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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagatttctacaaagaagagaactaagcatgtaaaactacgtttccagGTATCTAGAGAACAGCAATTGTGTTGGAATGTGCGTAAATATGTGTAAAATTCCCACCCAGGATTTCTTCACAAATGACTTTGGGTTGCCTCTCACCATG

Basic information

species Selaginella moellendorffii
transcript EFJ25335
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ25335 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA02G09680.2 (Glycine max), 3'ss of exon 4
------------------------------------------------gtgagatttctacaaagaagagaactaagcatgtaaaactacgtttcc--agGTATCTAGAGAACAGCAATTGTGTTGGAATGTGCGTAAATATGTGTAAAATTCCCACCCAGGATTTCTTCACAAATGACTTTGGGTTGCCTCTCACCATG
                                                || | | ||  || |       |      | |  | |  ||   ||    ||||| || ||||| ||    |||||||||||||| || |||||||| || ||||| ||||| ||||| ||||| ||||| |||||  | ||  | || |||
agctagtatttattttgaaatttacttcttgcattaattaaggccgttgtaacaatttcaccatttttccattgtttccttgatatttattcttgtgaagGTACCTGGAGAATAGTGGCTGTGTTGGAATGTGTGTCAATATGTGCAAGATTCCTACCCAAGATTTTTTCACTAATGAATTTGGACTTCCGTTAACAATG

upper sequence: EFJ25335 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA13G10340.1 (Glycine max), 3'ss of exon 4
------------------------------------------------gtgagatttctacaaagaagagaactaagcatgtaaaactacgtttcc--agGTATCTAGAGAACAGCAATTGTGTTGGAATGTGCGTAAATATGTGTAAAATTCCCACCCAGGATTTCTTCACAAATGACTTTGGGTTGCCTCTCACCATG
                                                || | | ||  |  |       |      | |  | |  ||   ||    ||||| || ||||| ||    |||||||||||||| || |||||||| || ||||| ||||| ||||| ||||| ||||| |||||  | ||  | || |||
aatagctagtatttattttgaaattcacttacattaattaaggccgttgtaacaatttcaacattttcccattgtttccttgatatttattcttgtgaagGTACCTGGAGAATAGTGGCTGTGTTGGAATGTGTGTCAATATGTGCAAGATTCCTACCCAAGATTTTTTCACTAATGAATTTGGACTTCCGTTAACAATG

upper sequence: EFJ25335 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: AT1G64680.1 (Arabidopsis thaliana), 3'ss of exon 1
-------------------------------gtgagatttctacaaagaagagaactaagcatg-taaaactac-gtttccagGTATCTAGAGAACAGCAATTGTGTTGGAATGTGCGTAAATATGTGTAAAATTCCCACCCAGGATTTCTTCACAAATGACTTTGGGTTGCCTCTCACCATG
                                  || | |||      ||  |    |  | || |   |||   | ||  |||||||| ||||||||    ||||| |||||||| || |||||||| || ||||| ||||| ||||||||||| ||||| |||||  | || |||||||||
gtaacaagtgaattccatcaaaatgactattactagttgtcttgttcaaaatgtgacagacttgctcctactgttgattgaagGTATCTGGAGAACAGTGGGTGTGTAGGAATGTGTGTGAATATGTGCAAGATTCCAACCCAAGATTTCTTCACCAATGAGTTTGGCCTCCCACTCACCATG

upper sequence: EFJ25335 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: Vv02s0025g02640.t01 (Vitis vinifera), 3'ss of exon 3
------------------------------------gtgagatttctacaaagaagagaactaagcatgt--------------aaaactacgtttccagGTATCTAGAGAACAGCAATTGTGTTGGAATGTGCGTAAATATGTGTAAAATTCCCACCCAGGATTTCTTCACAAATGACTTTGGGTTGCCTCTCACCATG
                                     | | ||     | ||  |   | ||     | |              |||    | | || ||||| || ||||||||    ||||| ||||||||||| |||||||| |||||||| || || ||||||||||| || || || ||| | ||| | || |||
catatgtcacagtaaccaaatttcaatatattagaaataaaataatgtccaactactaatctttcttttttttctttttctgacaaattctcctatcaagGTACCTGGAGAACAGTGGGTGTGTGGGAATGTGCGTGAATATGTGCAAAATTCCTACTCAAGATTTCTTCACCAACGAATTCGGGCTTCCTTTAACTATG

upper sequence: EFJ25335 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: PP1S6_190V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------------------------------------------gtgagatttctacaaagaagagaactaagcatgtaa-aactacgtttc----cagGTATCTAGAGAACAGCAATTGTGTTGGAATGTGCGTAAATATGTGTAAAATTCCCACCCAGGATTTCTTCACAAATGACTTTGGGTTGCCTCTCACCATG
                                                        || |  | | |  | ||  | | |||||  |   || | || ||  |     ||| || ||||| || ||    || || || |||||||| |||||||| ||||| || ||||||||||||||||| ||||| || ||  | || || || |||
gtacttgccatttttttccactcttgttttccctctattctgcttatcttgaatctgtcaagtgt-tgtagaggtg-gtactaatgacacaatagctgcggatgagaacagATACCTAGAAAATAGTGGATGCGTCGGGATGTGCGTCAATATGTGCAAAATCCCGACCCAGGATTTCTTCACCAATGAATTCGGTCTTCCACTTACTATG

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|169068945|gb|FE476662.1|FE476662
EST:     GAAGTGAATGGAGTGAAACAAAAAAGTGGTGTGAAGATTCTTAAATGCAG                         GTATCTAGAGAACAGCAATTGTGTTGGAATGTGCGTAAATATGTGTAAAAT
genomic: GAAGTGAATGGAGTGAAACAAAAAAGTGGTGTGAAGATTCTTAAATGCAGgtgagatttc ... acgtttccagGTATCTAGAGAACAGCAATTGTGTTGGAATGTGCGTAAATATGTGTAAAAT
EST: gi|169077052|gb|FE485367.1|FE485367
EST:     GAAGTGAATGGAGTGAAACAAAACAGCGGTGTGAAGATTCTTAAATGCAG                         GTATCTAGAGAACAGCAACTGTGTTGGAATGTGCGTAAATATGTGTAAAAT
genomic: GAAGTGAATGGAGTGAAACAAAAAAGTGGTGTGAAGATTCTTAAATGCAGgtgagatttc ... acgtttccagGTATCTAGAGAACAGCAATTGTGTTGGAATGTGCGTAAATATGTGTAAAAT
EST: gi|169101826|gb|FE500772.1|FE500772
EST:     GAAGTGAATGGAGTGAAACAAAACAGCGGTGTGAAGATTCTTAAATGCAG                         GTATCTAGAGAACAGCAACTGTGTTGGAATGTGCGTAAATATGTGTAAAAT
genomic: GAAGTGAATGGAGTGAAACAAAAAAGTGGTGTGAAGATTCTTAAATGCAGgtgagatttc ... acgtttccagGTATCTAGAGAACAGCAATTGTGTTGGAATGTGCGTAAATATGTGTAAAAT
EST: gi|169046384|gb|FE457388.1|FE457388
EST:     GAAGTGAATGGAGTGAAACAAAACAGCGGTGTGAAGATTCTTAAATGCAG                         GTATCTAGAGAACAGCAACTGTGTTGGAATGTGCGTAAATATGTGTAAAAT
genomic: GAAGTGAATGGAGTGAAACAAAAAAGTGGTGTGAAGATTCTTAAATGCAGgtgagatttc ... acgtttccagGTATCTAGAGAACAGCAATTGTGTTGGAATGTGCGTAAATATGTGTAAAAT
EST: gi|169101827|gb|FE500773.1|FE500773
EST:     GAAGTGAATGGAGTGAAACAAAACAGCGGTGTGAAGATTCTTAAATGCAG                         GTATCTAGAGAACAGCAACTGTGTTGGAATGTGCGTAAATATGTGTAAAAT
genomic: GAAGTGAATGGAGTGAAACAAAAAAGTGGTGTGAAGATTCTTAAATGCAGgtgagatttc ... acgtttccagGTATCTAGAGAACAGCAATTGTGTTGGAATGTGCGTAAATATGTGTAAAAT
EST: gi|169068806|gb|FE478499.1|FE478499
EST:     GAAGTGAATGGAGTGAAACAAAACAGCGGTGTGAAGATTCTTAAATGCAG                         GTATCTAGAGAACAGCAACTGTGTTGGAATGTGCGTAAATATGTGTAAAAT
genomic: GAAGTGAATGGAGTGAAACAAAAAAGTGGTGTGAAGATTCTTAAATGCAGgtgagatttc ... acgtttccagGTATCTAGAGAACAGCAATTGTGTTGGAATGTGCGTAAATATGTGTAAAAT
EST: gi|169068944|gb|FE476661.1|FE476661
EST:     GAAGTGAATGGAGTGAAACAAAAAAGTGGTGTGAAGATTCTTAAATGCAG                         GTATCTAGAGAACAGCAATTGTGTTGGAATGTGCGTAAATATGTGTAAAAT
genomic: GAAGTGAATGGAGTGAAACAAAAAAGTGGTGTGAAGATTCTTAAATGCAGgtgagatttc ... acgtttccagGTATCTAGAGAACAGCAATTGTGTTGGAATGTGCGTAAATATGTGTAAAAT
EST: gi|169046385|gb|FE457389.1|FE457389
EST:     GAAGTGAATGGAGTGAAACAAAACAGCGGTGTGAAGATTCTTAAATGCAG                         GTATCTAGAGAACAGCAACTGTGTTGGAATGTGCGTAAATATGTGTAAAAT
genomic: GAAGTGAATGGAGTGAAACAAAAAAGTGGTGTGAAGATTCTTAAATGCAGgtgagatttc ... acgtttccagGTATCTAGAGAACAGCAATTGTGTTGGAATGTGCGTAAATATGTGTAAAAT
EST: gi|169107502|gb|FE511667.1|FE511667
EST:     GAAGTGAATGGAGTGAAACAAAACAGCGGTGTGAAGATTCTTAAATGCAG                         GTATCTAGAGAACAGCAACTGTGTTGGAATGTGCGTAAATATGTGTAAAAT
genomic: GAAGTGAATGGAGTGAAACAAAAAAGTGGTGTGAAGATTCTTAAATGCAGgtgagatttc ... acgtttccagGTATCTAGAGAACAGCAATTGTGTTGGAATGTGCGTAAATATGTGTAAAAT

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: 26 (upstream exon), 11 (downstream exon)
Score: 2

CGGTTTGAGGTAGAAGTGAATGGAGTGAAACAAAAAAGTGGTGTGAAGATTCTTAAATGCAGgtgagatttc ... acgtttccagGTATCTAGAGAACAGCAATTGTGTTGGAATGTGCGTAAATATGTGTAAAATTCCCACCCAGGATTTCTTCACAAATGACTTTGGGTTGCCTCTCACCATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgagatttctacaaagaagagaactaagcatgtaaaactacgtttccagGTATCTAGAGAACAGCAATTGTGTTGGAATGTGCGTAAATATGTGTAAAATTCCCACCCAGGATTTCTTCACAAATGACTTTGGGTTGCCTCTCACCATG
                                                  cgtttcc  CT-rich tract
                                   atgtaaaa  TA-rich tract