         GTGCTTATGGGTATGGGACCTAGATATAGTTCAGCCTTGGAGTTGGTTTCT
genomic: ACCAGCAAAACGTATATCAAGATGAGCGGCCCTTCATCAGCGCGAGAAAGgtatcgtgtt ... tggtatgcagGTGCTTATGGGTATGGGACCTAGATATAGTTCAGCCTTGGAGTTGGTTTCT
EST: gi|162246304|gb|FC421049.1|FC421049
EST:     ACCAGCAAAACGTATATCAAGATGAGCGGCCCTTCATCAGCGCGAGAAAG                         GTGCTTATGGGTATGGGACCTAGATATAGTTCAGCCTTGGAGTTGGTTTCT
genomic: ACCAGCAAAACGTATATCAAGATGAGCGGCCCTTCATCAGCGCGAGAAAGgtatcgtgtt ... tggtatgcagGTGCTTATGGGTATGGGACCTAGATATAGTTCAGCCTTGGAGTTGGTTTCT
EST: gi|162244637|gb|FC424604.1|FC424604
EST:     ACCAGCAAAACGTATATCAAGATGAGCGGCCCTTCATCAGCGCGAGAAAG                         GTGCTTATGGGTATGGGACCTAGATATAGTTCAGCCTTGGAGTTGGTTTCT
genomic: ACCAGCAAAACGTATATCAAGATGAGCGGCCCTTCATCAGCGCGAGAAAGgtatcgtgtt ... tggtatgcagGTGCTTATGGGTATGGGACCTAGATATAGTTCAGCCTTGGAGTTGGTTTCT
EST: gi|162188744|gb|FC364030.1|FC364030
EST:     ACCAGCAAAACGTATATCAAGATGAGCGGCCCTTCATCAGCGCGAGAAAG                         GTGCTTATGGGTATGGGACCTAGATATAGTTCAGCCTTGGAGTTGGTTTCT
genomic: ACCAGCAAAACGTATATCAAGATGAGCGGCCCTTCATCAGCGCGAGAAAGgtatcgtgtt ... tggtatgcagGTGCTTATGGGTATGGGACCTAGATATAGTTCAGCCTTGGAGTTGGTTTCT

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), 33 (downstream exon)
Score: 27

GATCGAGTTCTGTATCAGGGAAAGAGTTGTGTTGATGGCTGACGAGGTTTACCAGCAAAACGTATATCAAGATGAGCGGCCCTTCATCAGCGCGAGAAAGgtatcgtgtt ... tggtatgcagGTGCTTATGGGTATGGGACCTAGATATAGTTCAGCCTTGGAGTTGGTTTCTTTTCACACAGTGTCAAAGGGCTTCCTTGGAGAATGTGGACAGCGTGGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctgtgtgttgaaatcgtaggatatatctgttgtttttgtcttgtggtatgcagGTGCTTATGGGTATGGGACCTAGATATAGTTCAGCCTTGGAGTTGGTTTCTTTTCACACAGTGTCAAAGGGCTTCCTTGGAGAATGTGGACAGCGTGGTG
                      atatatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcgtgttgcaatgccattgctattctccttatgggtacctgagctcccttgtttcagaagttattatgcagtatttatctctgtgtgttgaaatcgtaggatatatctgttgtttttgtcttgtggtatgcagGTGCTTATGGGTATGGGACCTAGATATAGTTCAGCCTTGGAGTTGGTTTCTTTTCACACAGTGTCAAAGGGCTTCCTTGGAGAATGTGGACAGCGTGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA