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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttctttctcgatttcgcccgcattgcgtgcttccagctcctagatctcgccaaatgcgtactcggatctctagatcttaactctcttccctctttcttcctctcccccagCGGGAGATTGGCTCCAGGGACCATACGTTTACTTCCTCTACAGCCACTATGGCTTCCAGAAGGGGGATATTGGGCGGCTCTTCATCGCTGGCTTTGGATC

Basic information

species Selaginella moellendorffii
transcript EFJ11977
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ11977 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os10g37520.1 (Oryza sativa), 3'ss of exon 1
----------------------------------------gtgagttctttctcgatttcgcccgcattgcg-tgcttccagctcctagatctc-gccaaat-gcgtactcggatctctaga------tcttaactctcttccctctttcttcctc----------------tcccccagCGGGAGATTGGCTCCAGGGACCATACGTTTACTTCCTCTACAGCCACTATGGCTTCCAGAAGGGGGATATTGGGCGGCTCTTCATCGCTGGCTTTGGATC
                                         |       |  |||| ||| || ||   | | ||  |  | | |  ||||||  |||   | ||     |||||   | |       |  | || || || ||    |    | |                |    |||| || |||||||| ||||| || ||||| |||| |||||||||||| || |||||| | ||||| || ||||| || ||||||||||| ||||| || ||
gtgcgtaacgcctccccccgcccccagatttcccccccctttcccccaatcttcgagttcccctgcggcgtggtggctggatcgctcagatctgagccgggttgcaatgccggattgtttgggagggtttctgacgctgttgccgtggtgaatcgcgggtgtgggtgtgggtttttgcagCTGGGGATTGGCTGCAGGGGCCGTACGTGTACTACCTCTACAGCCAGTACGGCTTCGACAAGGGTGACATTGGCCGCCTCTTCATCGCCGGCTTCGGCTC

upper sequence: EFJ11977 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os03g02380.2 (Oryza sativa), 3'ss of exon 1
gtgagttctttctcgatttcgcccgcattgcgtgcttccagctcctagatctcgccaaatgcgtactcggatctctagatcttaactctcttccctctttcttcctctcccccagCGGGAGATTGGCTCCAGGGACCATACGTTTACTTCCTCTACAGCCACTATGGCTTCCAGAAGGGGGATATTGGGCGGCTCTTCATCGCTGGCTTTGGATC
                                 |  |     || | |||    |     || |  |||     |  |||||    |   |  | |   ||    |||    |||| || || ||||| || || || ||||| |||| |||||||||||| || |||||| | ||||| || || || || ||||||||||| ||||| |||||
---------------------------------gtatgtcattcttcgatt---cttggcgcattttcgtcctcccggatctgggattcatggctttcatcaa--tcttgtgcagCCGGGGACTGGCTGCAAGGGCCGTACGTGTACTACCTCTACAGCCAGTACGGCTTCGACAAGGGCGACATCGGCCGCCTCTTCATCGCCGGCTTCGGATC

upper sequence: EFJ11977 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G064563_T03 (Zea mays), 3'ss of exon 1
gtgagttctttctcgatttcgcccgcattgcgtgcttccagctcctagatctcgccaaatgcgtactcggatctctagatcttaactctcttccctctttct-----------tcctctcccccagCGGGAGATTGGCTCCAGGGACCATACGTTTACTTCCTCTACAGCCACTATGGCTTCCAGAAGGGGGATATTGGGCGGCTCTTCATCGCTGGCTTTGGATC
||  |  |    ||  |  |  || | |     | ||  | || | |   |        |  || ||      |     | ||  ||  | |||| | |              |    ||   |||| || || ||||| ||||| || ||||| |||| |||||||||||| ||||||||| | ||||| || || || || ||||||||||| ||||| |||||
gtacgccccccgtccctcccctccccttctttagtttagatctgcgaacgccgttgtggttggttctgatggtttcgcctgttgcctgccctcccgcctcgaatggggacgggtttgttcgtgcagCCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTATGGCTTCGACAAGGGCGACATCGGCCGCCTCTTCATCGCCGGCTTCGGATC

upper sequence: EFJ11977 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G067638_T01 (Zea mays), 3'ss of exon 1
-------------------------------gtgagttctttctcg-atttcgcccgcattgcgtgcttccagctcctagatctcg-ccaaatgcgtact--cg--gatctctagatcttaactctcttccctctttcttcctctcc------cccagCGGGAGATTGGCTCCAGGGACCATACGTTTACTTCCTCTACAGCCACTATGGCTTCCAGAAGGGGGATATTGGGCGGCTCTTCATCGCTGGCTTTGGATC
                                   |  ||| |||| ||| |    || | |||    | |  |  | |||||| | |     ||| | |  ||  | | | | |   |    |||||  | |  || | |  |  |        |||| || || ||||| ||||| || ||||| |||| |||||||||||| || |||||| | ||||| || ||||| || ||||||||||| ||||| || ||
gtacgcctcctgattcctgcttggtcccctccctcgcccttcctcgcattcccgttgcgtcgcggcactgcgccctccagatctggactgggggcgcaatgccggtggtatttggtggtctggtctctgacgttattgtgctccggcggatggtgcagCTGGGGACTGGCTGCAGGGGCCCTACGTGTACTACCTCTACAGCCAGTACGGCTTCGACAAGGGCGACATTGGCCGCCTCTTCATCGCCGGCTTCGGTTC

upper sequence: EFJ11977 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G077669_T01 (Zea mays), 3'ss of exon 1
gtgagttctttctcgatttcgcccgcattgcgtgcttccagctcctagatctcgccaaatgcgtactcggatctctagatcttaactctcttccctctttcttcctctcccccagCGGGAGATTGGCTCCAGGGACCATACGTTTACTTCCTCTACAGCCACTATGGCTTCCAGAAGGGGGATATTGGGCGGCTCTTCATCGCTGGCTTTGGATC
    || |   |||   ||| |     |||   | ||||  |   ||||||| || ||    ||  | |    |||  ||  | |   |     |   ||| | |        ||| || || ||||| ||||| || ||||| |||| |||||||||||| || |||||| | ||||| || || || || ||||||||||| ||||| |||||
----gtacgccctc--cttcccttctcttgttcggttcct-cgtttagatct-gcgaacgctgtggtgg---ttctgaatgatgatggttgggacggattcgtgc--------agCCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTACGGCTTCGACAAGGGCGACATCGGCCGCCTCTTCATCGCCGGCTTCGGATC

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|169047653|gb|FE454821.1|FE454821
EST:     CTTCAATGCCTTCAAGAACAATTACCTGGTGGTCTACTCGCTCATGATGG                         CGGGAGATTGGCTCCAGGGACCATACGTTTACTTCCTCTACAGCCACTATG
genomic: CTTCAATGCCTTCAAGAACAATTACCTGGTGGTCTACTCGCTCATGATGGgtgagttctt ... tctcccccagCGGGAGATTGGCTCCAGGGACCATACGTTTACTTCCTCTACAGCCACTATG
EST: gi|70671102|gb|DN839679.1|DN839679
EST:     CTTCAATGCCTTCAAGAACAATTACCTGGTGGTCTACTCGCTCATGATGG                         CGGGAGATTGGCTCCAGGGACCATACGTTTACTTCCTCTACAGCCACTATG
genomic: CTTCAATGCCTTCAAGAACAATTACCTGGTGGTCTACTCGCTCATGATGGgtgagttctt ... tctcccccagCGGGAGATTGGCTCCAGGGACCATACGTTTACTTCCTCTACAGCCACTATG

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), 35 (downstream exon)
Score: 18

GCACTCGAGTTTCGCCGTGGCAGCAAGGACCGGATCGTCGCGACATCGGCCTTCAATGCCTTCAAGAACAATTACCTGGTGGTCTACTCGCTCATGATGGgtgagttctt ... tctcccccagCGGGAGATTGGCTCCAGGGACCATACGTTTACTTCCTCTACAGCCACTATGGCTTCCAGAAGGGGGATATTGGGCGGCTCTTCATCGCTGGCTTTGGATC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcgtactcggatctctagatcttaactctcttccctctttcttcctctcccccagCGGGAGATTGGCTCCAGGGACCATACGTTTACTTCCTCTACAGCCACTATGGCTTCCAGAAGGGGGATATTGGGCGGCTCTTCATCGCTGGCTTTGGATC
                   tcttaac  putative branch site (score: 18)
           tctctagatcttaact  CT-rich tract
                  atcttaa  TA-rich tract