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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCACTAGCACTTGGTGGAACCGTGCTTGGCTTTTATCCTGTCAAGGTTCTGCCATCAAAGACAGCAATTTTACCTGTGAACCCTAAATTTCTTCCTCACgtaagtagacagataaatttacgttgcctgttaatgttaaatctctgtagtaaatgcattatcttcgttatcctgcag

Basic information

species Zea mays
transcript GRMZM5G814159_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G814159_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os06g35030.3 (Oryza sativa), 5'ss of exon 5
AGCACTAGCACTTGGTGGAACCGTGCTTGGCTTTTATCCTGTCAAGGTTCTGCCATCAAAGACAGCAATTTTACCTGTGAACCCTAAATTTCTTCCTCACgtaagtagacagataaatttacgttgcctgt-taatgttaaat---ctctgtagta-aatg--cattatcttcgttatcctgcag-------------------------------------------------
|||  || |||||||||||||||||||||| | ||| ||||| |  ||||||||||| ||||| || ||||| || ||||||||||||||| | ||||  ||||||| ||||||     ||  |||    | || |  |  ||   |||||||||  |||    ||| |  | |||    | |                                                   
AGCTTTAACACTTGGTGGAACCGTGCTTGGTTATTACCCTGTGAGAGTTCTGCCATCTAAGACCGCGATTTTGCCGGTGAACCCTAAATTTTTACCTCGAgtaagtaaacagattcgggtattttgatattatactaattgatttactctgtagtgtaataattattgtactagttgatttccgagatctgtagtgtaataattaattggcataatttcgtttctctctcgcag
















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|32911170|gb|CF015982.1|CF015982
EST:     TGCCATCAAAGACAGCAATTTTACCTGTGAACCCTAAATTTCTTCCTCAC                         ACTGATGATGAGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATT
genomic: TGCCATCAAAGACAGCAATTTTACCTGTGAACCCTAAATTTCTTCCTCACgtaagtagac ... tatcctgcagACTGATGATGAGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATT
EST: gi|78180693|gb|DV551066.1|DV551066
EST:     TGCCATCAAAGACAGCAATTTTACCTGTGAACCCTAAATTTCTTCCTCAC                         ACTGATGATGAGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATT
genomic: TGCCATCAAAGACAGCAATTTTACCTGTGAACCCTAAATTTCTTCCTCACgtaagtagac ... tatcctgcagACTGATGATGAGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATT
EST: gi|148929870|gb|EE285590.2|EE285590
EST:     TGCCATCAAAGACAGCAATTTTACCTGTGAACCCTAAATTTCTTCCTCAC                         ACTGATGATGAGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATT
genomic: TGCCATCAAAGACAGCAATTTTACCTGTGAACCCTAAATTTCTTCCTCACgtaagtagac ... tatcctgcagACTGATGATGAGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATT
EST: gi|71772178|gb|DR970115.1|DR970115
EST:     TGCCATCAAAGACAGCAATTTTACCTGTGAACCCTAAATTTCTTCCTCAC                         ACTGATGATGAGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATT
genomic: TGCCATCAAAGACAGCAATTTTACCTGTGAACCCTAAATTTCTTCCTCACgtaagtagac ... tatcctgcagACTGATGATGAGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATT
EST: gi|110932361|gb|EE152587.1|EE152587
EST:     TGCCATCAAAGACAGCAATTTTACCTGTGAACCCTAAATTTCTTCCTCAC                         ACTGATGATGAGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATT
genomic: TGCCATCAAAGACAGCAATTTTACCTGTGAACCCTAAATTTCTTCCTCACgtaagtagac ... tatcctgcagACTGATGATGAGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATT
EST: gi|18164011|gb|BM333850.1|BM333850
EST:     TGCCATCAAAGACAGCAATTTTACCTGTGAACCCTAAATTTCTTCCTCAC                         ACTGATGATGAGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATT
genomic: TGCCATCAAAGACAGCAATTTTACCTGTGAACCCTAAATTTCTTCCTCACgtaagtagac ... tatcctgcagACTGATGATGAGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATT
EST: gi|211122862|gb|FL458470.1|FL458470
EST:     TGTGAACCCTAAATTTCTTCCTCAC                         ACTGATGATGAGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATT
genomic: TGTGAACCCTAAATTTCTTCCTCACgtaagtagac ... tatcctgcagACTGATGATGAGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATT
EST: gi|6851486|gb|AW352496.1|AW352496
EST:     TGCCATCAAAGACAGCAATTTTACCTGTGAACCCTAAATTTCTTCCTCAC                         ACTGATGATGAGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATT
genomic: TGCCATCAAAGACAGCAATTTTACCTGTGAACCCTAAATTTCTTCCTCACgtaagtagac ... tatcctgcagACTGATGATGAGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATT
EST: gi|110190841|gb|EC872739.1|EC872739
EST:     TGCCATCAAAGACAGCAATTTTACCTGTGAACCCTAAATTTCTTCCTCAC                         ACTGATGATGAGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATT
genomic: TGCCATCAAAGACAGCAATTTTACCTGTGAACCCTAAATTTCTTCCTCACgtaagtagac ... tatcctgcagACTGATGATGAGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATT
EST: gi|76292409|gb|DV031977.1|DV031977
EST:     TGCCATCAAAGACAGCAATTTTACCTGTGAACCCTAAATTTTTTCCTCAC                         ACTGATGATGAGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATT
genomic: TGCCATCAAAGACAGCAATTTTACCTGTGAACCCTAAATTTCTTCCTCACgtaagtagac ... tatcctgcagACTGATGATGAGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATT
EST: gi|211513328|gb|FL030344.1|FL030344
EST:     TGCCATCAAAGACAGCAATTTTACCTGTGAACCCTAAATTTCTTCCTCAC                         ACTGATGATGAGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATT
genomic: TGCCATCAAAGACAGCAATTTTACCTGTGAACCCTAAATTTCTTCCTCACgtaagtagac ... tatcctgcagACTGATGATGAGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATT
EST: gi|32165016|gb|CD670334.1|CD670334
EST:     TGCCATCAAAGACAGCAATTTTACCTGTGAACCCTAAATTTCTTCCTCAC                         ACTGATGATGAGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATT
genomic: TGCCATCAAAGACAGCAATTTTACCTGTGAACCCTAAATTTCTTCCTCACgtaagtagac ... tatcctgcagACTGATGATGAGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATT
EST: gi|86467993|gb|DY234363.1|DY234363
EST:     TGCCATCAAAGACAGCAATTTTACCTGTGAACCCTAAATTTCTTCCTCAC                         ACTGATGATGAGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATT
genomic: TGCCATCAAAGACAGCAATTTTACCTGTGAACCCTAAATTTCTTCCTCACgtaagtagac ... tatcctgcagACTGATGATGAGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATT
EST: gi|32914736|gb|CF019548.1|CF019548
EST:     TGCCATCAAAGACAGCAATTTTACCTGTGAACCCTAAATTTCTTCCTCAC                         ACTGATGATGAGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATT
genomic: TGCCATCAAAGACAGCAATTTTACCTGTGAACCCTAAATTTCTTCCTCACgtaagtagac ... tatcctgcagACTGATGATGAGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATT
EST: gi|37395891|gb|CF635231.1|CF635231
EST:     TGCCATCAAAGACAGCAATTTTACCTGTGAACCCTAAATTTCTTCCTCAC                         ACTGATGATGAGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACTTT
genomic: TGCCATCAAAGACAGCAATTTTACCTGTGAACCCTAAATTTCTTCCTCACgtaagtagac ... tatcctgcagACTGATGATGAGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATT
EST: gi|67021641|gb|CO450390.1|CO450390
EST:     TGCCATCAAAGACAGCAATTTTACCTGTGAACCCTAAATTTCTTCCTCAC                         ACTGATGATGAGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATT
genomic: TGCCATCAAAGACAGCAATTTTACCTGTGAACCCTAAATTTCTTCCTCACgtaagtagac ... tatcctgcagACTGATGATGAGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATT
EST: gi|149099389|gb|EE185429.2|EE185429
EST:     TGCCATCAAAGACAGCAATTTTACCTGTGAACCCTAAATTTCTTCCTCAC                         ACTGATGATGAGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATT
genomic: TGCCATCAAAGACAGCAATTTTACCTGTGAACCCTAAATTTCTTCCTCACgtaagtagac ... tatcctgcagACTGATGATGAGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATT
EST: gi|31362976|gb|CD447333.1|CD447333
EST:     TGCCATCAAAGACAGCAATTTTACCTGTGAACCCTAAATTTCTTCCTCAC                         ACTGATGATGAGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATT
genomic: TGCCATCAAAGACAGCAATTTTACCTGTGAACCCTAAATTTCTTCCTCACgtaagtagac ... tatcctgcagACTGATGATGAGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATT

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), 48 (downstream exon)
Score: 200

AGCACTAGCACTTGGTGGAACCGTGCTTGGCTTTTATCCTGTCAAGGTTCTGCCATCAAAGACAGCAATTTTACCTGTGAACCCTAAATTTCTTCCTCACgtaagtagac ... tatcctgcagACTGATGATGAGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 85

AGCACTAGCACTTGGTGGAACCGTGCTTGGCTTTTATCCTGTCAAGGTTCTGCCATCAAAGACAGCAATTTTACCTGTGAACCCTAAATTTCTTCCTCACgtaagtagac ... tatcctgcagACTGATGATGAGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 120

AGCACTAGCACTTGGTGGAACCGTGCTTGGCTTTTATCCTGTCAAGGTTCTGCCATCAAAGACAGCAATTTTACCTGTGAACCCTAAATTTCTTCCTCACgtaagtagac ... tatcctgcagACTGATGATGAGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 211

AGCACTAGCACTTGGTGGAACCGTGCTTGGCTTTTATCCTGTCAAGGTTCTGCCATCAAAGACAGCAATTTTACCTGTGAACCCTAAATTTCTTCCTCACgtaagtagac ... tatcctgcagACTGATGATGAGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAG