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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGTTGGCAAATTTGCTTGGTTGTTGCTGTGAAGGCGATGAGAGATTGCTTGTTGCAGAATACATGCCCAATGATACGCTAGCGAAGCACCTTTTCCATTgtgagttctttgaaaacatagttatgtttagcattacaaaacaatttgcattcataatctgttgcttgactacaaggaattaaggatgatgccatgacat...

Basic information

species Zea mays
transcript GRMZM2G382104_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G382104_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os04g58750.2 (Oryza sativa), 5'ss of exon 4
-AGGTTGGCAAATTTGCTTGGTTGTTGCTGTGAAGGCGATGAGAGATTGCTTGTTGCAGAATACATGCCCAATGATACGCTAGCGAAGCACCTTTTCCATTgtgagtt-ctttgaaaacatagttatgtttagcattacaaaacaatttgcattcataatc-tgttgcttgactacaaggaattaaggatgatgccatgacat--
 ||||| |||| ||||||||| |||||||| ||||| || ||||||||||||||||||||||||||||||||||| || ||||||||||| ||||||||||||||||| |  || |    | ||    |   || |||  ||    | ||      | |||   |   ||    ||  ||   |    ||| |  |||  |    
AAGGTTAGCAA-TTTGCTTGGCTGTTGCTGCGAAGGTGACGAGAGATTGCTTGTTGCAGAATACATGCCCAATGACACACTAGCGAAGCATCTTTTCCATTgtgagttgccatgcatttcttgtcgcat---gcctta-gaacttttatgttgctgtcatcacatcaattagtaactgggttctgttcatggttacatttccgca

upper sequence: GRMZM2G382104_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA05G37870.1 (Glycine max), 5'ss of exon 5
AGGTTGGCAAATTTGCTTGGTTGTTGCTGTGAAGGCGATGAGAGATTGCTTGTTGCAGAATACATGCCCAATGATACGCTAGCGAAGCACCTTTTCCATTgtgagttctttgaaaaca--tagttatgtttagcattacaaaacaatttgcattcataatctgttgcttgactacaaggaattaaggatgatgccatgacat
|| |||  |||| ||||||| ||||| |||||||| || || || || |||||||||||||| ||||||||||||||  |  | |||||  | ||||||||| ||| | |    | ||  || ||  ||||  |  | ||  |   || ||||| |     |   | |  |   ||     |||      |  | ||    |
AGATTGATAAATCTGCTTGGATGTTGTTGTGAAGGTGAAGAAAGGTTACTTGTTGCAGAATATATGCCCAATGATACTTTGACAAAGCATTTATTCCATTgtaagtgcataactagcaattaattcagtttgcc--tgcattagctttggcatttacttgtttgggttctaggtcagactcttatcctgaacacaatctggt

upper sequence: GRMZM2G382104_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA08G01730.2 (Glycine max), 5'ss of exon 4
AGGTTGGCAAATTTGCTTGGTTGTTGCTGTGAAGGCGATGAGAGATTGCTTGTTGCAGAATACATGCCCAATGATACGCTAGCGAAGCACCTTTTCCATTgtgagttctttgaaaacatagttatgtttagcattacaaaacaatttgcattcataatctgtt-gcttgactacaaggaattaaggatgatgccatgacat--
|| |||  |||| ||||||| ||||| |||||||| || || || || |||||||||||||| ||||||||||||||  | || |||||  | ||||||||| ||| | |  ||   | | |||  || ||  |  ||  |  |  |       | |  |||| |  |   || |   || |       |  |  ||||    
AGATTGATAAATCTGCTTGGATGTTGTTGTGAAGGTGAAGAAAGGTTACTTGTTGCAGAATATATGCCCAATGATACTTTGGCAAAGCATTTATTCCATTgtaagtgcat--aactgacaatta-attcagtttgccagcattagctttgccatttacttgtttgtatttttaaatcaaactcttatctaaccagtgactgag

upper sequence: GRMZM2G382104_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA03G01300.2 (Glycine max), 5'ss of exon 4
AGGTTGGCAAATTTGCTTGGTTGTTGCTGTGAAGGCGATGAGAGATTGCTTGTTGCAGAATACATGCCCAATGATACGCTAGCGAAGCACCTTTTCCATTgt--gagttctttgaaaacatagttatgtttagcat-tacaaaacaatttgcattcata-atctgttgcttgactacaaggaattaaggatgatgccatgacat
||||||||||||||||||||||||||||||||||| || ||||| |||||||| |||||||| ||||||||||| || || || ||||||||||| ||||||  ||| || ||  |  |||  ||   |     |  |    |||| | || |||  ||  |||     || |  | | | | || | | |  ||         
AGGTTGGCAAATTTGCTTGGTTGTTGCTGTGAAGGGGAGGAGAGGTTGCTTGTGGCAGAATATATGCCCAATGAAACACTTGCAAAGCACCTTTTTCATTgtaagagctccttttatgcattttttaatcctttaagtgttgaaca-tctg-attggtatgtcttaaatttaataatatgtagtttacggttttgttgcctt--

upper sequence: GRMZM2G382104_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA07G07850.2 (Glycine max), 5'ss of exon 4
AGGTTGGCAAATTTGCTTGGTTGTTGCTGTGAAGGCGATGAGAGATTGCTTGTTGCAGAATACATGCCCAATGATACGCTAGCGAAGCACCTTTTCCATTgt--gagttctttgaaaacatagtt---atgtttagcattacaaaacaatttgcattcataatctgttgcttgactacaaggaattaaggatgatgccatgacat
||||||||||||||||||||||||||||||||||| || ||||| |||||||| |||||||| ||||||||||| || || || ||||||||||| ||||||  ||| || ||  |  |||  ||   ||   |   | | |  ||||  |       ||    |     |    |  | ||  ||   |||  |  | |     
AGGTTGGCAAATTTGCTTGGTTGTTGCTGTGAAGGAGAGGAGAGGTTGCTTGTGGCAGAATATATGCCCAATGAAACACTTGCAAAGCACCTTTTTCATTgtaagagctccttttatgcattttttttattcctttaagtgctgaacatctgatcactatgtcttaaatttatggtttacggttttgttgatttttgctt-----

upper sequence: GRMZM2G382104_T02 (Zea mays), 5'ss of exon 4
lower sequence: Vv15s0046g02900.t01 (Vitis vinifera), 5'ss of exon 4
AGGTTGGCAAATTTGCTTGGTTGTTGCTGTGAAGGCGATGAGAGATTGCTTGTTGCAGAATACATGCCCAATGATACGCTAGCGAAGCACCTTTTCCATTgtgagttctttgaaaacatagttatgtttagcattacaaaacaatttgcattcataatctgttgcttgactacaaggaattaaggatgatgccatgacat
|| ||||||||||||||||||||||| ||||| |   |||| || ||||| || || ||||| ||||||||||| || || || || ||||||||||||||| |||| || | | |   |    ||||    |   |  ||   ||      |||    |      ||  |   |    ||     || | |      ||
AGATTGGCAAATTTGCTTGGTTGTTGTTGTGAGGATAATGAAAGGTTGCTGGTGGCGGAATATATGCCCAATGAAACACTTGCAAAACACCTTTTCCATTgtaagtttttggtacaggaataactgttgtaaagctctcaatggttctttagcatgtgttagaagatgttttttaacctttgcacttgttcctgatgtat

upper sequence: GRMZM2G382104_T02 (Zea mays), 5'ss of exon 4
lower sequence: Vv02s0025g03550.t01 (Vitis vinifera), 5'ss of exon 5
AGGTTGGCAAATTTGCTTGGTTGTTGCTGTGAAGGCGATGAGAGATTGCTTGTTGCAGAATACATGCCCAATGATACGCTAGCGAAGCACCTTTTCCATTgtgagttctttgaaaacatagttatgtttagcattacaaaacaatttgcattcataatctgttgcttgactacaaggaattaaggatgatgccatgacat
|| ||||||||||||||||||||||| | |||||| |||||||| || ||||| |||||||  ||||||||||| || || || |||||||| || |||||| ||||  ||  | |   |        |  | || || |    || |||||  |      ||  ||   |  ||| |||  |   |   |  |    ||
AGATTGGCAAATTTGCTTGGTTGTTGTTCTGAAGGAGATGAGAGGTTACTTGTCGCAGAATTTATGCCCAATGACACACTTGCAAAGCACCTGTTTCATTgtaagtttcttagacatgcaacatctggtgaccttgcatatgctttagcatttgtgcaacatttattttatttaagaaatctatatttgggatactcaat

