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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATACACTGCCTTCGGAGTATGATTCGCGTGTAAAAGCTATGGAGGTTGATGAGAAACCTACAGAGGTGTACTCGGATATTGGTGGTCTGGATAAACAGgtgtgattgtcgttttagagttcaaatttcccgctgggttcttcaatatcatctacacaatctattccatatgagtgtcttagttctggttgagtttttt...

Basic information

species Physcomitrella patens
transcript PP1S218_133V6.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S218_133V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: LOC_Os06g07630.1 (Oryza sativa), 5'ss of exon 4
GGATACACTGCCTTCGGAGTATGATTCGCGTGTAAAAGCTATGGAGGTTGATGAGAAACCTACAGAGGTGTACTCGGATATTGGTGGTCTGGATAAACAGgtgtgattgtcgttttagagttcaaatttcc-cgctgggttcttcaatatcatctacaca-atctattccatatgagtgtcttagttctggttgagtttttt-----------------------------------------------------------------------------------
||| |||||||| || ||||||||||| || ||||| || |||||||| ||||| ||||| |||||||  |||   |||||||| ||||| || || |||||   ||||     | |  ||| ||| |||   | |   || |  ||    |  ||   | | | ||  | |  | |  |  |||  |   |||  |   ||                                                                                   
GGACACACTGCCATCAGAGTATGATTCACGAGTAAAGGCAATGGAGGTGGATGAAAAACCCACAGAGGACTACAATGATATTGGAGGTCTTGAAAAGCAGgtac-attgcttaataaatgttgaaagttcagtgttcctttttggaactggaaatattgacaaccatctctttagggaataatagagcaatttgtatcgcttcatgcatcaagcatgttacatttccatccatcttttccttttcataatttatcattctttccatcctattttattgaatatag

upper sequence: PP1S218_133V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: Vv14s0060g02260.t01 (Vitis vinifera), 5'ss of exon 4
GGATACACTGCCTTCGGAGTATGATTCGCGTGTAAAAGCTATGGAGGTTGATGAGAAACCTACAGAGGTGTACTCGGATATTGGTGGTCTGGATAAACAGgtgtgattgtcgttttagagttcaaatttcccgctgggttcttcaatatcatctacacaatctattccatatgagtgtcttagttctggttgagtttttt
 |||||  |||| || ||||||||||| || ||||| ||||||||||||||||| ||||| ||||| |  |||   ||||| || || ||||| || ||||   | ||  |  ||| | |   |  ||        |||| ||   | ||   |     ||   ||| |    |    |||   |||  ||         
AGATACTTTGCCATCTGAGTATGATTCTCGAGTAAAGGCTATGGAGGTTGATGAAAAACCAACAGAAGACTACAATGATATCGGAGGGCTGGAGAAGCAGgcaagttt--caattttgtgcatattttatggaagtggttgttgcttgtccgatttttgatactttcaactaaaa---cttgcctctaattacaacag--

upper sequence: PP1S218_133V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: EFJ15061 (Selaginella moellendorffii), 5'ss of exon 4
GGATACACTGCCTTCGGAGTATGATTCGCGTGTAAAAGCTATGGAGGTTGATGAGAAACCTACAGAGGTGTACTCGGATATTGGTGGTCTGGATAAACAGgtg--tgattgtcgttttagagttcaaatt-tcccgctgggttcttcaatatcatctacacaatctattccatatgagtgtcttagttctggttgagtttttt
||||||||| || || ||||||||||| ||||| || |||||||| || ||||||||||| |||||||  |||   |||||||| || || || ||||| ||   || ||    | || | |||    || | | | |       |   | | |                                                 
GGATACACTTCCGTCCGAGTATGATTCTCGTGTCAAGGCTATGGAAGTCGATGAGAAACCCACAGAGGACTACAGTGATATTGGAGGGCTTGACAAACAAgtaactgcttcatttctttgtgttttctttattctgatcaaaagcttggtgttag------------------------------------------------

upper sequence: PP1S218_133V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: EFJ37626 (Selaginella moellendorffii), 5'ss of exon 4
GGATACACTGCCTTCGGAGTATGATTCGCGTGTAAAAGCTATGGAGGTTGATGAGAAACCTACAGAGGTGTACTCGGATATTGGTGGTCTGGATAAACAGgtgtgattgtcgttttagagttcaaatttcccgctgggttcttcaatatcatctacacaatctattccatatgagtgtcttagttctggttgagtttttt
||||||||| || || ||||||||||| ||||| || |||||||| || ||||||||||| |||||||  |||   |||||||| || || || ||||| ||         | ||          |||||    ||  ||||| | | | ||| | |   |   ||  |                               
GGATACACTTCCGTCCGAGTATGATTCTCGTGTCAAGGCTATGGAAGTCGATGAGAAACCCACAGAGGACTACAGTGATATTGGAGGGCTTGACAAACAAgta-----actgcttc---------atttctttgtgttttctttattctgatc-aaaagcttggttttag------------------------------

