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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATGCATCTGGATGCTGAAAAGGAGATGATGTCACAGTGTGTGGCTCTTCTTGGGAAGTTTATTGCAGTCCGGGAGCCAAACATTCGGTACCTTGGTCTGgtaattgcatttcttattaatgtttacttgattaacaccttttgctggcagtcttgctttcacatcaagttgtgcaagtgtacaatttatcatattgaaacagtaatcgatccatctttcag

Basic information

species Zea mays
transcript GRMZM2G137236_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G137236_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os03g02150.1 (Oryza sativa), 5'ss of exon 9
CATGCATCTGGATGCTGAAAAGGAGATGATGTCACAGTGTGTGGCTCTTCTTGGGAAGTTTATTGCAGTCCGGGAGCCAAACATTCGGTACCTTGGTCTGgtaa-ttgcatt----------------------tcttattaatgtttacttgat-------taacacctt-------ttgctggcagtct-----tgctt---tcacatcaagttgt-gcaagtgtacaatttatcatattgaaacagtaatcgatccatcttt-cag
 |||||||| ||||||||||||||||||||||| ||||| ||||||||||||||||||||||||||||| ||||| ||||| ||| |||| ||||||||||||| ||| | |                      |  |||  ||||||  ||| |       |||    |        || |||  |||||     |||||   || ||| || |    |  |||| | | |||  |||| ||  |  ||| |  |||  ||||  |||
TATGCATCTTGATGCTGAAAAGGAGATGATGTCCCAGTGCGTGGCTCTTCTTGGGAAGTTTATTGCAGTTCGGGAACCAAATATTAGGTATCTTGGTCTGgtaagttgtactttgcaacagtaatactgtttgattctatatatgtttttttggtactttggtaatgtttcgttcacattcctgatagtctataaatgcttcattcgcattaaatccccgtgagtgaaaactttgccataatgtgatggtatttcatctgtcttcacag

upper sequence: GRMZM2G137236_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA17G05410.1 (Glycine max), 5'ss of exon 9
CATGCATCTGGATGCTGAAAAGGAGATGATGTCACAGTGTGTGGCTCTTCTTGGGAAGTTTATTGCAGTCCGGGAGCCAAACATTCGGTACCTTGGTCTGgtaatt------gcatttcttattaatgtttacttgattaacaccttttgctggcagtcttgctttcacat----caagttgtgcaag-------tgtacaatttatcatattgaaacagtaatcgatccatctttcag--------------------------------------------------------
 |||||||| ||||||||||| ||||||||||| || ||||||||||||||||| || |||||||| ||||| || ||||||||||| || |||||  |||||| |      ||||   | ||||||   || ||   |     ||| | ||   | |  || ||  |       ||||   |||| |       | | || |  ||   |||   | ||||   |         |                                                           
GATGCATCTTGATGCTGAAAAAGAGATGATGTCTCAATGTGTGGCTCTTCTTGGAAAATTTATTGCTGTCCGTGAACCAAACATTCGATATCTTGGCTTGgtaagtcggggggcatacttgattaatccatattt--ctcttttcttgttcttttatttctgtttgaaggagggacaaggattgcatgcccaatttctgcagtagatttcattatcatagtagaaggcttggtggtggtggtggttgtcataatgcaatgtcccagttcataacatatatgctattatggtgcag

upper sequence: GRMZM2G137236_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA12G30520.1 (Glycine max), 5'ss of exon 9
CATGCATCTGGATGCTGAAAAGGAGATGATGTCACAGTGTGTGGCTCTTCTTGGGAAGTTTATTGCAGTCCGGGAGCCAAACATTCGGTACCTTGGTCTGgtaatt------gcatttcttattaatgtttacttgattaacaccttttgctggcagtcttgctttcacatcaagttgtgcaagtgtacaatttatcatattgaaacagtaatcgatccatctttcag
 |||||||| ||||||||||| ||||||||||| |||||||||||||||||||| || |||||||| ||||| || ||||||||||| || |||||  |||||| |      |||    | |||||| | || ||   |     ||| |  |     | ||  |||    ||   |||       |  |||   ||   ||                           
GATGCATCTTGATGCTGAAAAAGAGATGATGTCTCAGTGTGTGGCTCTTCTTGGAAAATTTATTGCTGTCCGTGAACCAAACATTCGATATCTTGGCTTGgtaagttggggggcacacttgattaatctgtattt--ctcttttcttgtttttttttttttttttttttttctgtttgaagggaggggcaagg-attgcatgc-------------------------

upper sequence: GRMZM2G137236_T01 (Zea mays), 5'ss of exon 10
lower sequence: AT5G22770.1 (Arabidopsis thaliana), 5'ss of exon 9
CATGCATCTGGATGCTGAAAAGGAGATGATGTCACAGTGTGTGGCTCTTCTTGGGAAGTTTATTGCAGTCCGGGAGCCAAACATTCGGTACCTTGGTCTGgtaattgcatttcttattaatgtttacttgattaacaccttttgctggcagtcttgctttcacatcaagttgtgcaagtgtacaatttatcatattgaaacagtaatcgatccatctttcag
||||||||| |||||||| ||||| ||||||||||||||||| ||||||||||| ||||||||| | ||||| ||||| |||||  | || || ||  |||| |    || |   || |    || ||  ||  |  |||   |||||     | | ||    |     | |||       |  ||  ||  | |||| | | | |  |             
CATGCATCTTGATGCTGAGAAGGAAATGATGTCACAGTGTGTTGCTCTTCTTGGCAAGTTTATTTCTGTCCGTGAGCCCAACATCAGATATCTAGGCTTGgtga---gatcttgcat-accacttcctgcatctaagccta--gctggag---tagtttgtgaagtggttggtggtttctcatgatgcatt-ttttgacaaaattacag-------------

upper sequence: GRMZM2G137236_T01 (Zea mays), 5'ss of exon 10
lower sequence: AT5G22780.1 (Arabidopsis thaliana), 5'ss of exon 9
CATGCATCTGGATGCTGAAAAGGAGATGATGTCACAGTGTGTGGCTCTTCTTGGGAAGTTTATTGCAGTCCGGGAGCCAAACATTCGGTACCTTGGTCTGgtaattgcatttcttattaatgtttacttgattaacaccttttgctggcagtcttgctttcacatcaagt-tgtgcaagtgtacaatttatcatattgaaacagtaatcgatccatctttcag
||||||||| |||||||| ||||| ||||||||||||||||| ||||||||||| ||||||||| | ||||| ||||| |||||  | || || ||  |||| |    || |   ||      || ||  ||  |  |  || ||| | |   |   ||     | |||| | ||  |||| |  || |  | | |    |   |  | || | |  || |||
CATGCATCTTGATGCTGAGAAGGAAATGATGTCACAGTGTGTTGCTCTTCTTGGCAAGTTTATTTCTGTCCGTGAGCCCAACATCAGATATCTAGGCTTGgtga---gatcttgcatacccacttcctgcatctaagc--ttagctagaacagtaattt----gttaagtatttggtagtgcattatgtggcttctcatgatgcttgttga-caacattgcag

upper sequence: GRMZM2G137236_T01 (Zea mays), 5'ss of exon 10
lower sequence: Vv06s0061g01170.t01 (Vitis vinifera), 5'ss of exon 9
CATGCATCTGGATGCTGAAAAGGAGATGATGTCACAGTGTGTGGCTCTTCTTGGGAAGTTTATTGCAGTCCGGGAGCCAAACATTCGGTACCTTGGTCTGgtaa-ttgcatttcttattaatgtttacttgattaacaccttttgctggcagtcttgctttcacatcaagttgtgcaagtgtacaatttatcata--ttgaaacagtaatcgatccatctttcag----------------------------------------
||||||||||||||||||||| || |||||||| || ||||| ||  | |||||||| |||||||| || || |||||||| || || || |||||| |||||| || ||       |  || | | |||   | |   |||   ||     ||      | | | ||  |    |  |  | ||   | | | |  |||||    |    |      ||| | |                                        
CATGCATCTGGATGCTGAAAAAGAAATGATGTCTCAATGTGTTGCCTTGCTTGGGAAATTTATTGCTGTACGAGAGCCAAATATACGATATCTTGGTTTGgtaagttacaggatggttctatctgtgcttccgttatgtcttcacctat--atccaatgattaaagcatatcaaactggcatgcaccatgttagaatttgaatggattgatgtcattgcttgctgtctaactgcatgatttgacatttagattactctgctgcag

upper sequence: GRMZM2G137236_T01 (Zea mays), 5'ss of exon 10
lower sequence: EFJ34224 (Selaginella moellendorffii), 5'ss of exon 9
CATGCATCTGGATGCTGAAAAGGAGATGATGTCACAGTGTGTGGCTCTTCTTGGGAAGTTTATTGCAGTCCGGGAGCCAAACATTCGGTACCTTGGTCTGgtaattgcatttctta--ttaatgtttacttgattaacaccttttgctggcagtcttgctttcacatcaagttgtgcaagtgtacaatttatcatattgaaacagtaatcgatccatctttcag
 |||||| | || || || || || |||||| |||| ||||| | ||| ||||| ||||||||||| ||||| ||||| |||||||| || ||||| ||||||     |||| |    |||   | ||||| |        |||  ||| |||                                                                       
GATGCATTTAGACGCAGAGAAAGATATGATGGCACAATGTGTTGGTCTACTTGGAAAGTTTATTGCTGTCCGTGAGCCCAACATTCGATATCTTGGACTGgtatggatatttgtggccttacgctatactttacct-tgtttttcactg-cag-----------------------------------------------------------------------

upper sequence: GRMZM2G137236_T01 (Zea mays), 5'ss of exon 10
lower sequence: EFJ21842 (Selaginella moellendorffii), 5'ss of exon 9
CATGCATCTGGATGCTGAAAAGGAGATGATGTCACAGTGTGTGGCTCTTCTTGGGAAGTTTATTGCAGTCCGGGAGCCAAACATTCGGTACCTTGGTCTGgtaattgcatttcttat--taatgtttacttgattaacaccttttgctggcagtcttgctttcacatcaagttgtgcaagtgtacaatttatcatattgaaacagtaatcgatccatctttcag
 |||||| | || || || || || |||||| |||| ||||| | ||| ||||| ||||||||||| ||||| ||||| |||||||| || ||||| ||||||     |||| |     ||   | ||||| |        |||  ||| |||                                                                       
GATGCATTTAGACGCAGAGAAAGATATGATGGCACAATGTGTTGGTCTACTTGGAAAGTTTATTGCTGTCCGTGAGCCCAACATTCGATATCTTGGACTGgtatggatatttgtggccctacgctatactttacct-tgtttttcactg-cag-----------------------------------------------------------------------

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: 47 (upstream exon), 49 (downstream exon)
Score: 145

CATGCATCTGGATGCTGAAAAGGAGATGATGTCACAGTGTGTGGCTCTTCTTGGGAAGTTTATTGCAGTCCGGGAGCCAAACATTCGGTACCTTGGTCTGgtaattgcat ... catctttcagGAAAACATGACTAGGATGCTGTTAGTAACAGATGTGCAGGATATCATTAAAAGGCACCAGGCTCAGATCATCACATCTTTGAAGGATCCAGATATCAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 130

CATGCATCTGGATGCTGAAAAGGAGATGATGTCACAGTGTGTGGCTCTTCTTGGGAAGTTTATTGCAGTCCGGGAGCCAAACATTCGGTACCTTGGTCTGgtaattgcat ... catctttcagGAAAACATGACTAGGATGCTGTTAGTAACAGATGTGCAGGATATCATTAAAAGGCACCAGGCTCAGATCATCACATCTTTGAAGGATCCAGATATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 89

CATGCATCTGGATGCTGAAAAGGAGATGATGTCACAGTGTGTGGCTCTTCTTGGGAAGTTTATTGCAGTCCGGGAGCCAAACATTCGGTACCTTGGTCTGgtaattgcat ... catctttcagGAAAACATGACTAGGATGCTGTTAGTAACAGATGTGCAGGATATCATTAAAAGGCACCAGGCTCAGATCATCACATCTTTGAAGGATCCAGATATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 186

CATGCATCTGGATGCTGAAAAGGAGATGATGTCACAGTGTGTGGCTCTTCTTGGGAAGTTTATTGCAGTCCGGGAGCCAAACATTCGGTACCTTGGTCTGgtaattgcat ... catctttcagGAAAACATGACTAGGATGCTGTTAGTAACAGATGTGCAGGATATCATTAAAAGGCACCAGGCTCAGATCATCACATCTTTGAAGGATCCAGATATCAG