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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTGGAGAATCACTGAGAGATTTCTACAAGAGGACAAATATGTACTGGCAAATGGCTGCCTATGAGCACACTCAACACACTGGAAAGgttagtttccatttctcgaatttccatcattggtcagctagtatatcatccttaataaaacgtgttgcatgtaatcctgtacacccaacggcag

Basic information

species Zea mays
transcript GRMZM2G100815_T01
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G100815_T01 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os04g40740.4 (Oryza sativa), 5'ss of exon 10
-------------CCTGGAGAATCACTGAGAGATTTCTACAAGAGGACAAATATGTACTGGCAAATGGCTGCCTATGAGCACACTCAACACACTGGAAAGgttagtttccatttctcgaatttccatcattggtca-----gctagtatatcatcc------ttaataaaacg----tgttgcatgtaatcctgtacacccaacggcag
             || ||||| ||||| | ||||||||||||||| ||  ||||||||||||| |||||||| ||||||||||||||||||||||||||||||||||||   | ||  | | ||  |||   ||||     | ||  ||||  ||        |   |  | |    || || || || || ||  || |||| | |||
CACACTTTTAAAGCCAGGAGAGTCACTAAAAGATTTCTACAAGAGAACGGATATGTACTGGCAGATGGCTGCATATGAGCACACTCAACACACTGGAAAGgttagtttctgctccttaagtatct-tcacccgtcatacctgttatcatattctctaggttgctggcagtatgagtttgctgtatttattcgtgctcatccaatgccag

upper sequence: GRMZM2G100815_T01 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os04g40740.1 (Oryza sativa), 5'ss of exon 18
CCTGGAGAATCACTGAGAGATTTCTACAAGAGGACAAATATGTACTGGCAAATGGCTGCCTATGAGCACACTCAACACACTGGAAAGgttagtttccatttctcgaatttccatcattggtca-----gctagtatatcatcc------ttaataaaacg----tgttgcatgtaatcctgtacacccaacggcag
|| ||||| ||||| | ||||||||||||||| ||  ||||||||||||| |||||||| ||||||||||||||||||||||||||||||||||||   | ||  | | ||  |||   ||||     | ||  ||||  ||        |   |  | |    || || || || || ||  || |||| | |||
CCAGGAGAGTCACTAAAAGATTTCTACAAGAGAACGGATATGTACTGGCAGATGGCTGCATATGAGCACACTCAACACACTGGAAAGgttagtttctgctccttaagtatct-tcacccgtcatacctgttatcatattctctaggttgctggcagtatgagtttgctgtatttattcgtgctcatccaatgccag

upper sequence: GRMZM2G100815_T01 (Zea mays), 5'ss of exon 15
lower sequence: GLYMA04G36770.1 (Glycine max), 5'ss of exon 18
CCTGGAGAATCACTGAGAGATTTCTACAAGAGGACAAATATGTACTGGCAAATGGCTGCCTATGAGCACACTCAACACACTGGAAAGgttagtttccatttctcgaatttcc--atcat-tggtcagctagtatatcatccttaataaaacgtgttgcatg---taatcctgtacacccaacggcag
|| ||||||||  |||  |||||||||| | | ||||||||||| ||||||||||| ||| |||| || ||||||||||||||||| ||  |||| |  |  |    ||  |   | || || |   ||  ||  |   | |||||| ||  | |   ||    |||     |    |||  |  | 
CCAGGAGAATCCTTGAAGGATTTCTACAGGCGTACAAATATGTATTGGCAAATGGCAGCCCATGAACATACTCAACACACTGGAAAAgtaggttttctctcttttctttctctagttatgtgattctcttataacttccctttaatataaattttctaattctctaaattaatcattccattgttat

upper sequence: GRMZM2G100815_T01 (Zea mays), 5'ss of exon 15
lower sequence: GLYMA06G18170.1 (Glycine max), 5'ss of exon 17
-------------CCTGGAGAATCACTGAGAGATTTCTACAAGAGGACAAATATGTACTGGCAAATGGCTGCCTATGAGCACACTCAACACACTGGAAAGgttagtttccatttctcgaatttccatcat-tggtcagctagtatatcatccttaataaaa-cgtgttgcat---gtaatcctgtacacccaacggcag---
             || ||||||||  |||| |||||||||| | | ||||||||||| ||||||||||| ||| |||| || ||||||||||||||||| ||  |||| |  || ||    |    | || || |   ||  |||| | |||    ||||| | | ||   |   |||||    |       | |       
GTTGCATCCCAAGCCAGGAGAATCCTTGAGGGATTTCTACAGGCGTACAAATATGTATTGGCAAATGGCAGCCCATGAACATACTCAACACACTGGAAAAgtaggttttctcttttctttctctagttatatgattctct--tataacttcccatgtaaaatcatattatctttggtaatttgatttgttttatgaacctag

upper sequence: GRMZM2G100815_T01 (Zea mays), 5'ss of exon 15
lower sequence: AT5G50310.1 (Arabidopsis thaliana), 5'ss of exon 18
CCTGGAGAATCACTGAGAGATTTCTACAAGAGGACAAATATGTACTGGCAAATGGCTGCCTATGAGCACACTCAACACACTGGAAAGgt-----tagtttccatttctcgaatttccat-cattggtcagctagtatatcatccttaataaaacgtgttgcatgtaatcctgtacacccaacggcag-----
||||||||| |  |||  |||||||| ||| | ||||||||||||||||||||||||||||| ||||| || ||||| ||||| |||||     || | |   | | || |     |||  | ||         | || || | ||  |     ||  |     | ||    | |||     ||||      
CCTGGAGAAACTTTGAAGGATTTCTATAAGCGCACAAATATGTACTGGCAAATGGCTGCCTACGAGCATACCCAACATACTGGCAAGgtatgcttaatctgtgtgtttcaatcaagcatataatgactcatatttgtagcaactttgtt---ctgtccttggcatgatatgattcacatgttggcattgtag

upper sequence: GRMZM2G100815_T01 (Zea mays), 5'ss of exon 15
lower sequence: Vv17s0000g10130.t01 (Vitis vinifera), 5'ss of exon 18
CCTGGAGAATCACTGAGAGATTTCTACAAGAGGACAAATATGTACTGGCAAATGGCTGCCTATGAGCACACTCAACACACTGGAAAGgttagtttccatttctcgaatttccatcattggtcagctagtatatcatccttaataaaacgtgttgcatgtaatcctgtacacccaacggcag--------
||||||||| |  |||  || ||||| ||| | || ||| |||||||||||||||| ||  ||||||||||||||||||||||||||||  |||   |  | |  |  ||   |  | |      |  | | | | |  |  |  |  || ||  || |   | ||  ||  |||  |  |        
CCTGGAGAAACCTTGAAGGACTTCTATAAGCGTACCAATTTGTACTGGCAAATGGCAGCACATGAGCACACTCAACACACTGGAAAGgtctgttcataagttttaatattagctggtagacattttgctctcttagctcttgttcattgtcttcaatttg--cttgaccaatcaattgaggtgaaggta

upper sequence: GRMZM2G100815_T01 (Zea mays), 5'ss of exon 15
lower sequence: EFJ09772 (Selaginella moellendorffii), 5'ss of exon 16
CCTGGAGAATCACTGAGAGATTTCTACAAGAGGACAAATATGTACTGGCAAATGGCTGCCTATGAGCACACTCAACACACTGGAAAGgttagtttccatttctcgaatttccatcattggtcagctagtatatcatccttaataaaacgtgttgcatgtaatcctgtacacccaacggcag
||||| ||| | ||||||||||| | |    |||| |  ||||| |||||||||||||| || || ||||| ||||||||||||||||| |     ||  | |    ||||  || ||  |||     | |  ||||  | |                                       
CCTGGGGAAACGCTGAGAGATTTTTTCTCCCGGACGATCATGTATTGGCAAATGGCTGCTTACGACCACACCCAACACACTGGAAAGgtgatgacgcaggtttt--ctttcgctcgttcttcatgctctttg-catctatcag--------------------------------------

upper sequence: GRMZM2G100815_T01 (Zea mays), 5'ss of exon 15
lower sequence: EFJ11619 (Selaginella moellendorffii), 5'ss of exon 16
CCTGGAGAATCACTGAGAGATTTCTACAAGAGGACAAATATGTACTGGCAAATGGCTGCCTATGAGCACACTCAACACACTGGAAAGgttagtttccatttctcgaatttccatcattggtcagctagtatatcatccttaataaaacgtgttgcatgtaatcctgtacacccaacggcag
||||| ||| | ||||||||||| | |    |||| |  ||||| |||||||||||||| || || ||||| ||||||||||||||||| |     ||  | |    ||||  || ||  |||     | || ||||  | |                                       
CCTGGGGAAACGCTGAGAGATTTTTTCTCCCGGACGATCATGTATTGGCAAATGGCTGCTTACGACCACACCCAACACACTGGAAAGgtgatgacgcaggtttttt-tttcgctcgttcttcatgctcttta-catctatcag--------------------------------------

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|60351145|gb|DN218118.1|DN218118
EST:     ATATGTACTGGCAAATGGCTGCCTATGAGCACACTCAACACACTGGAAAG                         GAGCTCCGCAAAGACGGTTTTGATCTTGCCGAAACTCGATTCAAGGAACTG
genomic: ATATGTACTGGCAAATGGCTGCCTATGAGCACACTCAACACACTGGAAAGgttagtttcc ... ccaacggcagGAGCTCCGCAAAGACGGTTTTGATCTTGCCGAAACTCGATTCAAGGAACTG
EST: gi|148980754|gb|EE027321.2|EE027321
EST:     ATATGTACTGGCAAATGGCTGCCTATGAGCACACTCAACACACTGGAAAG                         GAGCTCCGCAAAGACGGTTTTGATCTTGCCGAAACTCGATTCAAGGAACTG
genomic: ATATGTACTGGCAAATGGCTGCCTATGAGCACACTCAACACACTGGAAAGgttagtttcc ... ccaacggcagGAGCTCCGCAAAGACGGTTTTGATCTTGCCGAAACTCGATTCAAGGAACTG
EST: gi|18179195|gb|BM380405.1|BM380405
EST:     CTGCCTATGAGCACACTCAACACACTGGAAAG                         GAGCTCCGCAAAGACGGTTTTGATCTTGCCGAAACTCGATTCAAGGAACTG
genomic: CTGCCTATGAGCACACTCAACACACTGGAAAGgttagtttcc ... ccaacggcagGAGCTCCGCAAAGACGGTTTTGATCTTGCCGAAACTCGATTCAAGGAACTG

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), 47 (downstream exon)
Score: 104

CCTGGAGAATCACTGAGAGATTTCTACAAGAGGACAAATATGTACTGGCAAATGGCTGCCTATGAGCACACTCAACACACTGGAAAGgttagtttcc ... ccaacggcagGAGCTCCGCAAAGACGGTTTTGATCTTGCCGAAACTCGATTCAAGGAACTGAAACCGATACTTGACGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 64

CCTGGAGAATCACTGAGAGATTTCTACAAGAGGACAAATATGTACTGGCAAATGGCTGCCTATGAGCACACTCAACACACTGGAAAGgttagtttcc ... ccaacggcagGAGCTCCGCAAAGACGGTTTTGATCTTGCCGAAACTCGATTCAAGGAACTGAAACCGATACTTGACGAG


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 45

CCTGGAGAATCACTGAGAGATTTCTACAAGAGGACAAATATGTACTGGCAAATGGCTGCCTATGAGCACACTCAACACACTGGAAAGgttagtttcc ... ccaacggcagGAGCTCCGCAAAGACGGTTTTGATCTTGCCGAAACTCGATTCAAGGAACTGAAACCGATACTTGACGAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 51

CCTGGAGAATCACTGAGAGATTTCTACAAGAGGACAAATATGTACTGGCAAATGGCTGCCTATGAGCACACTCAACACACTGGAAAGgttagtttcc ... ccaacggcagGAGCTCCGCAAAGACGGTTTTGATCTTGCCGAAACTCGATTCAAGGAACTGAAACCGATACTTGACGAG