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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCCCTTGAGAGATACACACATTATTATGAACGATGGGCAGCCAATCAGTCGgtaagtattgaatgtggttgaagtgacctgaaacttcaaatctacattagcatggagttcattcagagtgacaattgatgcatgccagctgttctgttgg...

Basic information

species Zea mays
transcript GRMZM5G876621_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G876621_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os04g41470.1 (Oryza sativa), 5'ss of exon 10
TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCCCTTGAGAGATACACACATTATTATGAACGATGGGCAGCCAATCAGTCGgtaagt-attgaatgtggttgaagtgacctgaaacttcaaatctacattagcatggagttcattcagagtgacaattgatgcatgccagctgttctgttgg--------------------------
||||||||||||||||||||||||||||||||||||||||| ||||||||||| ||||| ||||||||||| |||||||||||||||||||||||| ||||  |       |||| |||||||      | | |   |||     |   | |   ||| |  ||||  || |     |     | |  |||                          
TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCGgtaagttattgggtacaagaaaagttacctgaacaaagcattgtgttttacataagtagtaaaaaagatttccaatcaatactcaagaagaacttttctggtttcttaatatcttctcgttatgcag

upper sequence: GRMZM5G876621_T01 (Zea mays), 5'ss of exon 10
lower sequence: AT1G65430.1 (Arabidopsis thaliana), 5'ss of exon 10
TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCCCTTGAGAGATACACACATTATTATGAACGATGGGCAGCCAATCAGTCGgtaagta---ttgaatgtggtt-gaagtgacctgaaacttcaaatctacattagcatggagttcattcagagtgacaattgatgcatgccagctgttctgttgg
||||||||  ||||||   |  |||| |||||||||||||| ||||||||||| || || || |||||  |||||||| ||||||| |||||| |||   ||  ||    || ||| | || ||     |  |       ||     |||  |  || |||  ||   || |  | |   |    |  |  |  
TATGATGAGACTGAAAAACGCCGAGAGATGGCAAAGAACTCTCTTGAGAGATATACCCACTACTATGAGAGATGGGCAACCAATCAATCGgtatgtaaatttttatccatttagaattcacatgttttatttagctcctcttgaaggggaaat--ttaagaaagaattttcagccgtcaaattcatattcct--

upper sequence: GRMZM5G876621_T01 (Zea mays), 5'ss of exon 10
lower sequence: Vv00s0207g00090.t01 (Vitis vinifera), 5'ss of exon 10
TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCCCTTGAGAGATACACACATTATTATGAACGATGGGCAGCCAATCAGTCGgtaagtattgaatgtggttgaagtgac-ctgaaacttcaa-atctacattagcatggagttcattcagagtgacaattgatgcatgccagctgttctgttgg
||||||||  |||| |   |||| || ||||| ||||||||  | |||||||| || ||||||||||||||||||||  |||| || || ||| || |||| | |    ||     | ||    ||  || ||  ||||||     ||   |  | |       | ||  | || |   | |  ||  ||| 
TATGATGAGGCTGAGAAACGAAGGGATATGGCTAAGAACTCTTTGGAGAGATATACTCATTATTATGAACGATGGGCGACCAACCAATCTgtatgt-ttgacttttccagatcctcctcttttgctgtaatatggacattatttcagaaacccattatttcagaatttagtccaagattg-tcctcatttgc

upper sequence: GRMZM5G876621_T01 (Zea mays), 5'ss of exon 10
lower sequence: PP1S9_199V6.1 (Physcomitrella patens), 5'ss of exon 11
TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCCCTTGAGAGATACACACATTATTATGAACGATGGGCAGCCAATCAGTCGgtaagtattgaatgtggttgaagtgacctgaaacttcaaatctacattagc---atggagttcattcagagtgacaattgatgcatgccagctgttctgttgg---------------------------------------------------------
||||||||| | ||  ||||||| |||||||| ||||||||||||||  | |||||||| |||||||| || |||||  | ||  | || || |||| | |      ||||  ||        |||| |  |||| ||||    ||    ||  | |      ||| | ||          ||     |||                                                           
TATGATGAAGCAGAGCGGAGAAGGGAAATGGCGAAGAACTCCCTTGAACGTTACACACACTATTATGAGCGTTGGGCTACAAACGAATCTgtgagtactaa-----tttgagatggtgcacttcttcca--ctacgttagttatataatctttttcccataacacactagagatgcattgactacctggttaatttaatgtgatgtttttcatcatttcaatcttactcaaatccttctgatgtgtgcag

upper sequence: GRMZM5G876621_T01 (Zea mays), 5'ss of exon 10
lower sequence: PP1S178_72V6.2 (Physcomitrella patens), 5'ss of exon 11
TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCCCTTGAGAGATACACACATTATTATGAACGATGGGCAGCCAATCAGTCGgtaagtattgaatgtggttgaagtgacctgaaactt------------caaatctacattagca---tggagttcattcagagtgacaa-ttgatgc-atgccagctgt-tctgttgg-----------------------------------
|| |||||| | ||  |||| || |||||||| |||||||| |||||  | ||||||||||| |||||||| |||||  | ||| |||| ||||||  || ||   |||   |     |     ||              ||||| ||| | |    | |  ||    ||   |   || |||| |  |||    |||  | ||||                                     
TACGATGAAGCAGAGCGGAGGAGGGAAATGGCTAAGAACTCTCTTGAACGCTACACACATTACTATGAACGTTGGGCTACAAATGAGTCTgtaagtgctggattgcgtttgtgcattttttcttttgtcattcggtaatgaatctgcatgaactgtttaggattttgacatcatcctaacttgaggagatgtggtctgcatttgtttattcttgactatcgagagtttggtggtgttgtgcag

upper sequence: GRMZM5G876621_T01 (Zea mays), 5'ss of exon 10
lower sequence: PP1S156_28V6.1 (Physcomitrella patens), 5'ss of exon 10
TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCCCTTGAGAGATACACACATTATTATGAACGATGGGCAGCCAATCAGTCGgtaagtattgaatgtggttgaagtga----cctgaaacttcaaat---ctacattagcatggagttcattcagagtgacaattga---tgcatgcca-gctgttctgttgg-------------------------------------------
||||||||| | ||  |||| || || ||||| ||||||||||||||  | |||||||||||||||||||| |||||| | ||| | || || |||   |  |   |||     ||     ||   || | || |   ||   ||  |    | | ||   | | |||| ||  |   |  | || | | |||  |||  |                                           
TATGATGAAGCAGAGCGGAGGAGGGAGATGGCTAAGAACTCCCTTGAACGTTACACACATTATTATGAACGCTGGGCAACGAATGAATCTgtgagtgccggtttgagtttgcacgagttttcttctaccttaattgcgctgtcttttctcacactgcagatacattgactatgtaaattttaggcaatgatgtagtgtgagcttatatttatcatttctgttctaatttcttttatgtgtgcag

upper sequence: GRMZM5G876621_T01 (Zea mays), 5'ss of exon 10
lower sequence: EFJ15174 (Selaginella moellendorffii), 5'ss of exon 10
TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCCCTTGAGAGATACACACATTATTATGAACGATGGGCAGCCAATCAGTCGgt-aagtattgaatgtggttgaagtgacctgaaacttcaaatctacattagcatggagttcattcagagtgacaattgatgcatgccagctgttctgttgg
|| |||||| |||| ||||| ||||||||||| ||||||||  | |||||||| |||||||| || || ||||||||  | ||  | || ||  ||| |  ||| ||  | |  |||   |    ||| ||  |   | |   |  ||                                           
TACGATGAAGCTGAGAGGAGGAGAGAAATGGCTAAGAACTCGTTAGAGAGATATACACATTACTACGAGCGATGGGCCACGAACGAATCAgttgagtttccaatttgagt-atctgata-ggcctttctaacttcgttcatggtacag-------------------------------------------

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 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 132

TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCCCTTGAGAGATACACACATTATTATGAACGATGGGCAGCCAATCAGTCGgtaagtattg ... catggcgcagTCGAGGCAAAAGGCACTGGGGGACCTTCAAAGCCTACAGAATGACAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 115

TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCCCTTGAGAGATACACACATTATTATGAACGATGGGCAGCCAATCAGTCGgtaagtattg ... catggcgcagTCGAGGCAAAAGGCACTGGGGGACCTTCAAAGCCTACAGAATGACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 122

TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCCCTTGAGAGATACACACATTATTATGAACGATGGGCAGCCAATCAGTCGgtaagtattg ... catggcgcagTCGAGGCAAAAGGCACTGGGGGACCTTCAAAGCCTACAGAATGACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 93

TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCCCTTGAGAGATACACACATTATTATGAACGATGGGCAGCCAATCAGTCGgtaagtattg ... catggcgcagTCGAGGCAAAAGGCACTGGGGGACCTTCAAAGCCTACAGAATGACAAG