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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttttctttgtaatgccactgaacttaaaattcgtgctcagATGAAAGACTACATTGCTACCCCAAAACCCAATGGCTACCAAAGTCTACACACTAAAGTCATCCCATTTGGTTCAAAGACATTTTTCCCACTGGAAATTC

Basic information

species Selaginella moellendorffii
transcript EFJ30490
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ30490 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: LOC_Os03g22160.1 (Oryza sativa), 3'ss of exon 14
---------------------------gtaagtttttct--ttgtaatgccactgaacttaaaattcg--tgctcagATGAAAGACTACATTGCTACCCCAAAACCCAATGGCTACCAAAGTCTACACACTAAAGTCATCCCATTTGGTTCAAAGACATTTTTCCCACTGGAAATTC
                            ||| |||| |   || | ||    |      |||||  |   ||   || ||||||| |||||||| |||||||| || ||||| ||||||||||||||||| | ||| || ||||||       |||   | ||||   ||||| |||
gtgagttatctgctttccttattcattataatttttacctcttttgattttgccatttctaaaagccagctgtatagGTGAAAGATTACATTGCAACCCCAAAGCCTAATGGATACCAAAGTCTACACACGACAGTGATACCATTTCTGAATGAGAGTATGTTCCATTTGGAAGTTC

upper sequence: EFJ30490 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: GRMZM2G416698_T02 (Zea mays), 3'ss of exon 6
------------------------------------------------gtaagtttttctttgt-aatgccactgaacttaaaat---tcgtgct--cagATGAAAGACTACATTGCTACCCCAAAACCCAATGGCTACCAAAGTCTACACACTAAAGTCATCCCATTTGGTTCAAAGACATTTTTCCCACTGGAAATTC
                                                 | | | ||  ||||| ||| |||||   || | |||   |  || |  ||| || |||| |||||||| || |||||||| |||||||||||||| |||||||| | ||| || ||||||   | || || |                   
atatggacacccgttcctcaagctgtgagttatcttctttttgtcgtatttaatgttcttttgtgaattccacttttctaacaatcagttatgttaacagGTGGAAGATTACATTGCAACTCCAAAACCTAATGGCTACCAAAGCCTACACACAACAGTGATACCATTT---TTAATGAGA-------------------

upper sequence: EFJ30490 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: GRMZM2G416698_T01 (Zea mays), 3'ss of exon 7
------------------------gtaagtttttctttgt-aatgccactgaacttaaaat---tcgtgct--cagATGAAAGACTACATTGCTACCCCAAAACCCAATGGCTACCAAAGTCTACACACTAAAGTCATCCCATTTGGTTCAAAGACATTTTTCCCACTGGAAATTC-
                         | | | ||  ||||| ||| |||||   || | |||   |  || |  ||| || |||| |||||||| || |||||||| |||||||||||||| |||||||| | ||| || ||||||      |    || ||||    ||||| ||| 
gtgagttatcttctttttgtcgtatttaatgttcttttgtgaattccacttttctaacaatcagttatgttaacagGTGGAAGATTACATTGCAACTCCAAAACCTAATGGCTACCAAAGCCTACACACAACAGTGATACCATTTTTAATGAGAGTATGTTTCAT-TTGGAAGTTCA

upper sequence: EFJ30490 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: GRMZM2G353147_T01 (Zea mays), 3'ss of exon 13
------------------------gtaagtttttctttgtaa----tgccactgaacttaaaat---tcgtgct--cagATGAAAGACTACATTGCTACCCCAAAACCCAATGGCTACCAAAGTCTACACACTAAAGTCATCCCATTTGGTTCAAAGACATTTTTCCCACTGGAAATTC
                         ||| | ||  ||||| |    | | ||    || | |||   | |||    ||| || |||| |||||||| || |||||||| ||||| ||||||||||||||||| | ||| || ||||||  |    |||   | ||||   ||||| |||
gtgagttatcttcttttcgtcatattaaatgttcttttgtgaaatatacaacctttctaacaattaattgtgtcaacagGTGGAAGATTACATTGCAACTCCAAAACCTAATGGGTACCAAAGTCTACACACAACAGTGATACCATTTCTTAACGAGAGTATGTTCCATTTGGAAGTTC

upper sequence: EFJ30490 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: Vv07s0005g00770.t01 (Vitis vinifera), 3'ss of exon 14
-------------------------------------------------------gtaagtttttctttgtaatgccactga-acttaaaattcgtgct-cagATGAAAGACTACATTGCTACCCCAAAACCCAATGGCTACCAAAGTCTACACACTAAAGTCATCCCATTTGGTTCAAAGACATTTTTCCCACTGGAAATTC
                                                         || |   |  || |  |   | | | | || |  ||  |||  |||||||||||||| ||||| || |||||||| |||||||| |||||||| || || |  || || ||||||  ||   |||   | || | ||||||| |||
gtgtgtactttgctttgcacatcctttgaaatttgcttctaatttaagtatcagacaaaatgactagtttttctagaaataatattttatttttttgcaacagATGAAAGACTATATTGCAACTCCAAAACCTAATGGCTATCAAAGTCTCCATACAACTGTAATTCCATTTCTTTATGAGAGCATGTTTCGACTGGAAGTTC

upper sequence: EFJ30490 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: PP1S194_9V6.1 (Physcomitrella patens), 3'ss of exon 13
---------------------------------------------------------------gtaagtttttctttgtaa---tgccactgaacttaaaattcg-------tgctcagATGAAAGACTACATTGCTACCCCAAAACCCAATGGCTACCAAAGTCTACACACTAAAGTCATCCCATTTGGTTCAAAGACATTTTTCCCACTGGAAATTC
                                                               ||   ||    |||| ||   || |     |||||   |||        ||  ||||||||||||||||||||||| ||||| || ||||| || |||||| | ||||| | ||| || ||||| ||  || |||| |  |||||  | |||||||
gtgcgcagatcctaacttcgttgtggtacacccatgaggtgcatttaactttatgttttatccgttccttacagtttgcaatagtgtcgtgtgacttaggcttcactttggctgtgcagATGAAAGACTACATTGCTACACCAAAGCCTAATGGTTATCAAAGTTTGCACACCACAGTTATTCCATTCGGCACACAGACTTACTTCCCCATCGAAATTC

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: 21 (upstream exon), 32 (downstream exon)
Score: 19

GTCTGCTATCATGTTCTCGGACTGGTACACACATTATGGTCTCCTGTACCGCAAACCgtaagttttt ... tcgtgctcagATGAAAGACTACATTGCTACCCCAAAACCCAATGGCTACCAAAGTCTACACACTAAAGTCATCCCATTTGGTTCAAAGACATTTTTCCCACTGGAAATTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaagtttttctttgtaatgccactgaacttaaaattcgtgctcagATGAAAGACTACATTGCTACCCCAAAACCCAATGGCTACCAAAGTCTACACACTAAAGTCATCCCATTTGGTTCAAAGACATTTTTCCCACTGGAAATTC
                               tttttctttgtaat  TA-rich tract