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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctttttctgagttgcgcttgcaaagctggcaacaattcatttcactcgatgttttctcaaattttgtttttgcaaccaagtcctgctggtatctattttatggatgtcgcttcaattgaaatagttggtggatcttctttggagcatgcatgcttccttgtgcttagaaatgacgtcaaatgtgttgcttgtcagGGGTTGGAAGTGATTGAAGCTCACTATCTCTTCGGTGCTGATTACGATGACATTGATATTGTTGTCCATCCCCAATCAATCATTCATTCCATGGTGGAGA

Basic information

species Physcomitrella patens
transcript PP1S62_157V6.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S62_157V6.2 (Physcomitrella patens), 3'ss of exon 10
lower sequence: LOC_Os01g01710.2 (Oryza sativa), 3'ss of exon 8
gtaagctttttctgagttgcgcttgcaaagctggcaacaattcatttcactcgatgttttctcaaattttgtttttgcaaccaagtcctgctggtatctattttatggatgtcgcttcaattgaaatagttggtggatcttctttggagcatgcatgcttccttgtgcttagaaatgacgtcaaatgtgttgcttgtcagGGGTTGGAAGTGATTGAAGCTCACTATCTCTTCGGTGCTGATTACGATGACATTGATATTGTTGTCCATCCCCAATCAATCATTCATTCCATGGTGGAGA
                                                                                                                 |  |     | || | ||   | || ||  |  |  ||||   ||    || |||    ||||||  |||  ||  |       ||||| || ||||| |||||||| || ||| | || |||||||| |||||||||||||| |||||  |||| || ||||| ||||| || || ||| | || |
-----------------------------------------------------------------------------------------------------------------gtgtttgcagtaa-actttcagaattttactgaggtcatgttggcagtatt-tgcactaaaatga--tcacttgattcata---cagGGTTTAGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATACGATGACATTGAAATTGTGATCCACCCACAATCTATCATACACTCTATGATTGAAA

upper sequence: PP1S62_157V6.2 (Physcomitrella patens), 3'ss of exon 10
lower sequence: EFJ07179 (Selaginella moellendorffii), 3'ss of exon 9
gtaagctttttctgagttgcgcttgcaaagctggcaacaattcatttcactcgatgttttctcaaattttgtttttgcaaccaagtcctgctggtatctattttatggatgtcgcttcaattgaaatagttggtggatcttctttggagcatgcatgcttccttgtgcttagaaa-tgacgtcaaatgtgttgcttgtcagGGGTTGGAAGTGATTGAAGCTCACTATCTCTTCGGTGCTGATTACGATGACATTGATATTGTTGTCCATCCCCAATCAATCATTCATTCCATGGTGGAGA
                                                                                                                                                    | |   |  | |  || | |||      |||  | | || |  |||| | |||||  | || || ||||||||||||||| | || || ||||| || ||||||||||| |||||| ||||||||||||| || || || |||||| | ||||
----------------------------------------------------------------------------------------------------------------------------------------------------gtaaaaaaacatttttatacttgtctgctgaactaacatcttctgctgg-cagGGACTCGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGACATTGACATTGTTATCCATCCCCAATCCATTATACACTCCATGATCGAGA

upper sequence: PP1S62_157V6.2 (Physcomitrella patens), 3'ss of exon 10
lower sequence: EFJ09183 (Selaginella moellendorffii), 3'ss of exon 9
gtaagctttttctgagttgcgcttgcaaagctggcaacaattcatttcactcgatgttttctcaaattttgtttttgcaaccaagtcctgctggtatctattttatggatgtcgcttcaattgaaatagttggtggatcttctttggagcatgcatgcttccttgtgcttagaaa-tgacgtcaaatgtgttgcttgtcagGGGTTGGAAGTGATTGAAGCTCACTATCTCTTCGGTGCTGATTACGATGACATTGATATTGTTGTCCATCCCCAATCAATCATTCATTCCATGGTGGAGA
                                                                                                                                                    | |   |  | |  || | |||      |||  | | || |  |||| | |||||  | || || ||||||||||||||| | || || ||||| || ||||||||||| |||||| ||||||||||||| || || || |||||| | ||||
----------------------------------------------------------------------------------------------------------------------------------------------------gtaaaaaaacatttttatacttgtctgctgaactaacatcttctgctgg-cagGGACTCGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGACATTGACATTGTTATCCATCCCCAATCGATTATACACTCCATGATCGAGA