upper sequence: GRMZM2G382104_T02 (Zea mays), 5'ss of exon 4
lower sequence: PP1S122_66V6.1 (Physcomitrella patens), 5'ss of exon 3
AGGTTGGCAAATTTGCTTGGTTGTTGCTGTGAAGGCGATGAGAGATTGCTTGTTGCAGAATACATGCCCAATGATACGCTAGCGAAGCACCTTTTCCATTgtgagt------tctttgaaaacata-gttatgtttagcattacaaaacaatttgcattcataatctgttgcttgactacaaggaattaaggatgatgccatgacat-----------------------------------------------------------------------------------
|| ||||  |||||| | || |  |||||||| || |||||| |||| |||||||| ||||||||||||||||| || ||  | |  ||  | || || |||  ||      ||||  |   | |  ||| | |||    || |    || ||    | ||||       | |     | |    |   || || || |||     |                                                                                   
AGATTGGTGAATTTGATCGGCTACTGCTGTGAGGGTGATGAGCGATTACTTGTTGCGGAATACATGCCCAATGACACTCTTTCTAGACATTTATTTCACTgtaggtgctctttcttgtagtgcgtccgttttttttcttttttcttttcacttaagttgcata--tcacagatccttcatagaagacggagcattatcccaatctttacggttgagttgaagagcgcaattttatcgtttcggctttccgtaaagatggttaaggtttgttgatttttgaaaatgcacag

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: 48 (upstream exon), 49 (downstream exon)
Score: 155

AGGTTGGCAAATTTGCTTGGTTGTTGCTGTGAAGGCGATGAGAGATTGCTTGTTGCAGAATACATGCCCAATGATACGCTAGCGAAGCACCTTTTCCATTgtgagttctt ... catttctcagGGGAGTCACAATCAATGAAATGGACCATGAGATTAAGGGTTGTTCTCTGTCTCGCTGAGGCTTTAGAATATTGCACTAACAGGGGCCGTGCTCTCTACCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 88

AGGTTGGCAAATTTGCTTGGTTGTTGCTGTGAAGGCGATGAGAGATTGCTTGTTGCAGAATACATGCCCAATGATACGCTAGCGAAGCACCTTTTCCATTgtgagttctt ... catttctcagGGGAGTCACAATCAATGAAATGGACCATGAGATTAAGGGTTGTTCTCTGTCTCGCTGAGGCTTTAGAATATTGCACTAACAGGGGCCGTGCTCTCTACCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 119

AGGTTGGCAAATTTGCTTGGTTGTTGCTGTGAAGGCGATGAGAGATTGCTTGTTGCAGAATACATGCCCAATGATACGCTAGCGAAGCACCTTTTCCATTgtgagttctt ... catttctcagGGGAGTCACAATCAATGAAATGGACCATGAGATTAAGGGTTGTTCTCTGTCTCGCTGAGGCTTTAGAATATTGCACTAACAGGGGCCGTGCTCTCTACCA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 98

AGGTTGGCAAATTTGCTTGGTTGTTGCTGTGAAGGCGATGAGAGATTGCTTGTTGCAGAATACATGCCCAATGATACGCTAGCGAAGCACCTTTTCCATTgtgagttctt ... catttctcagGGGAGTCACAATCAATGAAATGGACCATGAGATTAAGGGTTGTTCTCTGTCTCGCTGAGGCTTTAGAATATTGCACTAACAGGGGCCGTGCTCTCTACCA