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|162195316|gb|FC370837.1|FC370837
EST:     ATGAGAAACCTACAGAGGTGTACTCGGATATTGGTGGTCTGGATAAACAG                         ATTCAAGAGTTGATGGAAGCAATTGTTCTTCCTATGACTCACAAAGAACGG
genomic: ATGAGAAACCTACAGAGGTGTACTCGGATATTGGTGGTCTGGATAAACAGgtgtgattgt ... tgtatgacagATTCAAGAGTTGATGGAAGCAATTGTTCTTCCTATGACTCACAAAGAACGG
EST: gi|162173415|gb|FC349794.1|FC349794
EST:     ATGAGAAACCTACAGAGGTGTACTCGGATATTGGTGGTCTGGATAAACAG                         ATTCAAGAGTTGATGGAAGCAATTGTTCTTCCTATGACTCACAAAGAACGG
genomic: ATGAGAAACCTACAGAGGTGTACTCGGATATTGGTGGTCTGGATAAACAGgtgtgattgt ... tgtatgacagATTCAAGAGTTGATGGAAGCAATTGTTCTTCCTATGACTCACAAAGAACGG
EST: gi|162176626|gb|FC352471.1|FC352471
EST:     ATGAGAAACCTACAGAGGTGTACTCGGATATTGGTGGTCTGGATAAACAG                         ATTCAAGAGTTGATGGAAGCAATTGTTCTTCCTATGACTCACAAAGAACGG
genomic: ATGAGAAACCTACAGAGGTGTACTCGGATATTGGTGGTCTGGATAAACAGgtgtgattgt ... tgtatgacagATTCAAGAGTTGATGGAAGCAATTGTTCTTCCTATGACTCACAAAGAACGG
EST: gi|100393599|gb|BY953447.1|BY953447
EST:     TGAGAAACCTACAGAGGTGTACTCGGATATTGGTGGTCTGGNATAA-CAG                         ATTCAAGAGTTGATGGAAGCAATTTGT-CTTCCTATGACTCANCAA-GA-
genomic: TGAGAAACCTACAGAGGTGTACTCGGATATTGGTGGTCTGG-ATAAACAGgtgtgattgt ... tgtatgacagATTCAAGAGTTGATGGAAGCAATT-GTTCTTCCTATGACTCA-CAAAGAA
EST: gi|208384557|gb|DC915029.1|DC915029
EST:     ATGAGAAACCTACAGAGGTGTACTCGGATATTGGTGGTCTGGATAAACAG                         ATTCAAGAGTTGATGGAA
genomic: ATGAGAAACCTACAGAGGTGTACTCGGATATTGGTGGTCTGGATAAACAGgtgtgattgt ... tgtatgacagATTCAAGAGTTGATGGAA
EST: gi|208379283|gb|DC927280.1|DC927280
EST:     ATGAGAAACCTACAGAGGTGTACTCGGATATTGGTGGTCTGGATAAACAG                         ATTCAAGAGTTGATGGAAGCAATTGTTCTTCCTATGACTCACAAAGAACGG
genomic: ATGAGAAACCTACAGAGGTGTACTCGGATATTGGTGGTCTGGATAAACAGgtgtgattgt ... tgtatgacagATTCAAGAGTTGATGGAAGCAATTGTTCTTCCTATGACTCACAAAGAACGG
EST: gi|208393155|gb|DC907978.1|DC907978
EST:     ATGAGAAACCTACAGAGGTGTACTCGGATATTGGTGGTCTGGATAACCAG                         ATTCAAGAGTTGATGG
genomic: ATGAGAAACCTACAGAGGTGTACTCGGATATTGGTGGTCTGGATAAACAGgtgtgattgt ... tgtatgacagATTCAAGAGTTGATGG
EST: gi|208367277|gb|DC939835.1|DC939835
EST:     ATGAGAAACCTACAGAGGTGTACTCGGATATTGGTGGTCTGGATAAACAG                         ATTCANGAGTTGATGGAAGCAATTGTTCTTCCTATGACTCACAAAGAACGG
genomic: ATGAGAAACCTACAGAGGTGTACTCGGATATTGGTGGTCTGGATAAACAGgtgtgattgt ... tgtatgacagATTCAAGAGTTGATGGAAGCAATTGTTCTTCCTATGACTCACAAAGAACGG
EST: gi|100362918|gb|BY947594.1|BY947594
EST:     ATGAGAAACCTACAGAGGTGTACTCGGATATTGGTGGTCTGGATAAACAG                         ATTCAAGAGTTGATGGAAGCAATTGTTCTTCCTATGACTCACAAAGAACGG
genomic: ATGAGAAACCTACAGAGGTGTACTCGGATATTGGTGGTCTGGATAAACAGgtgtgattgt ... tgtatgacagATTCAAGAGTTGATGGAAGCAATTGTTCTTCCTATGACTCACAAAGAACGG
EST: gi|162279775|gb|FC455683.1|FC455683
EST:     ATGAGAAACCTACAGAGGTGTACTCGGATATTGGTGGTCTGGATAAACAG                         ATTCAAGAGTTGATGGAAGCAATTGTTCTTCCTATGACTCACAAAGAACGG
genomic: ATGAGAAACCTACAGAGGTGTACTCGGATATTGGTGGTCTGGATAAACAGgtgtgattgt ... tgtatgacagATTCAAGAGTTGATGGAAGCAATTGTTCTTCCTATGACTCACAAAGAACGG
EST: gi|208373514|gb|DC931917.1|DC931917
EST:     ATGAGAAACCTACAGAGGTGTACTCGGATATTGGTGGTCTGGATAAACAG                         ATTCNAGAGTTGATGGAAGCAATTGTTCTTCCTATGACTCACAAAGAACGG
genomic: ATGAGAAACCTACAGAGGTGTACTCGGATATTGGTGGTCTGGATAAACAGgtgtgattgt ... tgtatgacagATTCAAGAGTTGATGGAAGCAATTGTTCTTCCTATGACTCACAAAGAACGG
EST: gi|100423272|gb|BY958215.1|BY958215
EST:     TGAGAAACCTACAGAGGTGTACTCGGATATGGGTGGTCTGGATAAAACAG                         AT-CAAGAGTTGATGGAAGCAATTTTGTCT-CCTATGACTC
genomic: TGAGAAACCTACAGAGGTGTACTCGGATATTGGTGGTCTGGATAAA-CAGgtgtgattgt ... tgtatgacagATTCAAGAGTTGATGGAAGCAATTGT-TCTTCCTATGACTC
EST: gi|162260448|gb|FC435061.1|FC435061
EST:     ATGAGAAACCTACAGAGGTGTACTCGGATATTGGTGGTCTGGATAAACAG                         ATTCAAGAGTTGATGGAAGCAATTGTTCTTCCTATGACTCACAAAGAACGG
genomic: ATGAGAAACCTACAGAGGTGTACTCGGATATTGGTGGTCTGGATAAACAGgtgtgattgt ... tgtatgacagATTCAAGAGTTGATGGAAGCAATTGTTCTTCCTATGACTCACAAAGAACGG
EST: gi|208351808|gb|DC910362.1|DC910362
EST:     ATGAGAAACCTACAGAGGTGTACTCGGATATTGGTGNTCTGGATAAACAG                         ATTCAAGAGTTGATGGAAGCAATTGTTCTTCCTATGACTCACAAAGAACGG
genomic: ATGAGAAACCTACAGAGGTGTACTCGGATATTGGTGGTCTGGATAAACAGgtgtgattgt ... tgtatgacagATTCAAGAGTTGATGGAAGCAATTGTTCTTCCTATGACTCACAAAGAACGG
EST: gi|100386534|gb|BY951330.1|BY951330
EST:     ATGAGAAACCTACAGAGGTGTACTCGGATATTGGTGGTCTGGATAAACAG                         ATTCAAGAGTTGATGGAAGCAATTGTTCTTCCTATGACTCACAAAGAACGG
genomic: ATGAGAAACCTACAGAGGTGTACTCGGATATTGGTGGTCTGGATAAACAGgtgtgattgt ... tgtatgacagATTCAAGAGTTGATGGAAGCAATTGTTCTTCCTATGACTCACAAAGAACGG
EST: gi|208357259|gb|DC910656.1|DC910656
EST:     ATGAGAAACCTACAGAGGTGTACTCGGATATTGGTGGTCTGGATAAACAG                         ATTCAAGAGTTGATGGAAGCAATTGTTCTTCCTATGACTCACAA-GANCGG
genomic: ATGAGAAACCTACAGAGGTGTACTCGGATATTGGTGGTCTGGATAAACAGgtgtgattgt ... tgtatgacagATTCAAGAGTTGATGGAAGCAATTGTTCTTCCTATGACTCACAAAGAACGG
EST: gi|208378607|gb|DC903638.1|DC903638
EST:     ATGAGAAACCTACAGAGGTGTACTCGGATATTGGTGGTCTGGATAAACAG                         ATTCAAGAGTTGATGGAAGCAATTGTTCTTCCTATGACTCACAAAGAACGG
genomic: ATGAGAAACCTACAGAGGTGTACTCGGATATTGGTGGTCTGGATAAACAGgtgtgattgt ... tgtatgacagATTCAAGAGTTGATGGAAGCAATTGTTCTTCCTATGACTCACAAAGAACGG
EST: gi|162155457|gb|FC330953.1|FC330953
EST:     ATGAGAAACCTACAGAGGTGTACTCGGATATTGGTGGTCTGGATAAACAG                         ATTCAAGAGTTGATGGAAGCAATTGTTCTTCCTATGACTCACAAAGAACGG
genomic: ATGAGAAACCTACAGAGGTGTACTCGGATATTGGTGGTCTGGATAAACAGgtgtgattgt ... tgtatgacagATTCAAGAGTTGATGGAAGCAATTGTTCTTCCTATGACTCACAAAGAACGG
EST: gi|100445979|gb|CJ970278.1|CJ970278
EST:     ATGAGAAACCTACAGAGGTGTACTCGGATATTGGTGGTCTGGATAAACAG                         ATTCAAGAGTTGATGGAAGCAATTGTTCTTCCTATGACTCACAAAGAACGG
genomic: ATGAGAAACCTACAGAGGTGTACTCGGATATTGGTGGTCTGGATAAACAGgtgtgattgt ... tgtatgacagATTCAAGAGTTGATGGAAGCAATTGTTCTTCCTATGACTCACAAAGAACGG
EST: gi|162167872|gb|FC344810.1|FC344810
EST:     ATGAGAAACCTACAGAGGTGTACTCGGATATTGGTGGTCTGGATAAACAG                         ATTCAAGAGTTGATGGAAGCAATTGTTCTTCCTATGACTCACAAAGAACGG
genomic: ATGAGAAACCTACAGAGGTGTACTCGGATATTGGTGGTCTGGATAAACAGgtgtgattgt ... tgtatgacagATTCAAGAGTTGATGGAAGCAATTGTTCTTCCTATGACTCACAAAGAACGG
EST: gi|162162468|gb|FC339199.1|FC339199
EST:     ATGAGAAACCTACAGAGGTGTACTCGGATATTGGTGGTCTGGATAAACAG                         ATTCAAGAGTTGATGGAAGCAATTGTTCTTCCTATGACTCACAAAGAACGG
genomic: ATGAGAAACCTACAGAGGTGTACTCGGATATTGGTGGTCTGGATAAACAGgtgtgattgt ... tgtatgacagATTCAAGAGTTGATGGAAGCAATTGTTCTTCCTATGACTCACAAAGAACGG
EST: gi|100399109|gb|BY954204.1|BY954204
EST:     ATGAGAAACCTACAGAGGTGTACTCGGATATTGGTGGTCTGGATAAACAG                         ATTCAAGAGTTGATGGAAGCAATTGTTCTTCCTATGACTCACAAAGAACGG
genomic: ATGAGAAACCTACAGAGGTGTACTCGGATATTGGTGGTCTGGATAAACAGgtgtgattgt ... tgtatgacagATTCAAGAGTTGATGGAAGCAATTGTTCTTCCTATGACTCACAAAGAACGG
EST: gi|162168240|gb|FC344970.1|FC344970
EST:     ATGAGAAACCTACAGAGGTGTACTCGGATATTGGTGGTCTGGATAAACAG                         ATTCAAGAGTTGATGGAAGCAATTGTTCTTCCTATGACTCACAAAGAACGG
genomic: ATGAGAAACCTACAGAGGTGTACTCGGATATTGGTGGTCTGGATAAACAGgtgtgattgt ... tgtatgacagATTCAAGAGTTGATGGAAGCAATTGTTCTTCCTATGACTCACAAAGAACGG

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), 32 (downstream exon)
Score: 19

GGATACACTGCCTTCGGAGTATGATTCGCGTGTAAAAGCTATGGAGGTTGATGAGAAACCTACAGAGGTGTACTCGGATATTGGTGGTCTGGATAAACAGgtgtgattgt ... tgtatgacagATTCAAGAGTTGATGGAAGCAATTGTTCTTCCTATGACTCACAAAGAACGGTTTGAAAGCTTAGGTGTCCGACCTCCCAAAGGAGTGTTGTTATATGGCC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATACACTGCCTTCGGAGTATGATTCGCGTGTAAAAGCTATGGAGGTTGATGAGAAACCTACAGAGGTGTACTCGGATATTGGTGGTCTGGATAAACAGgtgtgattgtcgttttagagttcaaatttcccgctgggttcttcaatatcatctacacaatctattccatatgagtgtcttagttctggttgagtttttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG