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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttctcgtgagttcttgtctttcacgccattttttgtcactgttgagctttggatcttacgacttagATGGGAAAAACAAGGACACAGTCCCTCTTTTGGCTACGACTTTTGGTATCAACCTCGTCACAAAACGATGATCAGTAGTTCCTGGGGGGCGCCCTCTGCG

Basic information

species Selaginella moellendorffii
transcript EFJ11187
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ11187 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: LOC_Os01g68770.1 (Oryza sativa), 3'ss of exon 3
------------------gtaagttctcgtgagttcttgtctt---tcacgccattttttgtcactgttgag-------ctttggatcttacgact--tagATGGGAAAAACAAGGACACAGTCCCTCTTTTGGCTACGACTTTTGGTATCAACCTCGTCACAAAACGATGATCAGTAGTTCCTGGGGGGCGCCCTCTGCG
                   || |||| | |||  | |    ||   | || |   |||   | ||| ||||        | | | || |  |  ||   || |||||||| | ||| ||||| ||||  |||||||| || | ||||||||||||||||||||| || |||||||||   || ||||| || ||  | || 
cataatgcccattccaggatatgttc-catgaaatgtcaatttatgttacacatatttgcatgacttttgaaagataaccatagtatttcccttctcgcagTTGGGAAAAGCCAGGTCACAGCCCCTTGTTTGGCTATGATTATTGGTATCAACCTCGTCACAAGACAATGATCAGTTCATCATGGGGAGCACCTGCAGCT

upper sequence: EFJ11187 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM2G103812_T02 (Zea mays), 3'ss of exon 3
-------------------------------gtaagttctcgtgagttcttgtctt--tcacgccattttttgtcactgttgagctttggatcttacgacttagATGGGAAAAACAAGGACACAGTCCCTCTTTTGGCTACGACTTTTGGTATCAACCTCGTCACAAAACGATGATCAGTAGTTCCTGGGGGGCGCCCTCTGCG
                               | ||        || |  || |  |  || |    | |||  |   | || || ||  |    ||| |   || |||||||| | ||| ||||||||||  ||||| || ||||| ||||| || ||||| ||||| ||||||||||||   || ||||| || ||  | |||
tgcagatgtatggtaaaattgcttgacatgtgaaaaacagacagattcattatgatgatctcagtgtctttattacttattaagtttctg---ctac-atgcagTTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACTTCTGGTACCAGCCTCGCCACAAGACGATGATCAGTTCGTCATGGGGAGCCCCTGCAGCG

upper sequence: EFJ11187 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: Vv05s0029g00240.t01 (Vitis vinifera), 3'ss of exon 3
--------------------------gtaagttctcgtgagttcttgtctttcacgccattttttg---tcactgttgagctttggatcttacgacttagATGGGAAAAACAAGGACACAGTCCCTCTTTTGGCTACGACTTTTGGTATCAACCTCGTCACAAAACGATGATCAGTAGTTCCTGGGGGGCGCCCTCTGCG
                           |||  |      |  |||    ||   | |  | ||||    |   | ||   ||     |  ||    | |||||||| |||| ||| || ||||| |||||||||||||| || ||||| ||||| |||||||| || |||||||||   || ||||| || ||  | || 
gaacatgtccagggaatggttttagtataacatgagccaacctctgacattgagcacagtattttaagtttgattttccactccttttgatatatatcagATGGGAGAAACCAGGGCATAGTCCGTCTTTTGGCTACGATTTCTGGTACCAACCCCGTCACAAGACAATGATCAGTTCATCATGGGGAGCACCTGCAGCT

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|169111355|gb|FE510904.1|FE510904
EST:     CAAGGAGCTGGATTCTTGCTCTTGGATGGAGAATTCAACATCAAAGGAAG                         ATGGGAAAAACAAGGACACAGTCCCTCTTTTGGCTACGACTTTTGGTATCA
genomic: CAAGGAGCTGGATTCTTGCTCTTGGATGGAGAATTCAACATCAAAGGAAGgtaagttctc ... tacgacttagATGGGAAAAACAAGGACACAGTCCCTCTTTTGGCTACGACTTTTGGTATCA
EST: gi|169035104|gb|FE444900.1|FE444900
EST:     CAAGGAGCTGGATTCTTGCTCTTGGATGGAGAATTCAACATCAAAGGAAG                         ATGGGAAAAACAAGGACACAGTCCCTCTTTTGGCTACGACTTTTGGTATCA
genomic: CAAGGAGCTGGATTCTTGCTCTTGGATGGAGAATTCAACATCAAAGGAAGgtaagttctc ... tacgacttagATGGGAAAAACAAGGACACAGTCCCTCTTTTGGCTACGACTTTTGGTATCA
EST: gi|169059197|gb|FE467199.1|FE467199
EST:     CAAGGAGCTGGATTCTTGCTCTTGGATGGAGAATTCAACATCAAAGGAAG                         --GG-AAAAACAAGGACACAGTCCCTCTTTTGGCTACGACTTTTGGTATCA
genomic: CAAGGAGCTGGATTCTTGCTCTTGGATGGAGAATTCAACATCAAAGGAAGgtaagttctc ... tacgacttagATGGGAAAAACAAGGACACAGTCCCTCTTTTGGCTACGACTTTTGGTATCA
EST: gi|169070384|gb|FE479349.1|FE479349
EST:     CAAGGAGCTGGATTCTTGCTCTTGGATGGAGAATTCAACATCAAAGGAAG                         ATGGGAAAAACAAGGACACAGTCCCTCTTTTGGCTACGACTTTTGGTATCA
genomic: CAAGGAGCTGGATTCTTGCTCTTGGATGGAGAATTCAACATCAAAGGAAGgtaagttctc ... tacgacttagATGGGAAAAACAAGGACACAGTCCCTCTTTTGGCTACGACTTTTGGTATCA
EST: gi|169103453|gb|FE507573.1|FE507573
EST:     CAAGGAGCTGGATTCTTGCTCTTGGATGGAGAATTCAACATCAAAGGAAG                         ATGGGAAAAACAAGGACACAGTCCCTCTTTTGGCTACGACTTTTGGTATCA
genomic: CAAGGAGCTGGATTCTTGCTCTTGGATGGAGAATTCAACATCAAAGGAAGgtaagttctc ... tacgacttagATGGGAAAAACAAGGACACAGTCCCTCTTTTGGCTACGACTTTTGGTATCA
EST: gi|169064647|gb|FE471378.1|FE471378
EST:     CAAGGAGCTGGATTCTTGCTCTTGGATGGAGAATTCAACATCAAAGGAAG                         ATGGGAAAAACAAGGACACAGTCCCTCTTTTGGCTACGACTTTTGGTATCA
genomic: CAAGGAGCTGGATTCTTGCTCTTGGATGGAGAATTCAACATCAAAGGAAGgtaagttctc ... tacgacttagATGGGAAAAACAAGGACACAGTCCCTCTTTTGGCTACGACTTTTGGTATCA
EST: gi|169099417|gb|FE501007.1|FE501007
EST:     CAAGGAGCTGGATTCTTGCTCTTGGATGGAGAATTCAACATCAAAGGAAG                         ATGGGAAAAACAAGGACACAGTCCCTCTTTTGGCTACGACTTTTGGTATCA
genomic: CAAGGAGCTGGATTCTTGCTCTTGGATGGAGAATTCAACATCAAAGGAAGgtaagttctc ... tacgacttagATGGGAAAAACAAGGACACAGTCCCTCTTTTGGCTACGACTTTTGGTATCA
EST: gi|169057338|gb|FE466799.1|FE466799
EST:     CAAGGAGCTGGATTCTTGCTCTTGGATGGAGAATTCAACATCAAAGGAAG                         ATGGGAAAAACAAGGACACAGTCCCTCTTTTGGCTACGACTTTTGGTATCA
genomic: CAAGGAGCTGGATTCTTGCTCTTGGATGGAGAATTCAACATCAAAGGAAGgtaagttctc ... tacgacttagATGGGAAAAACAAGGACACAGTCCCTCTTTTGGCTACGACTTTTGGTATCA
EST: gi|169026696|gb|FE433982.1|FE433982
EST:     CAAGGAGCTGGATTCTTGCTCTTGGATGGAGAATTCAACATCAAAGGAAG                         ATGGGAAAAACAAGGACACAGTCCCTCTTTTGGCTACGACTTTTGGTATCA
genomic: CAAGGAGCTGGATTCTTGCTCTTGGATGGAGAATTCAACATCAAAGGAAGgtaagttctc ... tacgacttagATGGGAAAAACAAGGACACAGTCCCTCTTTTGGCTACGACTTTTGGTATCA
EST: gi|169069404|gb|FE479487.1|FE479487
EST:     CAAGGAGCTGGATTCTTGCTCTTGGATGGAGAATTCAACATCAAAGGAAG                         ATGGGAAAAACAAGGACACAGTCCCTCTTTTGGCTACGACTTTTGGTATCA
genomic: CAAGGAGCTGGATTCTTGCTCTTGGATGGAGAATTCAACATCAAAGGAAGgtaagttctc ... tacgacttagATGGGAAAAACAAGGACACAGTCCCTCTTTTGGCTACGACTTTTGGTATCA
EST: gi|169024774|gb|FE433308.1|FE433308
EST:     CAAGGAGCTGGATTCTTGCTCTTGGATGGAGAATTCAACATCAAAGGAAG                         ATGGGAAAAACAAGGACACAGTCCCTCTTTTGGCTACGACTTTTGGTATCA
genomic: CAAGGAGCTGGATTCTTGCTCTTGGATGGAGAATTCAACATCAAAGGAAGgtaagttctc ... tacgacttagATGGGAAAAACAAGGACACAGTCCCTCTTTTGGCTACGACTTTTGGTATCA
EST: gi|169038580|gb|FE446905.1|FE446905
EST:     CAAGGAGCTGGATTCTTGCTCTTGGATGGAGAATTCAACATCAAAGGAAG                         ATGGGAAAAACAAGGACACAGTCCCTCTTTTGGCTACGACTTTTGGTATCA
genomic: CAAGGAGCTGGATTCTTGCTCTTGGATGGAGAATTCAACATCAAAGGAAGgtaagttctc ... tacgacttagATGGGAAAAACAAGGACACAGTCCCTCTTTTGGCTACGACTTTTGGTATCA

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: 34 (upstream exon), 34 (downstream exon)
Score: 52

CTTCCGGTGAGATTATGATCTCGTGCCTTGGAGACAAAGAAGGACGAGCACAAGGAGCTGGATTCTTGCTCTTGGATGGAGAATTCAACATCAAAGGAAGgtaagttctc ... tacgacttagATGGGAAAAACAAGGACACAGTCCCTCTTTTGGCTACGACTTTTGGTATCAACCTCGTCACAAAACGATGATCAGTAGTTCCTGGGGGGCGCCCTCTGCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgtctttcacgccattttttgtcactgttgagctttggatcttacgacttagATGGGAAAAACAAGGACACAGTCCCTCTTTTGGCTACGACTTTTGGTATCAACCTCGTCACAAAACGATGATCAGTAGTTCCTGGGGGGCGCCCTCTGCG
                                         atcttac  putative branch site (score: 52)
                attttttgt  TA-rich tract