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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagaccatattttttagatgcattgtatagactttccgttccgccttagactctcaagctttcaacttcaaatggtttttgttggttcgaaccgttacagGTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAG

Basic information

species Physcomitrella patens
transcript PP1S277_10V6.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S277_10V6.3 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA10G30220.1 (Glycine max), 3'ss of exon 3
-----------------------------------------------tagaccatat-tttttagatgcattgtatagactttccgttccgccttagactctcaagctttcaacttcaaatggt--ttttgttggttcgaaccgttacagGTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAG
                                               || ||| | |  | ||     |  | | | | |  |     | |    |    ||  |  || ||  | ||  || |   ||  |   | |          ||||||| ||||| || ||| ||||  | ||||||||||||||||||||| |||||||||| ||  |  |||| |
gtaagctgtttttacttccagtcatggtgtgcattcttcttcatctctaaaccctgtactcttcctctctcttttttggccatgaaacctgtaccattgactttattttccatgtgcatttgataacttcttcaatacttggatgactagGTGGGTGCAGAAAACAATCTACTTGTGAAGGATCACACTCACACTTTTGTTAACAAAGGGGGTCAAATTGGTG

upper sequence: PP1S277_10V6.3 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA20G37170.1 (Glycine max), 3'ss of exon 3
--------------------------------------tagaccatattttttagatgcattgtatagactttccgttccgcct----tagactctcaagctttcaacttcaaatggtttttgttggttcgaaccgtta-----cagGTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAG
                                      |   || | |||||| |          |  ||| |    |     |    |  ||  |  | || || | ||  |||   || |  |  ||| |  | |        ||||||| || || || ||| ||||  | ||||||||||||||||||||| |||||||||| ||  |  ||||||
gtaagctgtttttacttcatctctaaaacctgttttcttcttccctcttttttggccatgaaacctgtactattgactttatttttcgtgtacattgtatctgtccattt--aataacttctacttcttcaatgcttggatgactagGTGGGTGCGGATAACAATCTACTTGTAAAGGATCACACTCACACTTTTGTTAACAAAGGGGGTCAAATTGGAG
















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|100389821|gb|BY971173.1|BY971173
EST:     TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAG                         GTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
genomic: TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAGgtactttcac ... accgttacagGTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
EST: gi|162165520|gb|FC340631.1|FC340631
EST:     TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAG                         GTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
genomic: TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAGgtactttcac ... accgttacagGTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
EST: gi|100447940|gb|CJ972239.1|CJ972239
EST:     TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAG                         GTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
genomic: TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAGgtactttcac ... accgttacagGTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
EST: gi|162172589|gb|FC349362.1|FC349362
EST:     TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAG                         GTGGGGGCAGACAATAATTTACTACTCAAGGATCA
genomic: TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAGgtactttcac ... accgttacagGTGGGGGCAGACAATAATTTACTACTCAAGGATCA
EST: gi|162155413|gb|FC332027.1|FC332027
EST:     TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAG                         GTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
genomic: TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAGgtactttcac ... accgttacagGTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
EST: gi|100352075|gb|BY964693.1|BY964693
EST:     -ACATGTCTTTTTCGGGTGCTACAACA-TCCGTTTCGGCTCCTAGCTAAG                         GTGGGGGGCAGACA-TAATTTACTACTC
genomic: TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAGgtactttcac ... accgttacagGTGGGGG-CAGACAATAATTTACTACTC
EST: gi|18327722|gb|BJ159725.1|BJ159725
EST:     TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAG                         GTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
genomic: TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAGgtactttcac ... accgttacagGTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
EST: gi|100396902|gb|BY953885.1|BY953885
EST:     TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAG                         GTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
genomic: TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAGgtactttcac ... accgttacagGTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
EST: gi|208399548|gb|DC908545.1|DC908545
EST:     TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAG                         GTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
genomic: TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAGgtactttcac ... accgttacagGTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
EST: gi|162151154|gb|FC327153.1|FC327153
EST:     CAACAATCTGTTTCGCCTCCTAGCTAAG                         GTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
genomic: CAACAATCTGTTTCGCCTCCTAGCTAAGgtactttcac ... accgttacagGTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
EST: gi|100424082|gb|BY976656.1|BY976656
EST:     TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAG                         GTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
genomic: TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAGgtactttcac ... accgttacagGTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
EST: gi|162198693|gb|FC373474.1|FC373474
EST:     TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAG                         GTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
genomic: TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAGgtactttcac ... accgttacagGTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
EST: gi|100423760|gb|BY976531.1|BY976531
EST:     TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAG                         GTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTTAT
genomic: TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAGgtactttcac ... accgttacagGTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTT-AT
EST: gi|208351706|gb|DC910066.1|DC910066
EST:     TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAG                         GTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
genomic: TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAGgtactttcac ... accgttacagGTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
EST: gi|100367017|gb|BY948326.1|BY948326
EST:     TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAG                         GTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
genomic: TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAGgtactttcac ... accgttacagGTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
EST: gi|100440953|gb|BY962441.1|BY962441
EST:     TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAG                         GTGGGGGCAGACAATAATTTACTACTCAAGGAACACACTCACACTTTTATT
genomic: TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAGgtactttcac ... accgttacagGTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
EST: gi|162167140|gb|FC343616.1|FC343616
EST:     TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAG                         GTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
genomic: TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAGgtactttcac ... accgttacagGTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
EST: gi|100376253|gb|BY986096.1|BY986096
EST:     ACATGGCTTTTTTCGGGTGCTACAACAATCTGTTTCCCCTCCTAGCTTAG                         GTGGGGGCAGACAATAAT
genomic: ACATGTCTTTTT-CGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAGgtactttcac ... accgttacagGTGGGGGCAGACAATAAT
EST: gi|162159709|gb|FC336095.1|FC336095
EST:     TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAG                         GTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
genomic: TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAGgtactttcac ... accgttacagGTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
EST: gi|162167477|gb|FC344194.1|FC344194
EST:     TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAG                         GTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
genomic: TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAGgtactttcac ... accgttacagGTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
EST: gi|208349541|gb|DC905651.1|DC905651
EST:     TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAG                         GTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
genomic: TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAGgtactttcac ... accgttacagGTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
EST: gi|100390582|gb|BY971337.1|BY971337
EST:     TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAG                         GTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTTAT
genomic: TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAGgtactttcac ... accgttacagGTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTT-AT
EST: gi|100387464|gb|BY988335.1|BY988335
EST:     TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAG                         GTGGGGGCAGACAATAATTTACTACTCAGGGATCACACTCACACTTTTATT
genomic: TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAGgtactttcac ... accgttacagGTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
EST: gi|208397089|gb|DC908103.1|DC908103
EST:     TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAG                         GTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
genomic: TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAGgtactttcac ... accgttacagGTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
EST: gi|162168664|gb|FC343926.1|FC343926
EST:     TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAG                         GTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
genomic: TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAGgtactttcac ... accgttacagGTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
EST: gi|162170376|gb|FC346781.1|FC346781
EST:     TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAG                         GTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
genomic: TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAGgtactttcac ... accgttacagGTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
EST: gi|162176795|gb|FC352809.1|FC352809
EST:     TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAG                         GTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
genomic: TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAGgtactttcac ... accgttacagGTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
EST: gi|162267926|gb|FC444007.1|FC444007
EST:     TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAG                         GTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
genomic: TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAGgtactttcac ... accgttacagGTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
EST: gi|100450706|gb|CJ974398.1|CJ974398
EST:     TACATGTCTTTTTCGGGTGCTACAACAATCTGTTACGCCTCCTAGCTAAG                         GTGGGGGCAGACANTAATTTACTACTCAAGGATCACACTCACACTTTTTAT
genomic: TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAGgtactttcac ... accgttacagGTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTT-AT
EST: gi|100443101|gb|BY981727.1|BY981727
EST:     TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAG                         GTGGGGGCAGACNATAATTTACTACTNCA-GGATCACACTCACACTTTTAT
genomic: TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAGgtactttcac ... accgttacagGTGGGGGCAGACAATAATTTACTACT-CAAGGATCACACTCACACTTTTAT
EST: gi|162166539|gb|FC343236.1|FC343236
EST:     TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAG                         GTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
genomic: TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAGgtactttcac ... accgttacagGTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT

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: 25

TAAAGTGGGGTCCTTTAAAGATAAGGATGGAAACCATATCGAGATGGGTTTACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAGgtactttcac ... accgttacagGTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagactctcaagctttcaacttcaaatggtttttgttggttcgaaccgttacagGTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAG
                              tttttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagaccatattttttagatgcattgtatagactttccgttccgccttagactctcaagctttcaacttcaaatggtttttgttggttcgaaccgttacagGTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG