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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctcggtgcatagttttttgtgctacttgaatcattcaagattttgctttacgttcagGAAGGTCCTAGGACAATGGTTGGAGTTGCAACGTTTGATTCAACTATACACTTCTACAATTTGAGTAAAGACCTGCAACAG

Basic information

species Selaginella moellendorffii
transcript EFJ37282
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ37282 (Selaginella moellendorffii), 3'ss of exon 7
lower sequence: GRMZM2G075680_T01 (Zea mays), 3'ss of exon 7
------------------------------------gtaagc-tcggtgcatagttttttgtgctacttgaatcattcaagattttgct-ttacgttcagGAAGGTCCTAGGACAATGGTTGGAGTTGCAACGTTTGATTCAACTATACACTTCTACAATTTGAGTAAAGACCTGCAACAG
                                     ||    |   | ||  |  |  | |   | |||   |||| |   |||| || |    |||||||||||||| |||||||||||||| ||||||| ||||||||  |||| |||||||||| | | |     |  | ||| |||
agttgagtattttttgagtagatggattggtttcttttacatattatttcaagggatggtatttgatttgtgacattaactgtttttctgtcttattcagGAAGGTCCTCGGACAATGGTTGGAATTGCAACATTTGATTCTGCTATTCACTTCTACAGTCTTAAACGTGCTCAGCAGCAG

upper sequence: EFJ37282 (Selaginella moellendorffii), 3'ss of exon 7
lower sequence: GRMZM2G019236_T03 (Zea mays), 3'ss of exon 7
-----------------------------------gtaagctcggtgcatagtttt-ttgtgctacttgaatcattcaagattttgct--ttacgttcagGAAGGTCCTAGGACAATGGTTGGAGTTGCAACGTTTGATTCAACTATACACTTCTACAATTTGAGTAAAGACCTGCAACAG
                                   |     |   ||  ||| | | |||    | |||   || | ||  ||||     |    || ||||||||||| |||||||||||||| ||||||| ||||||||  |||| |||||||||| | | |     |  | ||| |||
cattgttccaattccaaaattgaccacatgtatttgagtattttttgactagatgtattggttgatttgtgacactaaatgttttttctgtcttatttagGAAGGTCCTCGGACAATGGTTGGAATTGCAACATTTGATTCTGCTATTCACTTCTACAGTCTTAAACGTGCTCAGCAGCAG

upper sequence: EFJ37282 (Selaginella moellendorffii), 3'ss of exon 7
lower sequence: GLYMA20G24330.1 (Glycine max), 3'ss of exon 9
-------------------------------------gtaagctcggtgcatagttttttgtgctacttgaatcattcaagattttg--ctttacgtt-cagGAAGGTCCTAGGACAATGGTTGGAGTTGCAACGTTTGATTCAACTATACACTTCTACAATTTGAGTAAAGACCTGCAACAG
                                       ||         || ||||    | |   ||  || | | ||  |||||  |||   | | ||||| |||||| | ||| |||| ||||||||||| ||||||||||| || || |||||||| ||||     |   |||| |||
tttgggttttttccttgtgttgtgaccagagattcttacaaatatctcatattgtttgacatacacttt--atgactaaattttttggtcttgttgctacagGAGGGTCCTCGCACATTGGTGGGAGTTGCAACTTTTGATTCAACAATTCATTTCTACAACTTGAAACGTGCATTGCAGCAG

upper sequence: EFJ37282 (Selaginella moellendorffii), 3'ss of exon 7
lower sequence: AT3G44340.2 (Arabidopsis thaliana), 3'ss of exon 9
--------------------------------------------------------------------------------------------------------gtaag-ctcggtgcatagttttttgtgctacttgaatcattcaagattttgctttacgtt---cagGAAGGTCCTAGGACAATGGTTGGAGTTGCAACGTTTGATTCAACTATACACTTCTACAATTTGAGTAAAGACCTGCAACAG
                                                                                                         | |  ||   |  | |  ||||  | | || | | |    |||  | ||| | ||| ||   |||||||||||||||||| | |||||| |||| |||||||| ||||| || ||||| || |||||||     |  ||||| |||
gtaaatcttctcgctctttccagtgatagacatgtattttttattttttatttcttataaacagttgagttgggaaatgaggctaggatatggtcactagagtaatgattctaaatagacatgttttgcttcaacattattttaacaaagtcttg-tatacattttgcagGAAGGTCCTAGGACATTTGTTGGAATTGCCACGTTTGACTCAACAATTCACTTTTATAATTTGAAGCGTGCACTGCAGCAG

upper sequence: EFJ37282 (Selaginella moellendorffii), 3'ss of exon 7
lower sequence: AT4G32640.1 (Arabidopsis thaliana), 3'ss of exon 8
--------------------------------gtaagctcggtgcatagttttttgtgctac--ttgaatcattcaagattttgctttacg----ttcagGAAGGTCCTAGGACAATGGTTGGAGTTGCAACGTTTGATTCAACTATACACTTCTACAATTTGAGTAAAGACCTGCAACAG
                                    |||   |   |  | ||||||    |  ||  |  ||| |   |||| || ||      |||||||||||||||||||| | |||||  |||| || ||||| ||||| || |||||||| |||||||     |  ||||| |||
gtgaacttttgttatggtatggttatgttaccaatggctttataattcttattttgtatcgccattagacaattaattttttttctgtattcgttttcagGAAGGTCCTAGGACATTTGTTGGGATTGCTACATTTGACTCAACAATCCACTTCTATAATTTGAAACGTGCACTGCAGCAG

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|169044000|gb|FE451586.1|FE451586
EST:     GCAGCTTGCAGTGCTATTCAGAGAGTTCTGGCGGATATTGCA                         GAAGGTCCTAGGACAATGGTTGGAGTTGCAACGTTTGATTCAACTATACAC
genomic: GCAGCTTGCAGTGCTATTCAGAGAGTTCTGGCGGATATTGCAgtaagctcgg ... ttacgttcagGAAGGTCCTAGGACAATGGTTGGAGTTGCAACGTTTGATTCAACTATACAC




















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: 32 (upstream exon), 34 (downstream exon)
Score: 8

AGTGTTCTTCTTTCTGGTGGATGTCTCAGCTAATGCTATCAAGACGGGAGCGGCCGCCGCAGCTTGCAGTGCTATTCAGAGAGTTCTGGCGGATATTGCAgtaagctcgg ... ttacgttcagGAAGGTCCTAGGACAATGGTTGGAGTTGCAACGTTTGATTCAACTATACACTTCTACAATTTGAGTAAAGACCTGCAACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cggtgcatagttttttgtgctacttgaatcattcaagattttgctttacgttcagGAAGGTCCTAGGACAATGGTTGGAGTTGCAACGTTTGATTCAACTATACACTTCTACAATTTGAGTAAAGACCTGCAACAG
                                      ttttgcttt  CT-rich tract
      atagtttttt  TA-rich tract