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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgctacaaactatgtcttttcttcctgcggttgtcatcttaatgctttcttccgaagTTGTATGCAGAATCTCTGGCTCGCTTTCAAGGCGGTTCCCCTTATATTTATCCGCTCTATGGCTTGGGAGAACTTCCTCAG

Basic information

species Selaginella moellendorffii
transcript EFJ11673
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ11673 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: LOC_Os05g34540.1 (Oryza sativa), 3'ss of exon 6
---------------------------gtactgctacaaact--atgtcttttcttcctgcggtt--gtcatcttaat--gctttcttccga------agTTGTATGCAGAATCTCTGGCTCGCTTTCAAGGCGGTTCCCCTTATATTTATCCGCTCTATGGCTTGGGAGAACTTCCTCAG
                             ||||||      |  || |  ||||||  ||  |||  || |  || ||  | | ||||| |       |||| |||||||| || || || ||||||||||| ||||| |||||||||||||| || || ||  |||| || || || |||
cttactagtgttcctcttttagctgtgtcactgctgttttgtgaatattctttctttatggagttcagttacatttattggttatcttctgttcttgtagTTATATGCAGAGTCCCTTGCACGCTTTCAAGGAGGTTCACCTTATATTTATCCACTGTACGGTCTGGGTGAGCTGCCACAG

upper sequence: EFJ11673 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GRMZM2G047431_T01 (Zea mays), 3'ss of exon 6
---------------------------------gtactgctacaaactatgtcttttcttcctgcggttgtcatcttaatgctttcttccga------agTTGTATGCAGAATCTCTGGCTCGCTTTCAAGGCGGTTCCCCTTATATTTATCCGCTCTATGGCTTGGGAGAACTTCCTCAG-------------------
                                  || || |||   |  |    |   |   ||   || |     |||  || | ||   |      || | |||||||||||  |||||||||||||||| || || || |||||||||||  | ||||| || |||||||| || |||                   
aggatagcacgattgccttgtttctgtttattgttaatgttacttgcattcaaatccgtctttgacattatttatctaacactattttagaatatttcagCTTTATGCAGAATCAGTGGCTCGCTTTCAAGGAGGATCACCATATATTTATCCCTTGTATGGTTTAGGAGAACTGCCACAGGGTTTTGCAAGACTTAGCG

upper sequence: EFJ11673 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GRMZM2G117507_T01 (Zea mays), 3'ss of exon 6
--------------------------------------------------------------gtactgctacaaac-tatgtcttttct-tcctgcggttgtcat--cttaatgctttcttccgaagTTGTATGCAGAATCTCTGGCTCGCTTTCAAGGCGGTTCCCCTTATATTTATCCGCTCTATGGCTTGGGAGAACTTCCTCAG
                                                               || ||||   ||  ||| || ||| | |  ||| ||| |  |  | || ||  | | |    || | |||||||| ||||| || ||||||||||| || || |||||||| ||||| || ||||| ||||| || || || |||
gtaagtcttggccaaagctgctccctagctgttgctatggatacacttgtgtcgtgtggttcctaatgcttggaatatatttcctttatatagtgcagttatatttacctattgtgtgccttt--agCTATATGCAGACTCTCTTGCACGCTTTCAAGGAGGCTCACCTTATATCTATCCACTATATGGGTTGGGTGAGCTACCACAG

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|169083495|gb|FE491926.1|FE491926
EST:     ACGATAGATACTTATCTGAGCCGGCTCTGGAAACGGTGAAGAGATTTAAG                         TTGTATGCAGAATCTCTGGCTCGCTTTCAAGGCGGTTCCCCTTATATTTAT
genomic: ACGATAGATACTTATCTGAGCCGGCTCTGGAAACGGTGAAGAGATTTAAGgtactgctac ... tcttccgaagTTGTATGCAGAATCTCTGGCTCGCTTTCAAGGCGGTTCCCCTTATATTTAT
EST: gi|169024779|gb|FE435471.1|FE435471
EST:     ACGATAGATACTTATCTGAGCCGGCTCTGGAAACGGTGAAGAGATTTAAG                         TTGTATGCAGAATCTCTGGCTCGCTTTCAAGGCGGTTCCCCTTATATTTAT
genomic: ACGATAGATACTTATCTGAGCCGGCTCTGGAAACGGTGAAGAGATTTAAGgtactgctac ... tcttccgaagTTGTATGCAGAATCTCTGGCTCGCTTTCAAGGCGGTTCCCCTTATATTTAT
EST: gi|169038310|gb|FE445309.1|FE445309
EST:     ACGATAGATACTTATCTGAGCCGGCTCTGGAAACGGTGAAGAGATTTAAG                         TTGTATGCAGAATCTCTGGCTCGCTTTCAAGGCGGTTCCCCTTATATTTAT
genomic: ACGATAGATACTTATCTGAGCCGGCTCTGGAAACGGTGAAGAGATTTAAGgtactgctac ... tcttccgaagTTGTATGCAGAATCTCTGGCTCGCTTTCAAGGCGGTTCCCCTTATATTTAT
EST: gi|169070711|gb|FE477310.1|FE477310
EST:     ACGATAGATACTTATCTGAGCCGGCTCTGGAAACGGTGAAGAGATTTAAG                         TTGTATGCAGAATCTCTGGCTCGCTTTCA-GGCGGTTCCCCTTATATT-AT
genomic: ACGATAGATACTTATCTGAGCCGGCTCTGGAAACGGTGAAGAGATTTAAGgtactgctac ... tcttccgaagTTGTATGCAGAATCTCTGGCTCGCTTTCAAGGCGGTTCCCCTTATATTTAT
EST: gi|169093397|gb|FE492701.1|FE492701
EST:     ACGATAGATACTTATCTGAGCCGGCTCTGGAAACGGTGAAGAGATTTAAG                         TTGTATGCAGAATCTCTGGCTCGCTTTCAAGGCGGTT
genomic: ACGATAGATACTTATCTGAGCCGGCTCTGGAAACGGTGAAGAGATTTAAGgtactgctac ... tcttccgaagTTGTATGCAGAATCTCTGGCTCGCTTTCAAGGCGGTT
EST: gi|169092638|gb|FE493658.1|FE493658
EST:     ACGATAGATACTTATCTGAGCCGGCTCTGGAAACGGTGAAGAGATTTAAG                         TTGTATGCAGAATCTCTGGCTCGCTTTCAAGGCGGTTCCCCTTATATTTAT
genomic: ACGATAGATACTTATCTGAGCCGGCTCTGGAAACGGTGAAGAGATTTAAGgtactgctac ... tcttccgaagTTGTATGCAGAATCTCTGGCTCGCTTTCAAGGCGGTTCCCCTTATATTTAT

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), 30 (downstream exon)
Score: 28

TGACGATAACACCATCGATTTTATTGGCCACTCACTGGCATTGCACCGGGACGATAGATACTTATCTGAGCCGGCTCTGGAAACGGTGAAGAGATTTAAGgtactgctac ... tcttccgaagTTGTATGCAGAATCTCTGGCTCGCTTTCAAGGCGGTTCCCCTTATATTTATCCGCTCTATGGCTTGGGAGAACTTCCTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctacaaactatgtcttttcttcctgcggttgtcatcttaatgctttcttccgaagTTGTATGCAGAATCTCTGGCTCGCTTTCAAGGCGGTTCCCCTTATATTTATCCGCTCTATGGCTTGGGAGAACTTCCTCAG
                                  tcttaat  putative branch site (score: 28)
                                        tgctttcttcc  CT-rich tract
                                 atcttaat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactgctacaaactatgtcttttcttcctgcggttgtcatcttaatgctttcttccgaagTTGTATGCAGAATCTCTGGCTCGCTTTCAAGGCGGTTCCCCTTATATTTATCCGCTCTATGGCTTGGGAGAACTTCCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA