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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gggttttcataacgtaagagcccatgtttccgtcttatactgcgttatggctttgaaatgtagtagttaagtgatatttagtcatgatgcgcgtgatcagGTACTATCATGACCATCGCCAAAGATCGCGTAAAGCCATCTCCTCTGCCTGACAGTTGGAAGTTGAGGGAGATTTTTGGTGTCGGTGTTGTGCTCGGCAC

Basic information

species Physcomitrella patens
transcript PP1S6_11V6.1
intron # 13
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|162193951|gb|FC371764.1|FC371764
EST:     GTTCGACTTTTCACCATTCATGGTTCTTGTCATTGCCATTCTCAATGACG                         GTACTATCATGACCATCGCCAAAGATCGCGTAAAGCCATCTCCTCTGCCTG
genomic: GTTCGACTTTTCACCATTCATGGTTCTTGTCATTGCCATTCTCAATGACGgtatgtgcgc ... gcgtgatcagGTACTATCATGACCATCGCCAAAGATCGCGTAAAGCCATCTCCTCTGCCTG
EST: gi|162198821|gb|FC374304.1|FC374304
EST:     GTTCGACTTTTCACCATTCATGGTTCTTGTCATTGCCATTCTCAATGACG                         GTACTATCATGACCATCGCCAAAGATCGCGTAAAGCCATCTCCTCTGCCTG
genomic: GTTCGACTTTTCACCATTCATGGTTCTTGTCATTGCCATTCTCAATGACGgtatgtgcgc ... gcgtgatcagGTACTATCATGACCATCGCCAAAGATCGCGTAAAGCCATCTCCTCTGCCTG
EST: gi|162174468|gb|FC350747.1|FC350747
EST:     GTTCGACTTTTCACCAT-CATGGTTCTTGTCATTGCCATTCTCAATGACG                         GTACTATCATGACCAT
genomic: GTTCGACTTTTCACCATTCATGGTTCTTGTCATTGCCATTCTCAATGACGgtatgtgcgc ... gcgtgatcagGTACTATCATGACCAT
EST: gi|162252827|gb|FC428858.1|FC428858
EST:     GTTCGACTTTTCACCATTCATGGTTCTTGTCATTGCCATTCTCAATGACG                         GTACTATCATGACCATCGCCAAAGATCGCGTAAAGCCATCTCCTCTGCCTG
genomic: GTTCGACTTTTCACCATTCATGGTTCTTGTCATTGCCATTCTCAATGACGgtatgtgcgc ... gcgtgatcagGTACTATCATGACCATCGCCAAAGATCGCGTAAAGCCATCTCCTCTGCCTG
EST: gi|162267612|gb|FC444675.1|FC444675
EST:     GTTCGACTTTTCACCATTCATGGTTCTTGTCATTGCCATTCTCAATGACG                         GTACTATCATGACCATCGCCAAAGATCGCGTAAAGCCATCTCCTCTGCCTG
genomic: GTTCGACTTTTCACCATTCATGGTTCTTGTCATTGCCATTCTCAATGACGgtatgtgcgc ... gcgtgatcagGTACTATCATGACCATCGCCAAAGATCGCGTAAAGCCATCTCCTCTGCCTG
EST: gi|162185478|gb|FC362560.1|FC362560
EST:     GTTCGACTTTTCACCATTCATGGTTCTTGTCATTGCCATTCTCAATGACG                         GTACTATCATGACCATCGCCAAAGATCGCGTAAAGCCATCTCCTCTGCCTG
genomic: GTTCGACTTTTCACCATTCATGGTTCTTGTCATTGCCATTCTCAATGACGgtatgtgcgc ... gcgtgatcagGTACTATCATGACCATCGCCAAAGATCGCGTAAAGCCATCTCCTCTGCCTG
EST: gi|162198374|gb|FC375547.1|FC375547
EST:     GTTCGACTTTTCACCATTCATGGTTCTTGTCATTGCCATTCTCAATGACG                         GTACTATCATGACCATCGCCAAAGATCGCGTAAAGCCATCTCCTCTGCCTG
genomic: GTTCGACTTTTCACCATTCATGGTTCTTGTCATTGCCATTCTCAATGACGgtatgtgcgc ... gcgtgatcagGTACTATCATGACCATCGCCAAAGATCGCGTAAAGCCATCTCCTCTGCCTG
EST: gi|100379616|gb|BY949858.1|BY949858
EST:     TTCGACTTTTCACCATTCATGGTTCTTGTCATTGCCATTTCTCA-TGACG                         GTACTATCATGACCATCGCCAAAGATCGCGTNAAGCCATCTCCTCTGCCTG
genomic: TTCGACTTTTCACCATTCATGGTTCTTGTCATTGCCATT-CTCAATGACGgtatgtgcgc ... gcgtgatcagGTACTATCATGACCATCGCCAAAGATCGCGTAAAGCCATCTCCTCTGCCTG
EST: gi|162183362|gb|FC359277.1|FC359277
EST:     GTTCGACTTTTCACCATTCATGGTTCTTGTCATTGCCATTCTCAATGACG                         GTACTATCATGACCATCGCCAAAGATCGCGTAAAGCCATCTCCTCTGCCTG
genomic: GTTCGACTTTTCACCATTCATGGTTCTTGTCATTGCCATTCTCAATGACGgtatgtgcgc ... gcgtgatcagGTACTATCATGACCATCGCCAAAGATCGCGTAAAGCCATCTCCTCTGCCTG
EST: gi|162184822|gb|FC361124.1|FC361124
EST:     GTTCGACTTTTCACCATTCATGGTTCTTGTCATTGCCATTCTCAATGACG                         GTACTATCATGACCATCGCCAAAGATCGCGTAAAGCCATCTCCTCTGCCTG
genomic: GTTCGACTTTTCACCATTCATGGTTCTTGTCATTGCCATTCTCAATGACGgtatgtgcgc ... gcgtgatcagGTACTATCATGACCATCGCCAAAGATCGCGTAAAGCCATCTCCTCTGCCTG
EST: gi|162179356|gb|FC356305.1|FC356305
EST:     GTTCGACTTTTCACCATTCATGGTTCTTGTCATTGCCATTCTCAATGACG                         GTACTATCATGACCATCGCCAAAGATCGCGTAAAGCCATCTCCTCTGCCTG
genomic: GTTCGACTTTTCACCATTCATGGTTCTTGTCATTGCCATTCTCAATGACGgtatgtgcgc ... gcgtgatcagGTACTATCATGACCATCGCCAAAGATCGCGTAAAGCCATCTCCTCTGCCTG
EST: gi|162176072|gb|FC351866.1|FC351866
EST:     GTTCGACTTTTCACCATTCATGGTTCTTGTCATTGCCATTCTCAATGACG                         GTACTATCATGACCATCGCCAAAGATCGCGTAAAGCCATCTCCTCTGCCTG
genomic: GTTCGACTTTTCACCATTCATGGTTCTTGTCATTGCCATTCTCAATGACGgtatgtgcgc ... gcgtgatcagGTACTATCATGACCATCGCCAAAGATCGCGTAAAGCCATCTCCTCTGCCTG
EST: gi|162159442|gb|FC336231.1|FC336231
EST:     TTCGACTTTTCACCATTCATGGTTCTTGTCATTGCCATTCTNCA-TGACG                         GTACTATCATGACCAT
genomic: TTCGACTTTTCACCATTCATGGTTCTTGTCATTGCCATTCT-CAATGACGgtatgtgcgc ... gcgtgatcagGTACTATCATGACCAT
EST: gi|162178407|gb|FC354131.1|FC354131
EST:     GTTCGACTTTTCACCATTCATGGTTCTTGTCATTGCCATTCTCAATGACG                         GTACTATCATGACCATCGCCAAAGATCGCGTAAAGCCATCTCCTCTGCCTG
genomic: GTTCGACTTTTCACCATTCATGGTTCTTGTCATTGCCATTCTCAATGACGgtatgtgcgc ... gcgtgatcagGTACTATCATGACCATCGCCAAAGATCGCGTAAAGCCATCTCCTCTGCCTG
EST: gi|162198177|gb|FC375480.1|FC375480
EST:     GTTCGACTTTTCACCATTCATGGTTCTTGTCATTGCCATTCTCAATGACG                         GTACTATCATGACCATCGCCAAAGATCGCGTAAAGCCATCTCCTCTGCCTG
genomic: GTTCGACTTTTCACCATTCATGGTTCTTGTCATTGCCATTCTCAATGACGgtatgtgcgc ... gcgtgatcagGTACTATCATGACCATCGCCAAAGATCGCGTAAAGCCATCTCCTCTGCCTG
EST: gi|162197978|gb|FC373993.1|FC373993
EST:     GTTCGACTTTTCACCATTCATGGTTCTTGTCATTGCCATTCTCAATGACG                         GTACTATCATGACCATCGCCAAAGATCGCGTAAAGCCATCTCCTCTGCCTG
genomic: GTTCGACTTTTCACCATTCATGGTTCTTGTCATTGCCATTCTCAATGACGgtatgtgcgc ... gcgtgatcagGTACTATCATGACCATCGCCAAAGATCGCGTAAAGCCATCTCCTCTGCCTG
EST: gi|162168958|gb|FC345640.1|FC345640
EST:     GTTCGACTTTTCACCATTCATGGTTCTTGTCATTGCCATTCTCAATGACG                         GTACTATCATGACCATCGCCAAAGATCGCGTAAAGCCATCTCCTCTGCCTG
genomic: GTTCGACTTTTCACCATTCATGGTTCTTGTCATTGCCATTCTCAATGACGgtatgtgcgc ... gcgtgatcagGTACTATCATGACCATCGCCAAAGATCGCGTAAAGCCATCTCCTCTGCCTG
EST: gi|162153187|gb|FC329593.1|FC329593
EST:     GTTCGACTTTTCACCATTCATGGTTCTTGTCATTGCCATTCTCAATGACG                         GTACTATCATGACCATCGCCAAAGATCGCGTAAAGCCATCTCCTCTGCCTG
genomic: GTTCGACTTTTCACCATTCATGGTTCTTGTCATTGCCATTCTCAATGACGgtatgtgcgc ... gcgtgatcagGTACTATCATGACCATCGCCAAAGATCGCGTAAAGCCATCTCCTCTGCCTG
EST: gi|162185798|gb|FC362354.1|FC362354
EST:     GTTCGACTTTTCACCATTCATGGTTCTTGTCATTGCCATTCTCAATGACG                         GTACTATCATGACCATCGCCAAAGATCGCGTAAAGCCATCTCCTCTGCCTG
genomic: GTTCGACTTTTCACCATTCATGGTTCTTGTCATTGCCATTCTCAATGACGgtatgtgcgc ... gcgtgatcagGTACTATCATGACCATCGCCAAAGATCGCGTAAAGCCATCTCCTCTGCCTG
EST: gi|162163564|gb|FC339474.1|FC339474
EST:     GTTCGACTTTTCACCATTCATGGTTCTTGTCATTGCCATTCTCAATGACG                         GTACTATCATGACCATCGCCAAAGATCGCGTAAAGCCATCTCCTCTGCCTG
genomic: GTTCGACTTTTCACCATTCATGGTTCTTGTCATTGCCATTCTCAATGACGgtatgtgcgc ... gcgtgatcagGTACTATCATGACCATCGCCAAAGATCGCGTAAAGCCATCTCCTCTGCCTG

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: 31 (upstream exon), 30 (downstream exon)
Score: 8

CTTGGATTTATGCTACTGGCCTTGATATGGAAGTTCGACTTTTCACCATTCATGGTTCTTGTCATTGCCATTCTCAATGACGgtatgtgcgc ... gcgtgatcagGTACTATCATGACCATCGCCAAAGATCGCGTAAAGCCATCTCCTCTGCCTGACAGTTGGAAGTTGAGGGAGATTTTTGGTGTCGGTGTTGTGCTCGGCAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatggctttgaaatgtagtagttaagtgatatttagtcatgatgcgcgtgatcagGTACTATCATGACCATCGCCAAAGATCGCGTAAAGCCATCTCCTCTGCCTGACAGTTGGAAGTTGAGGGAGATTTTTGGTGTCGGTGTTGTGCTCGGCAC
                     ttaagtgatattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gggttttcataacgtaagagcccatgtttccgtcttatactgcgttatggctttgaaatgtagtagttaagtgatatttagtcatgatgcgcgtgatcagGTACTATCATGACCATCGCCAAAGATCGCGTAAAGCCATCTCCTCTGCCTGACAGTTGGAAGTTGAGGGAGATTTTTGGTGTCGGTGTTGTGCTCGGCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT