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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcatgtcattaaactagtttcggtgacttattgtttttcttacagTTGCCACAGACCAATCCCGGATTTAACAACCCTCCTTTCAAATTTACGAAGTACTCCAATGCATACATGCTTGTATATATCAGAGAGAGCGATAAGGACA

Basic information

species Selaginella moellendorffii
transcript EFJ19227
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ13603 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: GLYMA14G04890.1 (Glycine max), 3'ss of exon 12
------------------------gtaagcatgtcattaaac---tagtt-tcggtgactta----ttgtttttcttacagTTGCCACAGACCAATCCCGGATTTAACAACCCTCCTTTCAAATTTACGAAGTACTCCAATGCATACATGCTTGTATATATCAGAGAGAGCGATAAGGACA
                        ||  ||||||  || |||   || || ||||| | |||     |  | || | |||||| |||||||| ||||| |||||||||||| ||||||| ||||| || || || || ||||| || ||||| || |||||  | ||    || |||||||
gtaattgcttttttgcaattggctgtg-gcatgtatttgaacatttacttgtcggttatttaaccacttgtattttaacagTTACCACAGACAAATCCTGGATTTAACAACACTCCTTTTAAATTCACCAAATATTCAAATGCTTATATGCTGGTGTATATACGTGAAGCTGACAAGGACA

upper sequence: EFJ13603 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: AT5G06600.2 (Arabidopsis thaliana), 3'ss of exon 12
--------------------------------gtaagcatgtc---attaaactagtttcggtgacttattgt--ttttcttacagTTGCCACAGACCAATCCCGGATT---TAACAACCCTCCTTTCAAATTTACGAAGTACTCCAATGCATACATGCTTGTATATATCAGAGAGAGCGATAAGGACA
                                | |  |   ||   |||   ||||  |     | ||  | |  | |  || ||| | |||||||| ||||| || ||   ||| ||||||||||||||||| || |||||||| ||||| |||||||||||||||||| |||| || || || |   
gttttattttcttgctccattttccatgatttgaaccccaatcctaattcctctagcctgacatatttgctttcgtgtcttttcagCTACCACAGACTAATCCTGGTTTCAATAATAACCCTCCTTTCAAATTCACAAAGTACTCGAATGCTTACATGCTTGTATATATCCGAGAAAGTGACAAAG---

upper sequence: EFJ13603 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: AT3G11910.2 (Arabidopsis thaliana), 3'ss of exon 12
---------------------------------gtaagcatgtcattaaactagtttcggtgacttatt-gtttttcttacagTTGCCACAGACCAATCCCGGATTTAACAACCCTCCTTTCAAATTTACGAAGTACTCCAATGCATACATGCTTGTATATATCAGAGAGAGCGATAAGGACA
                                  |    || |  ||  |||   ||   |  |  ||| | |||   | ||||| || ||||  ||||| || || || || || ||||||||||| || || ||||| ||||||||||||||||| |||||  | || || || ||||| |
gtagcactctctttcgaggttttctttattttctttgttatttttttttactgaatttactttcaaatttggtttctcttcagTTACCGCAGAATAATCCTGGTTTCAATAATCCACCTTTCAAATTCACAAAATACTCGAATGCATACATGCTTGTTTATATTCGGGAAAGTGACAAGGATA

upper sequence: EFJ13603 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: Vv13s0073g00610.t01 (Vitis vinifera), 3'ss of exon 12
-------------------------------------gtaagcatgtcattaaactagtttcggtgacttattgtttttctt------acagTTGCCACAGACCAATCCCGGATTTAACAACCCTCCTTTCAAATTTACGAAGTACTCCAATGCATACATGCTTGTATATATCAGAGAGAGCGATAAGGACA
                                      ||    | |  | |   || | |     |  |  | | | |||       |||| | || ||||| ||||||||||| |||||| |||| ||||||||||| || ||||| ||||||||||||||||| |||||  | || || || ||||| |
gtaatttattcacaagcatagattgtaagttttctttctacttttattttaatcttattcttatcaatattatatctgtctgtatccaacagCTACCCCAGACAAATCCCGGATTCAACAACTCTCCATTCAAATTTACAAAATACTCAAATGCATACATGCTTGTGTATATACGTGAAAGTGACAAGGAGA

upper sequence: EFJ13603 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 12
----------------------------------------------gtaagcatgtcattaaactagtttcggtgacttattgtttttcttacagTTGCCACAGACCAATCCCGGATTTAACAACCCTCCTTTCAAATTTACGAAGTACTCCAATGCATACATGCTTGTATATATCAGAGAGAGCGATAAGGACA
                                              ||||   ||| | | | || ||| |  |  | |  | | | |   ||||||||||||||| || || ||||| |||||| |||| || ||||| ||||| ||||| ||||||||||||||||| |||||  | || || || ||||| |
gcatgtctttaccagtgtttctttactccgtcaactttattcttgggtaattgtgt-actgatctggttaccttctcctgct-tgtatgaaacagTTGCCACAGACAAACCCTGGATTCAACAACACTCCATTTAAATTCACGAAATACTCAAATGCATACATGCTTGTGTATATACGTGAAAGTGACAAGGAGA

upper sequence: EFJ13603 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 12
-----------------------------------------------------gtaagcatgtcatt--aaact---agtttcggtgactta--ttgtt--tttcttacagTTGCCACAGACCAATCCCGGATTTAACAACCCTCCTTTCAAATTTACGAAGTACTCCAATGCATACATGCTTGTATATATCAGAGAGAGCGATAAGGACA
                                                         ||||||  ||   ||||     |||     ||||    ||||  |   | |||| |||| ||||| ||||| ||||| || ||| | || || |||||||||||||| || |||||||||||||| || |||||  | || || || |||||||
gtaatgttttcttgagtttagctcataatttttgagtctatttgttattcttcacttgcatgttctttcgaactcatgctttttcctactttgcctgttaatgattaacagCTGCCCCAGACAAATCCTGGATTGAATAACACCCCCTTTAAATTTACGAAGTATTCAAATGCATACATGCTGGTGTATATACGTGAAAGTGACAAGGACA

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|169097066|gb|FE497092.1|FE497092
EST:     AGGAGGAAGTTAAAAGGGCTTTTGAGGAGCAGTATGGTGGAGAAGAGGAA                         TTGCCACAGACCAATCCCGGATTTAACAACCCTCCTTTCAAATTTACGAAG
genomic: AGGAGGAAGTTAAAAGGGCTTTTGAGGAGCAGTATGGTGGAGAAGAGGAAgtaagcatgt ... tttcttacagTTGCCACAGACCAATCCCGGATTTAACAACCCTCCTTTCAAATTTACGAAG




















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), 29 (downstream exon)
Score: 15

GTACAAGTTCGACGATGAACGGGTGACAAAGGAGGAAGTTAAAAGGGCTTTTGAGGAGCAGTATGGTGGAGAAGAGGAAgtaagcatgt ... tttcttacagTTGCCACAGACCAATCCCGGATTTAACAACCCTCCTTTCAAATTTACGAAGTACTCCAATGCATACATGCTTGTATATATCAGAGAGAGCGATAAGGACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaagcatgtcattaaactagtttcggtgacttattgtttttcttacagTTGCCACAGACCAATCCCGGATTTAACAACCCTCCTTTCAAATTTACGAAGTACTCCAATGCATACATGCTTGTATATATCAGAGAGAGCGATAAGGACA
                                         cttattgtttttctt  CT-rich tract
                                     ttattgtttttctta  TA-rich tract