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|162203496|gb|FC380412.1|FC380412
EST:     CTGCCACGCTCATGAACAAG                         GGGTTGGAAGTGATTGAAGCTCACTATCTCTTCGGTGCTGATTACGATGAC
genomic: CTGCCACGCTCATGAACAAGgtaagctttt ... tgcttgtcagGGGTTGGAAGTGATTGAAGCTCACTATCTCTTCGGTGCTGATTACGATGAC
EST: gi|162185513|gb|FC361237.1|FC361237
EST:     GGAGCATGGGCCGCAAAATTACGGTTGATTCTGCCACGCTCATGAACAAG                         GGGTTGGAAGTGATTGAAGCTCACTATCTCTTCGGTGCTGATTACGATGAC
genomic: GGAGCATGGGCCGCAAAATTACGGTTGATTCTGCCACGCTCATGAACAAGgtaagctttt ... tgcttgtcagGGGTTGGAAGTGATTGAAGCTCACTATCTCTTCGGTGCTGATTACGATGAC
EST: gi|100442899|gb|BY963394.1|BY963394
EST:     GGAGCATGGGCCGCAAAATTACGGTTGATTCTGCCACGCTCATGAACAAG                         GGGTTGGAAGTG
genomic: GGAGCATGGGCCGCAAAATTACGGTTGATTCTGCCACGCTCATGAACAAGgtaagctttt ... tgcttgtcagGGGTTGGAAGTG
EST: gi|162163958|gb|FC339868.1|FC339868
EST:     GGAGCATGGGCCGCAAAATTACGGTTGATTCTGCCACGCTCATGAACAAG                         GGGTTGGAAGTGATTGAAGCTCACTATCTCTTCGGTGCTGATTACGATGAC
genomic: GGAGCATGGGCCGCAAAATTACGGTTGATTCTGCCACGCTCATGAACAAGgtaagctttt ... tgcttgtcagGGGTTGGAAGTGATTGAAGCTCACTATCTCTTCGGTGCTGATTACGATGAC

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), 34 (downstream exon)
Score: 17

GGAGAAGTTGAAGGAGGTTAAAGTAGCAGATGCTTTGAAGCATCCCAACTGGAGCATGGGCCGCAAAATTACGGTTGATTCTGCCACGCTCATGAACAAGgtaagctttt ... tgcttgtcagGGGTTGGAAGTGATTGAAGCTCACTATCTCTTCGGTGCTGATTACGATGACATTGATATTGTTGTCCATCCCCAATCAATCATTCATTCCATGGTGGAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggagcatgcatgcttccttgtgcttagaaatgacgtcaaatgtgttgcttgtcagGGGTTGGAAGTGATTGAAGCTCACTATCTCTTCGGTGCTGATTACGATGACATTGATATTGTTGTCCATCCCCAATCAATCATTCATTCCATGGTGGAGA
                       ttagaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctttttctgagttgcgcttgcaaagctggcaacaattcatttcactcgatgttttctcaaattttgtttttgcaaccaagtcctgctggtatctattttatggatgtcgcttcaattgaaatagttggtggatcttctttggagcatgcatgcttccttgtgcttagaaatgacgtcaaatgtgttgcttgtcagGGGTTGGAAGTGATTGAAGCTCACTATCTCTTCGGTGCTGATTACGATGACATTGATATTGTTGTCCATCCCCAATCAATCATTCATTCCATGGTGGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA