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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgctccatcccctctctagcactcaaatgcatgtttatttgctattcctaagtggctgaagttacaagatttttcatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGCGTTATTGCAATAATTGTTGTTAAG

Basic information

species Zea mays
transcript GRMZM2G102903_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G102903_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os07g44350.1 (Oryza sativa), 3'ss of exon 8
------------------------------------------------------------------------------------------gtgctccatcccctctctagcactcaaatgcatgtttatttgctattcctaagtggctgaagttacaagatttttcatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGCGTTATTGCAATAATTGTTGTTAAG
                                                                                          |    |    | |  | | | ||  | ||| | || ||||||   |  ||  ||| ||  | ||||||||||  |   | |||||||| |||||||||||||| ||||| ||||| |||||||| |||||||| || |||||||| ||||||||||||
gttctctctctctctctccccccctgcacacacgtatgttactcgtttcgtcccaaaataagtgcagccctctagttcaaatttgaactagaaggctgcactcattttgggac--agatgga-gtatatttgaagtggct--gtgcctagacttacaagattcattgctgcagGTTGCAACTGACAAATGCATCATGGCATTCCTATTTCTGATAGTCTGTGGTGTGATTGCAATCATTGTTGTTAAG

upper sequence: GRMZM2G102903_T02 (Zea mays), 3'ss of exon 8
lower sequence: AT1G48240.1 (Arabidopsis thaliana), 3'ss of exon 8
--------------------------gtgctccatcccctctctagcactcaaatgcatgtttatttgctattcctaagtggctgaagttacaagatttt-tcatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGCGTTATTGCAATAATTGTTGTTAAG
                              || |   |    | |   || ||||   ||| ||  |  |||  |    |   |  |    |||   ||| |  |  ||||| ||||| || |||||||| ||||||||||||||||||||||||||||| ||||| || |||||  |||| |||
gtttgtatgatctctcacaggacataagattctaagacactgcaaaagctaaaat-tgtgtctaactattatcaccgtttcctttcaacctcaattctttcttgtcacagGTAGCTACAGATAAATGCATAATGGCGTTCCTGTTTCTGATTGTCTGTGGTGTTATAGCTATAATCATTGTGAAG

upper sequence: GRMZM2G102903_T02 (Zea mays), 3'ss of exon 8
lower sequence: AT3G17440.2 (Arabidopsis thaliana), 3'ss of exon 8
gtgctccatcccctctcta-gcactcaaatgcatgtttatttgctattcctaagtggctgaagttacaagatttttcatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGCGTTATTGCAATAATTGTTGTTAAG
       | | | | |  |   |   | ||  ||  || || |||   ||| |    |||||     | |  |  | ||||||||| ||||| || |||||||| |||| |||||||||||| ||||| || || ||  | || |||||  | || |||
----gtaacctcatatggacatatgtagatttatcctttttggcttgacctcaaaacctgaatgcttatgtctacttatttcagGTGGCTACCGATAAATGCATAATGGGGTTCCTGTTTCTCATTGTATGCGGTGTAGTAGCCATAATCATAGTGAAG

upper sequence: GRMZM2G102903_T02 (Zea mays), 3'ss of exon 8
lower sequence: AT3G17440.1 (Arabidopsis thaliana), 3'ss of exon 8
gtgctccatcccctctcta-gcactcaaatgcatgtttatttgctattcctaagtggctgaagttacaagatttttcatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGCGTTATTGCAATAATTGTTGTTAAG
|||    | | | | |  |   |   | ||  ||  || || |||   ||| |    |||||     | |  |  | ||||||||| ||||| || |||||||| |||| |||||||||||| ||||| || || ||  | || |||||  | || |||
gtgtgtaacctcatatggacatatgtagatttatcctttttggcttgacctcaaaacctgaatgcttatgtctacttatttcagGTGGCTACCGATAAATGCATAATGGGGTTCCTGTTTCTCATTGTATGCGGTGTAGTAGCCATAATCATAGTGAAG

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|18166823|gb|BM336662.1|BM336662
EST:     GCTTCTCACTGAAGAAGGCCAGTCAAATGGTGAAAGAGATTGGCCGTCAG                         GTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGC
genomic: ACTTCTCACTGAAGAAGGCCAGTCAAATGGTGAAAGAGATTGGCCGTCAGgtgctccatc ... ttcatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGC
EST: gi|78023758|gb|DV492145.1|DV492145
EST:     ACTTCTCACTGAAGAAGGCCAGTCAAATGGTGAAAGAGATTGGCCGTCAG                         GTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGC
genomic: ACTTCTCACTGAAGAAGGCCAGTCAAATGGTGAAAGAGATTGGCCGTCAGgtgctccatc ... ttcatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGC
EST: gi|108823916|gb|EC277924.1|EC277924
EST:     ACTTCTCACTGAACCACGCCAGTCAAATGGTGAAAGAGATTGGTCGTCAA                         GTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGC
genomic: ACTTCTCACTGAAGAAGGCCAGTCAAATGGTGAAAGAGATTGGCCGTCAGgtgctccatc ... ttcatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGC
EST: gi|26457562|gb|CA829145.1|CA829145
EST:     ACTTCTCACTGAAGAAGGCCAGTCAAATGGTGAAAGAGATTGGTCGTCAG                         GTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGC
genomic: ACTTCTCACTGAAGAAGGCCAGTCAAATGGTGAAAGAGATTGGCCGTCAGgtgctccatc ... ttcatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGC
EST: gi|26457605|gb|CA829188.1|CA829188
EST:     ACTTCTCACTGAAGAAGGCCAGTCAAATGGTGAAAGAGATTGGTCGTCAG                         GTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGC
genomic: ACTTCTCACTGAAGAAGGCCAGTCAAATGGTGAAAGAGATTGGCCGTCAGgtgctccatc ... ttcatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGC
EST: gi|22542296|gb|BU092734.1|BU092734
EST:     ACTTCTCACTGAAGAAGGCCAGTCAAATGGTGAAAGAGATTGGTCGTCAG                         GTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGC
genomic: ACTTCTCACTGAAGAAGGCCAGTCAAATGGTGAAAGAGATTGGCCGTCAGgtgctccatc ... ttcatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGC

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), 39 (downstream exon)
Score: 54

ACAGAGCAAATGAAGAGAATCGGCAATGAGTTAGATTCTGTTCACTTCTCACTGAAGAAGGCCAGTCAAATGGTGAAAGAGATTGGCCGTCAGgtgctccatc ... ttcatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGCGTTATTGCAATAATTGTTGTTAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 74

ACAGAGCAAATGAAGAGAATCGGCAATGAGTTAGATTCTGTTCACTTCTCACTGAAGAAGGCCAGTCAAATGGTGAAAGAGATTGGCCGTCAGgtgctccatc ... ttcatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGCGTTATTGCAATAATTGTTGTTAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 38

ACAGAGCAAATGAAGAGAATCGGCAATGAGTTAGATTCTGTTCACTTCTCACTGAAGAAGGCCAGTCAAATGGTGAAAGAGATTGGCCGTCAGgtgctccatc ... ttcatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGCGTTATTGCAATAATTGTTGTTAAG


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 104

ACAGAGCAAATGAAGAGAATCGGCAATGAGTTAGATTCTGTTCACTTCTCACTGAAGAAGGCCAGTCAAATGGTGAAAGAGATTGGCCGTCAGgtgctccatc ... ttcatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGCGTTATTGCAATAATTGTTGTTAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcatgtttatttgctattcctaagtggctgaagttacaagatttttcatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGCGTTATTGCAATAATTGTTGTTAAG
                                          tttttcatttc  CT-rich tract
                                      aagatttttcattt  TA-rich tract