Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatatttcgacgctttttcatgtggtttggatgagaatgtcttactcggaagcaacaccagcgttgttaatgggatccctgaattcaatttcaattacagGATAGGAGTTTCACTTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTCCTGAAAGCAGCAG

Basic information

species Physcomitrella patens
transcript PP1S46_69V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S46_69V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os03g03020.1 (Oryza sativa), 3'ss of exon 2
-tatatttcgacgctt---tttcatgtggtttggatgagaatgtcttactcggaagcaacaccagcgttgttaatgggatccctgaattcaatttcaattacagGATAGGAGTTTCACTTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTCCTGAAAGCAGCAG
 |    ||  |  | |   || ||     | ||  |||  |||  |  ||       ||     |   |  ||||   ||   ||  | |    |   || |||||||  |||||||| || ||||||||||| || |||||||| ||||||||||| || |||||||
gtgagcttaaaatcgtcaattccactgaatgtgtgtgaacatgcatctct-------aatgtgggtactcctaattatatgtgtgtttgcctggttttttgcagGATAAAAGTTTCACCTTTATCTTGAAGACCCCTCCTGCCTCAGTCCTTCTCCTCAAGGCAGCAG
















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:     CTGCTGACAAGCCTGGCTATATCATCCCCGTCGAGATCACAGTTTACGAT                         GATAGGAGTTTCACTTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTC
genomic: CTGCTGACAAGCCTGGCTATATCATCCCCGTCGAGATCACAGTTTACGATgtatgtggtt ... tcaattacagGATAGGAGTTTCACTTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTC
EST: gi|162277905|gb|FC453828.1|FC453828
EST:     CTGCTGACAAGCCTGGCTATATCATCCCCGTCGAGATCACAGTTTACGAT                         GATAGGAGTTTCACTTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTC
genomic: CTGCTGACAAGCCTGGCTATATCATCCCCGTCGAGATCACAGTTTACGATgtatgtggtt ... tcaattacagGATAGGAGTTTCACTTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTC
EST: gi|162228458|gb|FC405252.1|FC405252
EST:     CCTGGCTATATCATCCCCGTCGAGATCACAGTTTACGAT                         GATAGGAGTTTCACTTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTC
genomic: CCTGGCTATATCATCCCCGTCGAGATCACAGTTTACGATgtatgtggtt ... tcaattacagGATAGGAGTTTCACTTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTC
EST: gi|100411876|gb|BY992384.1|BY992384
EST:     CTGCTGACAAGCCTGGCTATATCATCCCCGTCGAGATCACAGTTTACGAT                         GATAGGAGTTTCACTTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTC
genomic: CTGCTGACAAGCCTGGCTATATCATCCCCGTCGAGATCACAGTTTACGATgtatgtggtt ... tcaattacagGATAGGAGTTTCACTTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTC
EST: gi|162234054|gb|FC410320.1|FC410320
EST:     CTGCTGACAAGCCTGGCTATATCATCCCCGTCGAGATCACAGTTTACGAT                         GATAGGAGTTTCACTTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTC
genomic: CTGCTGACAAGCCTGGCTATATCATCCCCGTCGAGATCACAGTTTACGATgtatgtggtt ... tcaattacagGATAGGAGTTTCACTTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTC
EST: gi|7147874|gb|AW509796.1|AW509796
EST:     CTGCTGACAAGCCTGGCTATATCATCCCCGTCGAGATCACAGATTACGAT                         GATAGGAGTTTCACTTTCATCTTGGAA-ACACCCACTGCCTCTGTCCTTCT
genomic: CTGCTGACAAGCCTGGCTATATCATCCCCGTCGAGATCACAGTTTACGATgtatgtggtt ... tcaattacagGATAGGAGTTTCACTTTCATCTTG-AAGACACCCCCTGCCTCTGTCCTTCT
EST: gi|162260840|gb|FC438196.1|FC438196
EST:     CTGCTGACAAGCCTGGCTATATCATCCCCGTCGAGATCACAGTTTACGAT                         GATAGGAGTTTCACTTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTC
genomic: CTGCTGACAAGCCTGGCTATATCATCCCCGTCGAGATCACAGTTTACGATgtatgtggtt ... tcaattacagGATAGGAGTTTCACTTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTC
EST: gi|19776753|gb|BQ039104.1|BQ039104
EST:     CTGCTGACAAGCCTGGCTATATCATCCCCGTCGAGATCACAGTTTACGAT                         GATAGGAGTTTCACTTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTC
genomic: CTGCTGACAAGCCTGGCTATATCATCCCCGTCGAGATCACAGTTTACGATgtatgtggtt ... tcaattacagGATAGGAGTTTCACTTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTC
EST: gi|162277904|gb|FC453827.1|FC453827
EST:     CTGCTGACAAGCCTGGCTATATCATCCCCGTCGAGATCACAGTTTACGAT                         GATAGGAGTTTCACTTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTC
genomic: CTGCTGACAAGCCTGGCTATATCATCCCCGTCGAGATCACAGTTTACGATgtatgtggtt ... tcaattacagGATAGGAGTTTCACTTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTC
EST: gi|208356326|gb|DC957360.1|DC957360
EST:     CTGCTGACAAGCCTGGCTATATCATCCCCGTCGAGATCACAGTTTACGAT                         GATAGGAGTTTCACTTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTC
genomic: CTGCTGACAAGCCTGGCTATATCATCCCCGTCGAGATCACAGTTTACGATgtatgtggtt ... tcaattacagGATAGGAGTTTCACTTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTC
EST: gi|162260841|gb|FC438197.1|FC438197
EST:     CTGCTGACAAGCCTGGCTATATCATCCCCGTCGAGATCACAGTTTACGAT                         GATAGGAGTTTCACTTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTC
genomic: CTGCTGACAAGCCTGGCTATATCATCCCCGTCGAGATCACAGTTTACGATgtatgtggtt ... tcaattacagGATAGGAGTTTCACTTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTC
EST: gi|162234055|gb|FC410321.1|FC410321
EST:     CTGCTGACAAGCCTGGCTATATCATCCCCGTCGAGATCACAGTTTACGAT                         GATAGGAGTTTCACTTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTC
genomic: CTGCTGACAAGCCTGGCTATATCATCCCCGTCGAGATCACAGTTTACGATgtatgtggtt ... tcaattacagGATAGGAGTTTCACTTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTC
EST: gi|208386417|gb|DC937084.1|DC937084
EST:     CTGCTGACAAGCCTGGCTATATCATCCCCGTCGAGATCACAGTTTACGAT                         GATAGGAGTTTCACTTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTC
genomic: CTGCTGACAAGCCTGGCTATATCATCCCCGTCGAGATCACAGTTTACGATgtatgtggtt ... tcaattacagGATAGGAGTTTCACTTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTC
EST: gi|19782770|gb|BQ039911.1|BQ039911
EST:     CTGCTGACAAGCCTGGCTATATCATCCCCGTCGAGATCACAGTTTACGAT                         GATAGGAGTTTCACTTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTC
genomic: CTGCTGACAAGCCTGGCTATATCATCCCCGTCGAGATCACAGTTTACGATgtatgtggtt ... tcaattacagGATAGGAGTTTCACTTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTC
EST: gi|19788061|gb|BQ040708.1|BQ040708
EST:     CTGCTGACAAGCCTGGCTATATCATCCCCGTCGAGATCACAGTTTACGAT                         GATAGGAGTTTCACTTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTC
genomic: CTGCTGACAAGCCTGGCTATATCATCCCCGTCGAGATCACAGTTTACGATgtatgtggtt ... tcaattacagGATAGGAGTTTCACTTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTC

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), 27 (downstream exon)
Score: 9

TTCCAAGGGTGTCAACATTATGGCTTTCTGCAAGGAATATAATGCCAAGACTGCTGACAAGCCTGGCTATATCATCCCCGTCGAGATCACAGTTTACGATgtatgtggtt ... tcaattacagGATAGGAGTTTCACTTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTCCTGAAAGCAGCAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcggaagcaacaccagcgttgttaatgggatccctgaattcaatttcaattacagGATAGGAGTTTCACTTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTCCTGAAAGCAGCAG
                   tgttaat  putative branch site (score: 9)
                                    aattcaatttcaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatatttcgacgctttttcatgtggtttggatgagaatgtcttactcggaagcaacaccagcgttgttaatgggatccctgaattcaatttcaattacagGATAGGAGTTTCACTTTCATCTTGAAGACACCCCCTGCCTCTGTCCTTCTCCTGAAAGCAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA