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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttcgtcgaatctcgattgagttcttcctctctttcttttctcatgttttcgctttcatcccttgcagACACTTCAAGTCACAAACCAAAGTGGACAAAGTCGTGGTTTTGTGGACTGCAAACACGGAACGCTACAGCGATGTGATTGTGGGCCTGAATGACACGAAG

Basic information

species Selaginella moellendorffii
transcript EFJ37320
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ37320 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: LOC_Os03g09250.2 (Oryza sativa), 3'ss of exon 4
--------------------gtacttcgtcgaatctcgattgagttcttcctct-----cttt---cttttctcatgttttcgctttcatccctt--gcagACACTTCAAGTCACAAACCAAAGTGGACAAAGTCGTGGTTTTGTGGACTGCAAACACGGAACGCTACAGCGATGTGATTGTGGGCCTGAATGACACGAAG
                     |  || |   ||  | ||   | || |  || |     || |   | ||   |||| | |   ||| ||  |||    ||  | ||||||  | | | |||||||||||| || ||||| ||||||||||||||||| ||| | |||||| ||||   ||| || || |||||||| | |
tagttccagtctgcattaagatggttggaacaacat-gacaaacttgtgactatgaatgctgtaaacattagacatgatattttttttattacttaaatagGGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGCAAACACTGAAAGGTACAGCAATGTCTGTGTTGGGCTCAATGACACAATG

upper sequence: EFJ37320 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: Vv07s0031g00920.t01 (Vitis vinifera), 3'ss of exon 4
-------------gtacttcgtcgaatctcgatt----gagttcttcctctctttcttttctcatgttttcgctttcatcccttgcagACACTTCAAGTCACAAACCAAAGTGGACAAAGTCGTGGTTTTGTGGACTGCAAACACGGAACGCTACAGCGATGTGATTGTGGGCCTGAATGACACGAAG
               | ||  |  ||  |  ||      | |          |||||| | |  || ||| |  |  ||   |   ||  | || |||     |||||| ||||| || || |||||  |||||||||| ||||| || || |||||  || |||||||||| ||||||||||| |  
gtagtcgtaatcttcaatttcttaaacatgaatcttaaaaatggaatgggcttttcttcttttctgattttgtatgtatgatt---agGGAGTTTAAGGAGGCAACCAAGGTGGATAAGGTGGTGGTGCTGTGGACTGCCAACACAGAGCGATACAGTAATTTGATTGTGGGACTGAATGACACCATA

upper sequence: EFJ37320 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: PP1S55_204V6.1 (Physcomitrella patens), 3'ss of exon 3
----------------------------------------------gtacttcgtcgaatctcgattgagttcttcctctctttcttttctcatgttttc-gctttcatcccttgcagACACTTCAAGTCACAAACCAAAGTGGACAAAGTCGTGGTTTTGTGGACTGCAAACACGGAACGCTACAGCGATGTGATTGTGGGCCTGAATGACACGAAG
                                              || ||||  | |     || |   ||||     | | |   |  |  ||  | | ||| |  |   ||||||  |||||||| | |||||||| || ||||| || |||||  ||||||| || ||||| || || |||||||| ||||| ||||| ||||||||||| |||
gtactcatccatcactgagaagcttctcaacgcattaccactcgccgtgcttctgccacaggtgaataccttctggtaatttatgaatatttctgaatccagctatttttggttgcagGAACTTCAAGGCGCAAACCAAGGTTGACAAGGTAGTGGTACTGTGGACCGCTAACACAGAGCGTTACAGCGACGTGATCGTGGGTCTGAATGACACCAAG

upper sequence: EFJ37320 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: PP1S267_10V6.1 (Physcomitrella patens), 3'ss of exon 4
----------------------------------------gtacttcgtcgaatctcgattgagttcttcctctctttcttttctcatgttttcgctttcatccc----ttgcagACACTTCAAGTCACAAACCAAAGTGGACAAAGTCGTGGTTTTGTGGACTGCAAACACGGAACGCTACAGCGATGTGATTGTGGGCCTGAATGACACGAAG
                                         |  ||| | ||   |      | ||  ||   ||  |   ||   ||| |   |     |        ||||||  |||| ||| | || | ||| ||||||||  |||| ||  |||||||||| ||||| ||||| ||||| |||||||| || || || ||||||||||||
gtagggcgtccgattctatacttcttccgagccctacagcctgtttc-tagagagttacggaaattgatcgcatcgatgcgtttgaatgctgaggtcaaaacattgtgattgcagGGACTTTAAGGCTCAGAACAAGGTGGACAAGATCGTTGTGCTGTGGACTGCTAACACCGAACGATACAGTGATGTGATCGTTGGTCTCAATGACACGAAG

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|169058097|gb|FE463979.1|FE463979
EST:     TTCAAAGGCTCCAAGAAAGAGAAGATGGATAAGATCATCGAGGACATCAG                         ACACTTCAAGTCACAAACCAAAGTGGACAAAGTCGTGGTTTTGTGGACTGC
genomic: TTCAAAGGCTCCAAGAAAGAGAAGATGGATAAGATCATCGAGGACATCAGgtacttcgtc ... tcccttgcagACACTTCAAGTCACAAACCAAAGTGGACAAAGTCGTGGTTTTGTGGACTGC
EST: gi|169059394|gb|FE467523.1|FE467523
EST:     TTCAAAGGCTCCAAGAAAGAGAAGATGGATAAGATCATCGAGGACATCAG                         ACACTTCAAGTCACAAACCAAAGTGGACAAAGTCGTGGTTTTGTGGACTGC
genomic: TTCAAAGGCTCCAAGAAAGAGAAGATGGATAAGATCATCGAGGACATCAGgtacttcgtc ... tcccttgcagACACTTCAAGTCACAAACCAAAGTGGACAAAGTCGTGGTTTTGTGGACTGC
EST: gi|169021157|gb|FE431468.1|FE431468
EST:     TTCAAAGGCTCCCAGAAAGAGAAGATGGATAAGATCATCGAGGACATCAG                         ACACTTCAAGTCACAAAC
genomic: TTCAAAGGCTCCAAGAAAGAGAAGATGGATAAGATCATCGAGGACATCAGgtacttcgtc ... tcccttgcagACACTTCAAGTCACAAAC
EST: gi|169059832|gb|FE467844.1|FE467844
EST:     TTCAAAGGCTCCAAGAAAGAGAAGATGGATAAGATCATCGAGGACATCAG                         ACACTTCAAGTCACAAACCAAAGTGGACAAAGTCGTGGTTTTGTGGACTGC
genomic: TTCAAAGGCTCCAAGAAAGAGAAGATGGATAAGATCATCGAGGACATCAGgtacttcgtc ... tcccttgcagACACTTCAAGTCACAAACCAAAGTGGACAAAGTCGTGGTTTTGTGGACTGC
EST: gi|169114320|gb|FE517077.1|FE517077
EST:     TTCAAAGGCTCCAAGAAAGAGAAGATGGATAAGATCATCGAGGACATCAG                         ACACTTCAAGTCACAAACCAAAGTGGACAAAGTCGTGGTTTTGTGGACTGC
genomic: TTCAAAGGCTCCAAGAAAGAGAAGATGGATAAGATCATCGAGGACATCAGgtacttcgtc ... tcccttgcagACACTTCAAGTCACAAACCAAAGTGGACAAAGTCGTGGTTTTGTGGACTGC
EST: gi|169097551|gb|FE497993.1|FE497993
EST:     TTCAAAGGCTCCAAGAAAGAGAAGATGGATAAGATCATCGAGGACATCAG                         ACACTTCAAGTC
genomic: TTCAAAGGCTCCAAGAAAGAGAAGATGGATAAGATCATCGAGGACATCAGgtacttcgtc ... tcccttgcagACACTTCAAGTC
EST: gi|169039349|gb|FE447230.1|FE447230
EST:     TTCAAAGGCTCCAAGAAAGAGAAGATGGATAAGATCATCGAGGACATCAG                         ACACTTCAAGTCACAAACCAAAGTGGACAAAGTCGTGGTTTTGTGGACTGC
genomic: TTCAAAGGCTCCAAGAAAGAGAAGATGGATAAGATCATCGAGGACATCAGgtacttcgtc ... tcccttgcagACACTTCAAGTCACAAACCAAAGTGGACAAAGTCGTGGTTTTGTGGACTGC
EST: gi|169026681|gb|FE433967.1|FE433967
EST:     TTCAAAGGCTCCAAGAAAGAGAAGATGGATAAGATCATCGAGGACATCAG                         ACACTTCAAGTCACAAACC
genomic: TTCAAAGGCTCCAAGAAAGAGAAGATGGATAAGATCATCGAGGACATCAGgtacttcgtc ... tcccttgcagACACTTCAAGTCACAAACC

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: 25 (upstream exon), 33 (downstream exon)
Score: 15

ACGACCCCGATTTCATTGCAGCCAACCAAGGTTCTCGCGCAAACAACATCTTCAAAGGCTCCAAGAAAGAGAAGATGGATAAGATCATCGAGGACATCAGgtacttcgtc ... tcccttgcagACACTTCAAGTCACAAACCAAAGTGGACAAAGTCGTGGTTTTGTGGACTGCAAACACGGAACGCTACAGCGATGTGATTGTGGGCCTGAATGACACGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgattgagttcttcctctctttcttttctcatgttttcgctttcatcccttgcagACACTTCAAGTCACAAACCAAAGTGGACAAAGTCGTGGTTTTGTGGACTGCAAACACGGAACGCTACAGCGATGTGATTGTGGGCCTGAATGACACGAAG
        ttcttcctctctttct  CT-rich tract
                   tttctttt  TA-rich tract