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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtctcctcacctcatttgctgcaactatagactgaattcgatcttgcagAACATGTACGCTCAGCTCCTTCCTCTGGCGCTGCCCGCTCCTCCGATGCCCGGCATGGGAGGCGGTCCTCCAGGATTCAACCCGGGCATGCCACCTCCTT

Basic information

species Selaginella moellendorffii
transcript EFJ24508
intron # 29
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 29
lower sequence: GRMZM5G822591_T01 (Zea mays), 3'ss of exon 6
---------------------------------gtttgtctcctcacctcat-ttgctgcaact------atagactgaattcgatcttgcagAACATGTACGCTCAGCTCCTTCCTCTGGCGCTGCCCGCTCCTCCGATGCCCGGCATGGGAGGCGGT---CCTCCAGGATTCAACCCGGGCATGCCACCTCCTT
                                 || |   |   ||  ||||  ||  |||  |      | |  ||   |||  | |||||||||||||| || || || |||||||| || ||||| ||||| || |||||||||||||| |||  |   |||||      |     ||||||||| ||     
gtacatctaaatcttcactcacatgttctgtttgtgtaattaaccatttcatgctgaggcagttggcatgacaagctacgttccgttttgcagAACATGTATGCGCAACTGCTTCCTCTTGCCCTGCCTGCTCCGCCAATGCCCGGCATGGGTGGCCCTCCACCTCCGATGGGCGGAATGGGCATGCCTCCGA---

upper sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 29
lower sequence: PP1S7_102V6.1 (Physcomitrella patens), 3'ss of exon 17
-------------------------------------------------------------------------------------------gtttgtctcctcacctcatttgctgcaactatagactgaattcgatcttgcagAACATGTACGCTCAGCTCCTTCCTCTGGCGCTGCCCGCTCCTCCGATGCCCGGCATGGGAGGCGGTCCTCCAGGATTCAACCCGGGCATGCCACCTCCTT--
                                                                                            |||| || |   | | ||    | |    |    |         |  ||||||||||||||||||||||| | |||||||| || || ||||| ||  |  |||| |||   ||   |      |   |   || | ||  |  |         
gtaagttttcggcctctacgaacatctcagtgctttcttgcagatttgcaagttcctgatatctagctacgttaattatgtaaaatattatctttggctgcatgcttgatgcaatactgacaagagcgacgaatttttatgcagAACATGTACGCTCAGCTCTTGCCTCTGGCTCTACCAGCTCCCCCTGTTGCCGGTATGCCTGGT--TTGGGTGGAGGTATGCCTGTGCCGGGTATGGGTGGAG

upper sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 29
lower sequence: PP1S147_10V6.1 (Physcomitrella patens), 3'ss of exon 17
--------------------------------------------------------------------------------------gtttgtctcctcacctcat----ttgctgcaactat----agactga-attcgatcttgcagAACATGTACGCTCAGCTCCTTCCTCTGGCGCTGCCCGCTCCTCCGATGCCCGGCATGGGAGGCGGTCCTCCAGGATTCAACCCGGGCATGCCACCTCCTT---
                                                                                      |||||  |   ||| |  |    ||    ||||  |    ||  ||| ||    || ||||||||||||||||||| ||| | |||||||| || || ||||||||  |  | || |||   ||    |||   ||  |   |   || ||||||   ||     
gtaagatctttggctagtttgcttttccgtttgtatgtattgattattttccctcgccatcctgatgtggattaggtgacgtgcgggtttgggtgtacacatggtgtcgttctctcaacgctgacaagtgtgacatattttcctgcagAACATGTACGCTCAACTCTTGCCTCTGGCTCTACCAGCTCCTCCTGTTGCTGGTATGACTGGTATGCCT---GGTATGGGCGGAGGTATGCCAATGCCGGGTA

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|169025121|gb|FE434708.1|FE434708
EST:     AGGAGGTCAAGAGCAAGGAGAAGGAAGAGAAGGATCTAGTGGCTCAACAG                         AACATGTACGCTCAGCTCCTTCCTCTGGCGCTGCCCGCTCCTCCGATGCCC
genomic: AGGAGGTCAAGAGCAAGGAGAAGGAAGAGAAGGATCTAGTGGCTCAACAGgtttgtctcc ... gatcttgcagAACATGTACGCTCAGCTCCTTCCTCTGGCGCTGCCCGCTCCTCCGATGCCC
EST: gi|169032179|gb|FE438786.1|FE438786
EST:     AGGAGGTCAAGAGCAAGGAGAAGGAAGAGAAGGATCTAGTGGCTCAACAG                         AACATGTACGCTCAGCTCCTTCCTCTGGCTCTGCCCGCTCCTCCGATGCCC
genomic: AGGAGGTCAAGAGCAAGGAGAAGGAAGAGAAGGATCTAGTGGCTCAACAGgtttgtctcc ... gatcttgcagAACATGTACGCTCAGCTCCTTCCTCTGGCGCTGCCCGCTCCTCCGATGCCC
EST: gi|169045877|gb|FE451733.1|FE451733
EST:     AGGAGGTCAAGAGCAAGGAGAAGGAAGAGAAGGATCTAGTGGCTCAACAG                         AACATGTACGCTCAGCTCCTTCCTCTGGCTCTGCCCGCTCCTCCGATGCCC
genomic: AGGAGGTCAAGAGCAAGGAGAAGGAAGAGAAGGATCTAGTGGCTCAACAGgtttgtctcc ... gatcttgcagAACATGTACGCTCAGCTCCTTCCTCTGGCGCTGCCCGCTCCTCCGATGCCC
EST: gi|169097271|gb|FE497648.1|FE497648
EST:     AGGAGGTCAAGAGCAAGGAGAAGGAAGAGAAGGATCTAGTGGCTCAACAG                         AACATGTACGCTCAGCTCCTTCCTCTGGCGCTGCCCGCTCCTCCGATGCCC
genomic: AGGAGGTCAAGAGCAAGGAGAAGGAAGAGAAGGATCTAGTGGCTCAACAGgtttgtctcc ... gatcttgcagAACATGTACGCTCAGCTCCTTCCTCTGGCGCTGCCCGCTCCTCCGATGCCC
EST: gi|169030493|gb|FE438697.1|FE438697
EST:     AGGAGGTCAAGAGCAAGGAGAAGGAAGAGAAGGATCTAGTGGCTCAACAG                         AACATGTACGCTCAGCTCCTTCCTCTGGCGCTGCCCGCTCCTCCGATGCCC
genomic: AGGAGGTCAAGAGCAAGGAGAAGGAAGAGAAGGATCTAGTGGCTCAACAGgtttgtctcc ... gatcttgcagAACATGTACGCTCAGCTCCTTCCTCTGGCGCTGCCCGCTCCTCCGATGCCC
EST: gi|169030494|gb|FE438698.1|FE438698
EST:     AGGAGGTCAAGAGCAAGGAGAAGGAAGAGAAGGATCTAGTGGCTCAACAG                         AACATGTACGCTCAGCTCCTTCCTCTGGCGCTGCCCGCTCCTCCGATGCCC
genomic: AGGAGGTCAAGAGCAAGGAGAAGGAAGAGAAGGATCTAGTGGCTCAACAGgtttgtctcc ... gatcttgcagAACATGTACGCTCAGCTCCTTCCTCTGGCGCTGCCCGCTCCTCCGATGCCC
EST: gi|169114798|gb|FE516059.1|FE516059
EST:     AGGAGGTCAAGAGCAAGGAGAAGGAAGAGAAGGATCTAGTGGCTCAACAG                         AACATGTACGCTCAGCTCCTTCCTCTGGCGCTGCCCGCTCCTCCGATGCCC
genomic: AGGAGGTCAAGAGCAAGGAGAAGGAAGAGAAGGATCTAGTGGCTCAACAGgtttgtctcc ... gatcttgcagAACATGTACGCTCAGCTCCTTCCTCTGGCGCTGCCCGCTCCTCCGATGCCC
EST: gi|169082004|gb|FE486447.1|FE486447
EST:     AGGAGGTCAAGAGCAAGGAGAAGGAAGAGAAGGATCTAGTGGCTCAACAG                         AACATGTACGCTCAGCTCCTTCCTCTGGCTCTGCCCGCTCCTCCGATGCCC
genomic: AGGAGGTCAAGAGCAAGGAGAAGGAAGAGAAGGATCTAGTGGCTCAACAGgtttgtctcc ... gatcttgcagAACATGTACGCTCAGCTCCTTCCTCTGGCGCTGCCCGCTCCTCCGATGCCC
EST: gi|169047381|gb|FE456214.1|FE456214
EST:     AGGAGGTCAAGAGCAAGGAGAAGGAAGAGAAGGATCTAGTGGCTCAACAG                         AACATGTACGCTCAGCTCCTTCCTCTGGCGCTGCCCGCTCCTCCGATGCCC
genomic: AGGAGGTCAAGAGCAAGGAGAAGGAAGAGAAGGATCTAGTGGCTCAACAGgtttgtctcc ... gatcttgcagAACATGTACGCTCAGCTCCTTCCTCTGGCGCTGCCCGCTCCTCCGATGCCC

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: 100

GTACACCAGCAAGGTGGACGATCTGATCAAAGACAAGCTAGCAGCCGACCAGGAGGTCAAGAGCAAGGAGAAGGAAGAGAAGGATCTAGTGGCTCAACAGgtttgtctcc ... gatcttgcagAACATGTACGCTCAGCTCCTTCCTCTGGCGCTGCCCGCTCCTCCGATGCCCGGCATGGGAGGCGGTCCTCCAGGATTCAACCCGGGCATGCCACCTCCTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttgtctcctcacctcatttgctgcaactatagactgaattcgatcttgcagAACATGTACGCTCAGCTCCTTCCTCTGGCGCTGCCCGCTCCTCCGATGCCCGGCATGGGAGGCGGTCCTCCAGGATTCAACCCGGGCATGCCACCTCCTT
         tcctcac  putative branch site (score: 100)
                              aactata  TA-rich tract