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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcgagcgtcttgtctgcgtgcttctcgtgttctaaacttctctcgcctctggtgacgcagCCCGAGATGATCGGACACTACCTGGGAGAGTTCTCCATCTCGTACAAGCCAGTCAAGCACGGGCGTCCCGGTATCGGTGCCACACACTCGTCCAGGTTTA

Basic information

species Selaginella moellendorffii
transcript EFJ26636
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ26636 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S47_42V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------------------------------------------------------------------------------------gtgagcgagcgtcttgtctgcgtgctt----ctcgtgttctaaacttctctcgcctctggtgac--gcagCCCGAGATGATCGGACACTACCTGGGAGAGTTCTCCATCTCGTACAAGCCAGTCAAGCACGGGCGTCCCGGTATCGGTGCCACACACTCGTCCAGGTTTA
| | | | | | | | | || || | ||| | | | | || | ||||||||||||||| |||||||| ||| ||||||||||||||||||||||| || |||||||| | |||||||| || || || ||||| || | ||||
gtaataagaattttccactctttcggaagtctaaacccggttcaattagattctttcatggtgatgtgatcaggattgttaattttggttttggtctcgaaggtgttttcccttttttcatttttaaatcttttattcaagagtattaatcatggtgtttctttgcagCCCGAGATGATTGGACACTATTTGGCTGAGTTCTCCATCTCGTACAAGCCCGTAAAGCACGGTAGGCCCGGTATTGGAGCTACCCACTCTTCGCGATTTA

upper sequence: EFJ26636 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S91_124V6.1 (Physcomitrella patens), 3'ss of exon 3
-------------------------------------------------------------------------------------------gtgagcgagcgtcttgt-ctgcgtgcttctcgtgttctaaacttctctcgcctctggtgacgcagCCCGAGATGATCGGACACTACCTGGGAGAGTTCTCCATCTCGTACAAGCCAGTCAAGCACGGGCGTCCCGGTATCGGTGCCACACACTCGTCCAGGTTTA
|| | | || || | ||| | | | || | ||| | |||||| |||||||| || |||||| ||| ||||||||||| ||||||||||| ||||||||||| | |||||||| || || || ||||| || | || |
gtataatattcggtcacgctatttttgactctccatcagtccgtgctatagggaagaattgattgaattcaatactagcttggacaacggagtagagggtggactggttccatttgcagcgtgaaagcctgaccttgtaaatgtct--ttgtgcagCCTGAGATGATTGGGCACTACTTGGCTGAGTTCTCCATTTCGTACAAGCCTGTCAAGCACGGTAGGCCCGGTATTGGAGCTACGCACTCTTCGCGATTCA

upper sequence: EFJ26636 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S13_413V6.1 (Physcomitrella patens), 3'ss of exon 3
---------------------------------------------------------------------------------------------------gtgagcgagcgtcttgtctgcgtgctt------ctcgtgttctaaactt--ctctcgcctc-tggtgacgcagCCCGAGATGATCGGACACTACCTGGGAGAGTTCTCCATCTCGTACAAGCCAGTCAAGCACGGGCGTCCCGGTATCGGTGCCACACACTCGTCCAGGTTTA
|| | | ||| | || | ||||| || || | | || | || |||||| |||||||| ||||||||| ||| |||||| ||||| ||||||||||| || ||||| || | ||||||||||| || || ||||| ||| | ||||
gtatagtgaatctatgcctttttcattaatgatcccatttggcatcaaacacattttatcaatgtggacatcgacaactgtcggaagttctgcgcatccctggtttgggttgttgaagaaaagattagagacttgaagttctgaatttaattttgatttcgttgttttgcagCCTGAGATGATTGGACACTACTTGGCAGAGTTTTCCATATCGTACAAGCCTGTGAAGCATGGTAGGCCCGGTATCGGAGCTACCCACTCCTCCCGATTTA

upper sequence: EFJ26636 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S223_96V6.1 (Physcomitrella patens), 3'ss of exon 4
----------------------------------------------------------------gtgagcgagcgtcttgtctgcgtgcttc----tcgtgttctaaacttctc-----tcgc-ctctggtg-----acgcagCCCGAGATGATCGGACACTACCTGGGAGAGTTCTCCATCTCGTACAAGCCAGTCAAGCACGGGCGTCCCGGTATCGGTGCCACACACTCGTCCAGGTTTA
|| | ||| || || | | || | || | ||| || ||| || | || || || ||||||||||||||| |||||||| ||| || || ||||| ||||||||||| || |||||||| || || |||||||| || || ||||| || | || |
gtaataatatatttattatgatcgacccagtagtctgaaaattcttgatgaagagtagttcatcctgtgagagtatcccctccccctagtttggcatggttatataatctactcaggattctcactttgatgtttccgtgcagCCCGAGATGATTGGACACTATTTGGCTGAATTTTCCATTTCGTACAAGCCTGTGAAGCACGGTCGGCCTGGTATCGGAGCTACCCACTCTTCGCGATTCA

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|169097202|gb|FE497124.1|FE497124
EST:     GCATCATTGGCGTCTACAACGGCAAGACGTTCAACCAGGTGGAGATCAAG                         CCCGAGATGATCGGACACTACCTGGGAGAGTTCTCCATCTCGTACAAGCCA
genomic: GCATCATTGGCGTCTACAACGGCAAGACGTTCAACCAGGTGGAGATCAAGgtgagcgagc ... ggtgacgcagCCCGAGATGATCGGACACTACCTGGGAGAGTTCTCCATCTCGTACAAGCCA
EST: gi|169027972|gb|FE435889.1|FE435889
EST:     GCATCATTGGCGTCTACAACGGCAAGACGTTCAACCAGGTGGAGATCAAG                         CCCGAGATGATCGGACACTACCTGGGAGAGTTCTCCATCTCGTACAAGCCA
genomic: GCATCATTGGCGTCTACAACGGCAAGACGTTCAACCAGGTGGAGATCAAGgtgagcgagc ... ggtgacgcagCCCGAGATGATCGGACACTACCTGGGAGAGTTCTCCATCTCGTACAAGCCA
EST: gi|169074868|gb|FE482749.1|FE482749
EST:     GCATCATTGGCGTCTACAACGGCAAGACGTTCAACCAGGTGGAGATCAAG                         CCCGAGATGATCGGACACTACCTGGGAGAGTTCTCCATCTCGTACAAGCCA
genomic: GCATCATTGGCGTCTACAACGGCAAGACGTTCAACCAGGTGGAGATCAAGgtgagcgagc ... ggtgacgcagCCCGAGATGATCGGACACTACCTGGGAGAGTTCTCCATCTCGTACAAGCCA

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), 31 (downstream exon)
Score: 61

AGTGCGAACGCATCTCCGGAGCATGATCATCGTCCCAGAGATGATTGGCAGCATCATTGGCGTCTACAACGGCAAGACGTTCAACCAGGTGGAGATCAAGgtgagcgagc ... ggtgacgcagCCCGAGATGATCGGACACTACCTGGGAGAGTTCTCCATCTCGTACAAGCCAGTCAAGCACGGGCGTCCCGGTATCGGTGCCACACACTCGTCCAGGTTTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtcttgtctgcgtgcttctcgtgttctaaacttctctcgcctctggtgacgcagCCCGAGATGATCGGACACTACCTGGGAGAGTTCTCCATCTCGTACAAGCCAGTCAAGCACGGGCGTCCCGGTATCGGTGCCACACACTCGTCCAGGTTTA
                        ttctaaa  putative branch site (score: 61)
 cttctctcgcctctg  CT-rich tract
 ttctaaa  TA-rich tract