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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatgtgtatttatatacgtagtgcacttgaatctttttcttcttttataatgggtgattgtgtatttacgtaaaattgctttggtttttaatgttgcagAGGTGCACAGTTGATCTGCCCGGTGGTCCGCTGGAAATTGAGTGGAGAGAATCGGACAACCACATCTACATGACCGGCCCTGCGAAGAGAGTATTTCAGG

Basic information

species Physcomitrella patens
transcript PP1S51_241V6.1
intron # 9
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|162269245|gb|FC445802.1|FC445802
EST:     GAGCTTGTGCGGTAGTTGTTGCTGCAGTGAAGGAAGGTCGCGCCGAAAGG                         AGGTGCACAGTTGATCTGCCCGGTGGTCCGCTGGAAATTGAGTGGAGAGAA
genomic: GAGCTTGTGCGGTAGTTGTTGCTGCAGTGAAGGAAGGTCGCGCCGAAAGGgtgagttcgt ... aatgttgcagAGGTGCACAGTTGATCTGCCCGGTGGTCCGCTGGAAATTGAGTGGAGAGAA
EST: gi|37834821|gb|BJ592833.1|BJ592833
EST:     GAGCTTGTGCGGTAGTTGTTGCTGCAGTGAAGGAAGGTCGCGCCGAAAGG                         AGGTGCACAGTTGATCTGCCCGGTGGTCCGCTGGAAATTGAGTGGAGAGAA
genomic: GAGCTTGTGCGGTAGTTGTTGCTGCAGTGAAGGAAGGTCGCGCCGAAAGGgtgagttcgt ... aatgttgcagAGGTGCACAGTTGATCTGCCCGGTGGTCCGCTGGAAATTGAGTGGAGAGAA
EST: gi|37835319|gb|BJ593331.1|BJ593331
EST:     GAGCTTGTGCGGTAGTTGTTGCTGCAGTGAAGGAAGGTCGCGCCGAAAGG                         AGGTGCACAGTTGATCTGCCCGGTGGTCCGCTGGAAATTGAGTGGAGAGAA
genomic: GAGCTTGTGCGGTAGTTGTTGCTGCAGTGAAGGAAGGTCGCGCCGAAAGGgtgagttcgt ... aatgttgcagAGGTGCACAGTTGATCTGCCCGGTGGTCCGCTGGAAATTGAGTGGAGAGAA
EST: gi|162186404|gb|FC362960.1|FC362960
EST:     GAGCTTGTGCGGTAGTTGTTGCTGCAGTGAAGGAAGGTCGCGCCGAAAGG                         AGGTGCACAGTTGATCTGCCCGGTGGTCCGCTGGAAATTGAGTGGAGAGAA
genomic: GAGCTTGTGCGGTAGTTGTTGCTGCAGTGAAGGAAGGTCGCGCCGAAAGGgtgagttcgt ... aatgttgcagAGGTGCACAGTTGATCTGCCCGGTGGTCCGCTGGAAATTGAGTGGAGAGAA
EST: gi|7584279|gb|AW700175.1|AW700175
EST:     GAGCTTGTGCGGTAGTTGTTGCTGCAGTGAAGGAAGGTCGCGCCGAAAGG                         AGGTGCACAGTTGATCTGCCCGGTGGTCCGCTGGAAATTGAGTGGAGAGAA
genomic: GAGCTTGTGCGGTAGTTGTTGCTGCAGTGAAGGAAGGTCGCGCCGAAAGGgtgagttcgt ... aatgttgcagAGGTGCACAGTTGATCTGCCCGGTGGTCCGCTGGAAATTGAGTGGAGAGAA
EST: gi|162252751|gb|FC428788.1|FC428788
EST:     GAGCTTGTGCGGTAGTTGTTGCTGCAGTGAAGGAAGGTCGCGCCGAAAGG                         AGGTGCACAGTTGTTCTGCCCGGTGGTCCGCTGGAAATTGAGTGGAGAGAA
genomic: GAGCTTGTGCGGTAGTTGTTGCTGCAGTGAAGGAAGGTCGCGCCGAAAGGgtgagttcgt ... aatgttgcagAGGTGCACAGTTGATCTGCCCGGTGGTCCGCTGGAAATTGAGTGGAGAGAA
EST: gi|67700556|gb|BJ960789.1|BJ960789
EST:     GAGCTTGTGCGGTAGTTGTTGCTGCAGTGAAGGAAGGTCGCGCCGAAAGG                         AGGTGCACAGTTGATCTGCCCGGTGGTCCGCTGGAAATTGAGTGGAGAGAA
genomic: GAGCTTGTGCGGTAGTTGTTGCTGCAGTGAAGGAAGGTCGCGCCGAAAGGgtgagttcgt ... aatgttgcagAGGTGCACAGTTGATCTGCCCGGTGGTCCGCTGGAAATTGAGTGGAGAGAA
EST: gi|162186405|gb|FC362961.1|FC362961
EST:     GAGCTTGTGCGGTAGTTGTTGCTGCAGTGAAGGAAGGTCGCGCCGAAAGG                         AGGTGCACAGTTGATCTGCCCGGTGGTCCGCTGGAAATTGAGTGGAGAGAA
genomic: GAGCTTGTGCGGTAGTTGTTGCTGCAGTGAAGGAAGGTCGCGCCGAAAGGgtgagttcgt ... aatgttgcagAGGTGCACAGTTGATCTGCCCGGTGGTCCGCTGGAAATTGAGTGGAGAGAA
EST: gi|22132121|gb|BQ826991.1|BQ826991
EST:     GAGCTTGTGCGGTAGTTGTTGCTGCAGTGAAGGAAGGTCGCGCCGAAAGG                         AGGTGCACAGTTGATCTGCCCGGTGGTCCGCTGGAAATTGAGTGGAGAGAA
genomic: GAGCTTGTGCGGTAGTTGTTGCTGCAGTGAAGGAAGGTCGCGCCGAAAGGgtgagttcgt ... aatgttgcagAGGTGCACAGTTGATCTGCCCGGTGGTCCGCTGGAAATTGAGTGGAGAGAA
EST: gi|22491789|gb|BU051712.1|BU051712
EST:     GAGCTTGTGCGGTAGTTGTTGCTGCAGTGAAGGAAGGTCGCGCCGAAAGG                         AGGTGCACAGTTGATCTGCCCGGTGGTCCGCTGGAAATTGAGTGGAGAGAA
genomic: GAGCTTGTGCGGTAGTTGTTGCTGCAGTGAAGGAAGGTCGCGCCGAAAGGgtgagttcgt ... aatgttgcagAGGTGCACAGTTGATCTGCCCGGTGGTCCGCTGGAAATTGAGTGGAGAGAA
EST: gi|37834965|gb|BJ592977.1|BJ592977
EST:     GAGCTTGTGCGGTAGTTGTTGCTGCAGTGAAGGAAGGTCGCGCCGAAAGG                         AGGTGCACAGTTGATCTGCCCGGTGGTCCGCTGGAAATTGAGTGGAGAGAA
genomic: GAGCTTGTGCGGTAGTTGTTGCTGCAGTGAAGGAAGGTCGCGCCGAAAGGgtgagttcgt ... aatgttgcagAGGTGCACAGTTGATCTGCCCGGTGGTCCGCTGGAAATTGAGTGGAGAGAA
EST: gi|162243414|gb|FC425110.1|FC425110
EST:     GAGCTTGTGCGGTAGTTGTTGCTGCAGTGAAGGAAGGTCGCGCCGAAAGG                         AGGTGCACAGTTGATCTGCCCGGTGGTCCGCTGGAAATTGAGTGGAGAGAA
genomic: GAGCTTGTGCGGTAGTTGTTGCTGCAGTGAAGGAAGGTCGCGCCGAAAGGgtgagttcgt ... aatgttgcagAGGTGCACAGTTGATCTGCCCGGTGGTCCGCTGGAAATTGAGTGGAGAGAA
EST: gi|67726581|gb|BJ976840.1|BJ976840
EST:     GAGCTTGTGCGGTAGTTGTTGCTGCAGTGAAGGAAGGTCGCGCCGAAAGG                         AGGTGCACAGTTGATCTGCCCGGTGGTCCGCTGGAAATTGAGTGGAGAGAA
genomic: GAGCTTGTGCGGTAGTTGTTGCTGCAGTGAAGGAAGGTCGCGCCGAAAGGgtgagttcgt ... aatgttgcagAGGTGCACAGTTGATCTGCCCGGTGGTCCGCTGGAAATTGAGTGGAGAGAA
EST: gi|162269244|gb|FC445801.1|FC445801
EST:     GAGCTTGTGCGGTAGTTGTTGCTGCAGTGAAGGAAGGTCGCGCCGAAAGG                         AGGTGCACAGTTGATCTGCCCGGTGGTCCGCTGGAAATTGAGTGGAGAGAA
genomic: GAGCTTGTGCGGTAGTTGTTGCTGCAGTGAAGGAAGGTCGCGCCGAAAGGgtgagttcgt ... aatgttgcagAGGTGCACAGTTGATCTGCCCGGTGGTCCGCTGGAAATTGAGTGGAGAGAA
EST: gi|37849296|gb|BJ607304.1|BJ607304
EST:     GAGCTTGTGCGGTAGTTGTTGCTGCAGTGAAGGAAGGTCGCGCCGAAAGG                         AGGTGCACAGTTGATCTGCCCGGTGGTCCGCTGGAAATTGAGTGGAGAGAA
genomic: GAGCTTGTGCGGTAGTTGTTGCTGCAGTGAAGGAAGGTCGCGCCGAAAGGgtgagttcgt ... aatgttgcagAGGTGCACAGTTGATCTGCCCGGTGGTCCGCTGGAAATTGAGTGGAGAGAA
EST: gi|37841391|gb|BJ599399.1|BJ599399
EST:     GAGCTTGTGCGGTAGTTGTTGCTGCAGTGAAGGAAGGTCGCGCCGAAAGG                         AGGTGCACAGTTGATCTGCCCGGTGGTCCGCTGGAAATTGAGTGGAGAGAA
genomic: GAGCTTGTGCGGTAGTTGTTGCTGCAGTGAAGGAAGGTCGCGCCGAAAGGgtgagttcgt ... aatgttgcagAGGTGCACAGTTGATCTGCCCGGTGGTCCGCTGGAAATTGAGTGGAGAGAA
EST: gi|37827317|gb|BJ585329.1|BJ585329
EST:     GAGCTTGTGCGGTAGTTGTTGCTGCAGTGAAGGAAGGTCGCGCCGAAAGG                         AGGTGCACAGTTGATCTGCCCGGTGGTCCGCTGGAAATTGAGTGGAGAGAA
genomic: GAGCTTGTGCGGTAGTTGTTGCTGCAGTGAAGGAAGGTCGCGCCGAAAGGgtgagttcgt ... aatgttgcagAGGTGCACAGTTGATCTGCCCGGTGGTCCGCTGGAAATTGAGTGGAGAGAA
EST: gi|162233272|gb|FC409614.1|FC409614
EST:     GAGCTTGTGCGGTAGTTGTTGCTGCAGTGAAGGAAGGTCGCGCCGAAAGG                         AGGTGCACAGTTGATCTGCCCGGTGGTCCGCTGGAAATTGAGTGGAGAGAA
genomic: GAGCTTGTGCGGTAGTTGTTGCTGCAGTGAAGGAAGGTCGCGCCGAAAGGgtgagttcgt ... aatgttgcagAGGTGCACAGTTGATCTGCCCGGTGGTCCGCTGGAAATTGAGTGGAGAGAA
EST: gi|162243413|gb|FC425109.1|FC425109
EST:     GAGCTTGTGCGGTAGTTGTTGCTGCAGTGAAGGAAGGTCGCGCCGAAAGG                         AGGTGCACAGTTGATCTGCCCGGTGGTCCGCTGGAAATTGAGTGGAGAGAA
genomic: GAGCTTGTGCGGTAGTTGTTGCTGCAGTGAAGGAAGGTCGCGCCGAAAGGgtgagttcgt ... aatgttgcagAGGTGCACAGTTGATCTGCCCGGTGGTCCGCTGGAAATTGAGTGGAGAGAA
EST: gi|162169969|gb|FC345909.1|FC345909
EST:     GAGCTTGTGCGGTAGTTGTTGCTGCAGTGAAGGAAGGTCGCGCCGAAAGG                         AGGTGCACAGTTGATTTGCCCGGTGGTCCGCTGGAAATTGAGTGGAGAGAA
genomic: GAGCTTGTGCGGTAGTTGTTGCTGCAGTGAAGGAAGGTCGCGCCGAAAGGgtgagttcgt ... aatgttgcagAGGTGCACAGTTGATCTGCCCGGTGGTCCGCTGGAAATTGAGTGGAGAGAA

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), 33 (downstream exon)
Score: 20

GTGCTACTCAGGCCTGTGGAACTGGAGCTTGTGCGGTAGTTGTTGCTGCAGTGAAGGAAGGTCGCGCCGAAAGGgtgagttcgt ... aatgttgcagAGGTGCACAGTTGATCTGCCCGGTGGTCCGCTGGAAATTGAGTGGAGAGAATCGGACAACCACATCTACATGACCGGCCCTGCGAAGAGAGTATTTCAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttataatgggtgattgtgtatttacgtaaaattgctttggtttttaatgttgcagAGGTGCACAGTTGATCTGCCCGGTGGTCCGCTGGAAATTGAGTGGAGAGAATCGGACAACCACATCTACATGACCGGCCCTGCGAAGAGAGTATTTCAGG
                                         ttttaat  putative branch site (score: 20)
                  tatttacgtaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taatgtgtatttatatacgtagtgcacttgaatctttttcttcttttataatgggtgattgtgtatttacgtaaaattgctttggtttttaatgttgcagAGGTGCACAGTTGATCTGCCCGGTGGTCCGCTGGAAATTGAGTGGAGAGAATCGGACAACCACATCTACATGACCGGCCCTGCGAAGAGAGTATTTCAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA