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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGACCATTGAGGCAGATTTTTGTGGAGTTTTTGGAGCGGTCTTGTACTGCAGAATTCTCCGGGTTTTTGTTGTACAAGGAATTGGGAAGGAGGCTGAAGgtcagtgcgcttacatctgccctgtggtttgattatctgagtccgttcatgtttttagttcatagtgtcccccggtacattaacatgccatcgctctatt...

Basic information

species Physcomitrella patens
transcript PP1S97_248V6.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S97_248V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: Vv08s0040g00390.t01 (Vitis vinifera), 5'ss of exon 1
GGGACCATTGAGGCAGATTTTTGTGGAGTTTTTGGAGCGGTCTTGTACTGCAGAATTCTCCGGGTTTTTGTTGTACAAGGAATTGGGAAGGAGGCTGAAGgtcagtgcgcttacatctgccctgtggtttgattatctgagtccgttcatgtttttagttcatagtgtcccccggtacattaacatgccatcgctctatt--
||| ||  | |||||||| ||||||||||| |||||| ||||||| ||||| || ||||| |||||| |  | ||||||||  | ||| | ||||| |||||  |      |  ||     |  | | ||  | ||        | || ||  ||| |||  |    |       | | |  | ||||    |   | |   
GGGTCCCCTCAGGCAGATCTTTGTGGAGTTCTTGGAGAGGTCTTGCACTGCTGAGTTCTCTGGGTTTCTTCTCTACAAGGAGCTTGGACGAAGGCTTAAGgtatggctttctttattccttcaattgatttctaatacagccatgctcctgggttttgttttttcaatgttt--atgcctctatatgcagctgaattttcaa
















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|162189138|gb|FC365971.1|FC365971
EST:     CAGAATTCTCCGGGTTTTTGTTGTACAAGGAATTGGGAAGGAGGCTGAAG                         AAGACAAACCCTGTGGTGGCTGAGATTTTCACCCTTATGTCAAGGGATGAA
genomic: CAGAATTCTCCGGGTTTTTGTTGTACAAGGAATTGGGAAGGAGGCTGAAGgtcagtgcgc ... atgtgaacagAAGACAAACCCTGTGGTGGCTGAGATTTTCACCCTTATGTCAAGGGATGAA
EST: gi|162217743|gb|FC394043.1|FC394043
EST:     CAGAATTCTCCGGGTTTTTGTTGTACAAGGAATTGGGAAGGAGGCTGAAG                         AAGACAAACCCTGTGGTGGCTGAGATTTTCACCCTTATGTCAAGGGATGAA
genomic: CAGAATTCTCCGGGTTTTTGTTGTACAAGGAATTGGGAAGGAGGCTGAAGgtcagtgcgc ... atgtgaacagAAGACAAACCCTGTGGTGGCTGAGATTTTCACCCTTATGTCAAGGGATGAA
EST: gi|162209497|gb|FC386130.1|FC386130
EST:     CAGAATTCTCCGGGTTTTTGTTGTACAAGGAATTGGGAAGGAGGCTGAAG                         AAGACAAACCCTGTGGTGGCTGAGATTTTCACCCTTATGTCAAGGGATGAA
genomic: CAGAATTCTCCGGGTTTTTGTTGTACAAGGAATTGGGAAGGAGGCTGAAGgtcagtgcgc ... atgtgaacagAAGACAAACCCTGTGGTGGCTGAGATTTTCACCCTTATGTCAAGGGATGAA
EST: gi|162260323|gb|FC435626.1|FC435626
EST:     CAGAATTCTCCGGGTTTTTGTTGTACAAGGAATTGGGAAGGAGGCTGAAG                         AAGACAAACCCTGTGGTGGCTGAGATTTTCACCCTTATGTCAAGGGATGAA
genomic: CAGAATTCTCCGGGTTTTTGTTGTACAAGGAATTGGGAAGGAGGCTGAAGgtcagtgcgc ... atgtgaacagAAGACAAACCCTGTGGTGGCTGAGATTTTCACCCTTATGTCAAGGGATGAA
EST: gi|162168656|gb|FC343918.1|FC343918
EST:     CAGAATTCTCCGGGTTTTTGTTGTACAAGGAATTGGGAAGGAGGCTGAAG                         AAGACAAACCCTGTGGTGGCTGAGATTTTCACCCTTATGTCAAGGGATGAA
genomic: CAGAATTCTCCGGGTTTTTGTTGTACAAGGAATTGGGAAGGAGGCTGAAGgtcagtgcgc ... atgtgaacagAAGACAAACCCTGTGGTGGCTGAGATTTTCACCCTTATGTCAAGGGATGAA
EST: gi|162247340|gb|FC423086.1|FC423086
EST:     CAGAATTCTCCGGGTTTTTGTTGTACAAGGAATTGGGAAGGAGGCTGAAG                         AAGACAAACCCTGTGGTGGCTGAGATTTTCACCCTTATGTCAAGGGATGAA
genomic: CAGAATTCTCCGGGTTTTTGTTGTACAAGGAATTGGGAAGGAGGCTGAAGgtcagtgcgc ... atgtgaacagAAGACAAACCCTGTGGTGGCTGAGATTTTCACCCTTATGTCAAGGGATGAA
EST: gi|162191054|gb|FC367316.1|FC367316
EST:     CAGAATTCTCCGGGTTTTTGTTGTACAAGGAATTGGGAAGGAGGCTGAAG                         AAGACAAACCCTGTGGTGGCTGAGATTTTCACCCTTATGTCAAGGGATGAA
genomic: CAGAATTCTCCGGGTTTTTGTTGTACAAGGAATTGGGAAGGAGGCTGAAGgtcagtgcgc ... atgtgaacagAAGACAAACCCTGTGGTGGCTGAGATTTTCACCCTTATGTCAAGGGATGAA
EST: gi|100389624|gb|BY952430.1|BY952430
EST:     CAGAGTTCTCCGGGTTTTTGTTGTACAAGGAATTGGGAAGGAGGCTGAAG                         AAGACAAACCCTGTGGTGGCTGAGATTTTCACCCTTATGTCAGGGGATGAA
genomic: CAGAATTCTCCGGGTTTTTGTTGTACAAGGAATTGGGAAGGAGGCTGAAGgtcagtgcgc ... atgtgaacagAAGACAAACCCTGTGGTGGCTGAGATTTTCACCCTTATGTCAAGGGATGAA
EST: gi|162161984|gb|FC338567.1|FC338567
EST:     CAGAATTCTCCGGGTTTTTGTTGTACAAGGAATTGGGAAGGAGGCTGAAG                         AAGACAAACCCTGTGGTGGCTGAGATTTTCACCCTTATGTCAAGGGATGAA
genomic: CAGAATTCTCCGGGTTTTTGTTGTACAAGGAATTGGGAAGGAGGCTGAAGgtcagtgcgc ... atgtgaacagAAGACAAACCCTGTGGTGGCTGAGATTTTCACCCTTATGTCAAGGGATGAA
EST: gi|162229195|gb|FC404554.1|FC404554
EST:     CAGAATTCTCCGGGTTTTTGTTGTACAAGGAATTGGGAAGGAGGCTGAAG                         AAGACAAACCCTGTGGTGGCTGAGATTTTCACCCTTATGTCAAGGGATGAA
genomic: CAGAATTCTCCGGGTTTTTGTTGTACAAGGAATTGGGAAGGAGGCTGAAGgtcagtgcgc ... atgtgaacagAAGACAAACCCTGTGGTGGCTGAGATTTTCACCCTTATGTCAAGGGATGAA
EST: gi|162182355|gb|FC357226.1|FC357226
EST:     CAGAATTCTCCGGGTTTTTGTTGTACAAGGAATTGGGAAGGAGGCTGAAG                         AAGACAAACCCTGTGGTGGCTGAGATTTTCACCCTTATGTCAAGGGATGAA
genomic: CAGAATTCTCCGGGTTTTTGTTGTACAAGGAATTGGGAAGGAGGCTGAAGgtcagtgcgc ... atgtgaacagAAGACAAACCCTGTGGTGGCTGAGATTTTCACCCTTATGTCAAGGGATGAA
EST: gi|162150906|gb|FC327386.1|FC327386
EST:     CAGAATTCTCCGGGTTTTTGTTGTACAAGGAATTGGGAAGGAGGCTGAAG                         AAGACAAACCCTGTGGTGGCTGAGATTTTCACCCTTATGTCAAGGGATGAA
genomic: CAGAATTCTCCGGGTTTTTGTTGTACAAGGAATTGGGAAGGAGGCTGAAGgtcagtgcgc ... atgtgaacagAAGACAAACCCTGTGGTGGCTGAGATTTTCACCCTTATGTCAAGGGATGAA
EST: gi|100390219|gb|BY952627.1|BY952627
EST:     CAGAATTCTCCGGGTTTTTGTTGTACAAGGAATTGGGAAGGAGGCTGAAG                         AAGACAAACCCTGTGGTGGCTGAGATTTTCACCCTTATGTCAAGGGATGAA
genomic: CAGAATTCTCCGGGTTTTTGTTGTACAAGGAATTGGGAAGGAGGCTGAAGgtcagtgcgc ... atgtgaacagAAGACAAACCCTGTGGTGGCTGAGATTTTCACCCTTATGTCAAGGGATGAA
EST: gi|162173960|gb|FC349760.1|FC349760
EST:     CAGAATTCTCCGGGTTTTTGTTGTACAAGGAATTGGGAAGGAGGCTGAAG                         AAGACAAACCCTGTGGTGGCTGAGATTTTCACCCTTATGTCAAGGGATGAA
genomic: CAGAATTCTCCGGGTTTTTGTTGTACAAGGAATTGGGAAGGAGGCTGAAGgtcagtgcgc ... atgtgaacagAAGACAAACCCTGTGGTGGCTGAGATTTTCACCCTTATGTCAAGGGATGAA

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: 26

GGGACCATTGAGGCAGATTTTTGTGGAGTTTTTGGAGCGGTCTTGTACTGCAGAATTCTCCGGGTTTTTGTTGTACAAGGAATTGGGAAGGAGGCTGAAGgtcagtgcgc ... atgtgaacagAAGACAAACCCTGTGGTGGCTGAGATTTTCACCCTTATGTCAAGGGATGAAGCCAGACATGCTGGCTTCTTGAACAAGGGACTGTCAGACTTCAACTTGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGACCATTGAGGCAGATTTTTGTGGAGTTTTTGGAGCGGTCTTGTACTGCAGAATTCTCCGGGTTTTTGTTGTACAAGGAATTGGGAAGGAGGCTGAAGgtcagtgcgcttacatctgccctgtggtttgattatctgagtccgttcatgtttttagttcatagtgtcccccggtacattaacatgccatcgctctatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG