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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttttcttcacctaccatttgcttttcatttcatattactttttgaattagactgacattcagtgttgctgtctccagGAGGTCACTGGGATATACACAAATAATTTTGACCTGTCTTTGAATACAAAGAATGGTTTCCCTGTTTTTGCCACAGTGGTTGAGGCAAACTATGTGGCAA

Basic information

species Zea mays
transcript GRMZM2G139894_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G139894_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os11g29380.1 (Oryza sativa), 3'ss of exon 8
gtaatttttcttcacctaccatttgcttttcatttcatattactttttgaattagactgacattcagtgttg--ctgtctccagGAGGTCACTGGGATATACACAAATAATTTTGACCTGTCTTTGAATACAAAGAATGGTTTCCCTGTTTTTGCCACAGTGGTTGAGGCAAACTATGTGGCAA
|||| | |||| ||  |||| |||   ||||  | ||| ||| | |   ||  |   |   ||| | | |    |  | | ||||||||||||||||||||||| || ||||||||| |||||||||||||||||||||||||||| |||||||||||||| || |||||||||||||||||||
gtaagtcttctgcatgtaccttttttatttc--tacatcttattgtagaaagcatgttctaattgactatctgcccatgttcagGAGGTCACTGGGATATACACCAACAATTTTGACTTGTCTTTGAATACAAAGAATGGTTTCCCAGTTTTTGCCACAGTAGTGGAGGCAAACTATGTGGCAA

upper sequence: GRMZM2G139894_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT1G44900.1 (Arabidopsis thaliana), 3'ss of exon 6
--gtaatttttcttcacctaccatttgcttttcattt-catat-tactttttgaattagac-tgacattcagtgttg--ctgtctccagGAGGTCACTGGGATATACACAAATAATTTTGACCTGTCTTTGAATACAAAGAATGGTTTCCCTGTTTTTGCCACAGTGGTTGAGGCAAACTATGTGGCAA
      |  |  |  |    || | |    | | |   || || ||  |  | ||| |  | ||  ||   |  |||   | | | |||||||| ||||| ||||| || || || |||||||| |||||||| ||||||||||| || || || |||||||| ||||| || || ||||||||  |||
gtacgttcatcatatattagccttctagaatacttgcacacatgtatatgatcaatcattcatgttatcttgcattggattttttgcagGAGGTTACTGGCATATATACCAACAACTTTGACCTATCTTTGAACACAAAGAATGGGTTTCCAGTCTTTGCCACTGTGGTGGAAGCTAACTATGTTACAA

upper sequence: GRMZM2G139894_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv01s0150g00390.t01 (Vitis vinifera), 3'ss of exon 7
------------------------------gtaatttttctt-cacct-accatttgcttttcatttcatattactttttgaattagactgacat--tcagtgttgctgtctccagGAGGTCACTGGGATATACACAAATAATTTTGACCTGTCTTTGAATACAAAGAATGGTTTCCCTGTTTTTGCCACAGTGGTTGAGGCAAACTATGTGGCAA
                               |  ||||| || ||| | |  ||     ||    |    ||| |    |||| |    | ||||  ||  |||   |   | ||||||||||| || || ||||| |||||||||||||| ||  ||||||| |||||||| || ||||| |||||||| || || |||||||| |||||  |||
gtaatacccttatgtctgcacttcttttatctggtttttgttgcacttgattatcctggttatgatagggattgccacctgaacttctgttacatgttccatgtgatttatttcagGAGGTCACAGGTATTTACACGAATAATTTTGACCTCTCCCTGAATACGAAGAATGGATTTCCTGTATTTGCCACTGTAGTCGAGGCAAATTATGTCACAA

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|211351168|gb|FL066628.1|FL066628
EST:     TCATACTTCTGAATGATCTGATTGACTGTGCTCGTCCAGGAGAGGAGATT                         GAGGTCACTGGGATATACACAAATAATTTTGACCTGTCTTTGAATACAAAG
genomic: TCATACTTCTGAATGATCTGATTGACTGTGCTCGTCCAGGAGAGGAGATTgtaatttttc ... ctgtctccagGAGGTCACTGGGATATACACAAATAATTTTGACCTGTCTTTGAATACAAAG
EST: gi|211351172|gb|FL066632.1|FL066632
EST:     TCATACTTCTGAATGATCTGATTGACTGTGCTCGTCCAGGAGAGGAGATT                         GAGGTCACTGGGATATACACAAATAATTTTGACCTGTCTTTGAATACAAAG
genomic: TCATACTTCTGAATGATCTGATTGACTGTGCTCGTCCAGGAGAGGAGATTgtaatttttc ... ctgtctccagGAGGTCACTGGGATATACACAAATAATTTTGACCTGTCTTTGAATACAAAG

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), 49 (downstream exon)
Score: 392

GGAAAGCCCAGGAATTGTTCCTGCTGGAAGGCTTCCCAGATACAAGGAAGTCATACTTCTGAATGATCTGATTGACTGTGCTCGTCCAGGAGAGGAGATTgtaatttttc ... ctgtctccagGAGGTCACTGGGATATACACAAATAATTTTGACCTGTCTTTGAATACAAAGAATGGTTTCCCTGTTTTTGCCACAGTGGTTGAGGCAAACTATGTGGCAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 71

GGAAAGCCCAGGAATTGTTCCTGCTGGAAGGCTTCCCAGATACAAGGAAGTCATACTTCTGAATGATCTGATTGACTGTGCTCGTCCAGGAGAGGAGATTgtaatttttc ... ctgtctccagGAGGTCACTGGGATATACACAAATAATTTTGACCTGTCTTTGAATACAAAGAATGGTTTCCCTGTTTTTGCCACAGTGGTTGAGGCAAACTATGTGGCAA


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 48

GGAAAGCCCAGGAATTGTTCCTGCTGGAAGGCTTCCCAGATACAAGGAAGTCATACTTCTGAATGATCTGATTGACTGTGCTCGTCCAGGAGAGGAGATTgtaatttttc ... ctgtctccagGAGGTCACTGGGATATACACAAATAATTTTGACCTGTCTTTGAATACAAAGAATGGTTTCCCTGTTTTTGCCACAGTGGTTGAGGCAAACTATGTGGCAA


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 20

GGAAAGCCCAGGAATTGTTCCTGCTGGAAGGCTTCCCAGATACAAGGAAGTCATACTTCTGAATGATCTGATTGACTGTGCTCGTCCAGGAGAGGAGATTgtaatttttc ... ctgtctccagGAGGTCACTGGGATATACACAAATAATTTTGACCTGTCTTTGAATACAAAGAATGGTTTCCCTGTTTTTGCCACAGTGGTTGAGGCAAACTATGTGGCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcatttcatattactttttgaattagactgacattcagtgttgctgtctccagGAGGTCACTGGGATATACACAAATAATTTTGACCTGTCTTTGAATACAAAGAATGGTTTCCCTGTTTTTGCCACAGTGGTTGAGGCAAACTATGTGGCAA
                           gactgac  putative branch site (score: 20)
                                             ctgtctcc  putative PPT
     tttcatattacttttt  TA-rich tract