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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgtattctggcatcttatttggttaacaatctttatattgacttctgtttgaaggatgaattactgatttactgttgatctgaggtgtaaattttgttcctattttaaatatatcttgtgataatatccattatatcaccggtttcttttggtttgtagGGTTATGGTTCCTTTCTACTTCGAGATCTACCATTTGATGCCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTG

Basic information

species Zea mays
transcript GRMZM2G042027_T05
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G042027_T05 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os05g29860.1 (Oryza sativa), 3'ss of exon 7
gtatgtgtattctggcatcttatttggt------------taacaatctttatattgacttctgtttgaaggatgaattactgatttactgttgatctgag---gtgtaaattttgttcctattttaaata----tatcttgtgataatatccatta-------tatcac-cggtttcttttggtttgtagGGTTATGGTTCCTTTCTACTTCGAGATCTACCATTTGATGCCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTG
|||||| | ||||| | || ||| ||||            || |    |  |   | | || ||||       |  ||| | |    | |  | || |||    || |||  |   ||  || || || |     ||   ||  | || |  ||||        | |||  | ||||||||| |||||||||| ||||| || ||| ||||||||||||| || ||||||||||| || ||||| || |||||||||||||||||||| |||||| |||||
gtatgtatcttctgacctcatatatggtggaacctgtatttagccgattcaactctaatttttgttatccctgtatatttcaggaaaaataattatttgaatctgtttaatatgcctttttaattgaattgttgttacaatggaaaaaaactcattgccttccttgtcatactgtttctttttgtttgtagGGATATGGATCATTTTTACTTCGAGATCTGCCTTTTGATGCCATTCAATTCTGTATATATGAGCAACTTCGAATTGGTTACAAAGTTGTG

upper sequence: GRMZM2G042027_T05 (Zea mays), 3'ss of exon 7
lower sequence: PP1S139_9V6.1 (Physcomitrella patens), 3'ss of exon 8
gtatgtgtattctggcatcttatttggttaacaatctttatattgactt--ctgtttgaaggatgaattactgatttactgttgatctgaggtgtaaattttgttcctattttaaatatatcttgtgataatatccattatatcaccggtttcttttggtttgtagGGTTATGGTTCCTTTCTACTTCGAGATCTACCATTTGATGCCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTA--CAAACTTGTG
   |  || ||   || |  |   || | |  | |||  ||  | |  |   | |||   |  ||     | |   | |   ||  |  ||    | ||  | |||| |         ||   ||   | ||    |   | |||  ||||     || |||  |||| | | |||| ||  |  | ||||| ||||||||||||||  ||||||| ||||| ||||||||| |    ||  | ||  ||||   |  
--gtaagtttttgagctttctgaatgatcag-agtctccatgcttatatgattcttttgcgtgtgttcgtccgccctgcccgtggac-aagtatcacataattttcccacaaccttgttagtatgaattcatgcttacactgtcattggttg----tgatttacagGGCTTTCGTTCATTCTTGTTACGAGACCTACCATTTGATGCATTCCAGTTTTGCATCTATGAGCAATTAAAGATCAGTTATGCAAAACGG--

upper sequence: GRMZM2G042027_T05 (Zea mays), 3'ss of exon 7
lower sequence: PP1S450_16V6.1 (Physcomitrella patens), 3'ss of exon 8
gtatgtgtattctggcatcttatttggttaacaatctttatattgacttctgtttgaaggatgaattactgatttactgttgatctgaggtgtaaattttgttcctattttaaatatatcttgtgataatatccattatatcaccggtttcttttggtttgtagGGTTATGGTTCCTTTCTACTTCGAGATCTACCATTTGATGCCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTG
                          ||     |||||| | ||  ||| | ||  |   ||          |  |    |    | | ||   | || | | | | |     |  | |  |  |||  | | || | ||      | |  |||||  ||| |||||| ||| || || || ||||||||| ||||||||||||| |||||||| |||||||| ||||| ||| || | ||||  ||    |||
--------------------------gtatgtgatctttctcttagcttgtcttcaagaaat----------tccatcactctcgttatgtcccatttatctgcatgtgcaggaagtgtacttcgat--tgtacactctaat----ggtctttttgaattgcagGGTTTTGGATCTTTCCTCCTTCGAGATTTACCATTTGATGCTATCCAGTTTTGCATTTACGAGCAGCTTAGATTGGGCTTGAAGAAAGTG

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|71436673|gb|DR817723.1|DR817723
EST:     ATGCTGTTCGTCTCATTGTTGCTAAAGAAGGATTTAAAGGACTGTACGCT                         GGTTATGGTTCCTTTCTACTTCGAGATCTACCATTT
genomic: ATGCTGTTCGTCTCATTGTTGCTAAAGAAGGATTTAAAGGACTGTACGCTgtatgtgtat ... tggtttgtagGGTTATGGTTCCTTTCTACTTCGAGATCTACCATTT
EST: gi|113702185|gb|EE679689.1|EE679689
EST:     AAGGACTGTACGCT                         GGTTATGGTTCCTTTCTACTTCGAGATCTACCATTTGATGCCATCCAGTTC
genomic: AAGGACTGTACGCTgtatgtgtat ... tggtttgtagGGTTATGGTTCCTTTCTACTTCGAGATCTACCATTTGATGCCATCCAGTTC
EST: gi|91056577|gb|EB166995.1|EB166995
EST:     ATGCTGTTCGTTTCATTGTTGCTAAAGAAGGATTTAAAGGACTGTACGCT                         GGTTATGGTTCCTTTCTACTTCGAGATTTACCATTTGATGCCATCCAGTTC
genomic: ATGCTGTTCGTCTCATTGTTGCTAAAGAAGGATTTAAAGGACTGTACGCTgtatgtgtat ... tggtttgtagGGTTATGGTTCCTTTCTACTTCGAGATCTACCATTTGATGCCATCCAGTTC
EST: gi|71302083|gb|DR787129.1|DR787129
EST:     ATGCTGTTCGTCTCATTGTTGCTAAAGAAGGATTTAAAGGACTGTACGCT                         GGTTATGGTTCCTTTCTACTTCGAGATCTACCATTTGATGCCATCCAGTTC
genomic: ATGCTGTTCGTCTCATTGTTGCTAAAGAAGGATTTAAAGGACTGTACGCTgtatgtgtat ... tggtttgtagGGTTATGGTTCCTTTCTACTTCGAGATCTACCATTTGATGCCATCCAGTTC
EST: gi|76011416|gb|DT938586.1|DT938586
EST:     ATGCTGTTCGTCTCATTGTTGCTAAAGAAGGATTTAAAGGACTGTACGCT                         GGTTATGGTTCCTTTCTACTTCGAGATCTACCATTTGATGCCATCCAGTTC
genomic: ATGCTGTTCGTCTCATTGTTGCTAAAGAAGGATTTAAAGGACTGTACGCTgtatgtgtat ... tggtttgtagGGTTATGGTTCCTTTCTACTTCGAGATCTACCATTTGATGCCATCCAGTTC
EST: gi|16918359|gb|BM073712.1|BM073712
EST:     ATGCTGTTCGTCTCATTGTTGCTAAAGAAGGATTTAAAGGACTGTACGCT                         GGTTATGGTTCCTTTCTACTTCGAGATCTACCATTTGATGCCATCCAGTTC
genomic: ATGCTGTTCGTCTCATTGTTGCTAAAGAAGGATTTAAAGGACTGTACGCTgtatgtgtat ... tggtttgtagGGTTATGGTTCCTTTCTACTTCGAGATCTACCATTTGATGCCATCCAGTTC
EST: gi|78092776|gb|DV521150.1|DV521150
EST:     TAAAGGACTGTACGCT                         GGTTATGGTTCCTTTCTACTTCGAGATCTACCATTTGATGCCATCCAGTTC
genomic: TAAAGGACTGTACGCTgtatgtgtat ... tggtttgtagGGTTATGGTTCCTTTCTACTTCGAGATCTACCATTTGATGCCATCCAGTTC
EST: gi|211226520|gb|FL435621.1|FL435621
EST:     ATGCTGTTCGTCTCATTGTTGCTAAAGAAGGATTTAAAGGACTGTACGCT                         GGTTATGGTTCCTTTCTACTTCGAGATCTACCATTTGATGCCATCCAGTTC
genomic: ATGCTGTTCGTCTCATTGTTGCTAAAGAAGGATTTAAAGGACTGTACGCTgtatgtgtat ... tggtttgtagGGTTATGGTTCCTTTCTACTTCGAGATCTACCATTTGATGCCATCCAGTTC
EST: gi|33092443|gb|CF052437.1|CF052437
EST:     GCTGTTCGTCTCATTGTTGCTAAAGAAGGATTTAAAGGACTGTACGCT                         GGTTATGGTTCCTTTCTACTTCGAGATCTACCATTTGATGCCATCCAGTTC
genomic: GCTGTTCGTCTCATTGTTGCTAAAGAAGGATTTAAAGGACTGTACGCTgtatgtgtat ... tggtttgtagGGTTATGGTTCCTTTCTACTTCGAGATCTACCATTTGATGCCATCCAGTTC
EST: gi|50325364|gb|CO520490.1|CO520490
EST:     ATGCTGTTCGTCTCATTGTTGCTAAAGAAGGATTTAAAGGACTGTACGCT                         GGTTATGGTTCCTTTCTACTTCGAGATCTACCATTTGATGCCATCCAGTTC
genomic: ATGCTGTTCGTCTCATTGTTGCTAAAGAAGGATTTAAAGGACTGTACGCTgtatgtgtat ... tggtttgtagGGTTATGGTTCCTTTCTACTTCGAGATCTACCATTTGATGCCATCCAGTTC
EST: gi|60342707|gb|DN209680.1|DN209680
EST:     ATGCTGTTCGTCTCATTGTTGCTAAAGAAGGATTTAAAGGACTGTACGCT                         GGTTATGGTTCCTTTCTACTTCGAGATCTACCATTTGATGCCATCCAGTTC
genomic: ATGCTGTTCGTCTCATTGTTGCTAAAGAAGGATTTAAAGGACTGTACGCTgtatgtgtat ... tggtttgtagGGTTATGGTTCCTTTCTACTTCGAGATCTACCATTTGATGCCATCCAGTTC
EST: gi|91054196|gb|EB164614.1|EB164614
EST:     ATGCTGTTCGTCTCATTGTTGCTAAAGAAGGATTTAAAGGACTGTACGCT                         GGTTATGGTTCCTTTCTACTTCGAGATCTACCATTTGATGCCATCCAGTTC
genomic: ATGCTGTTCGTCTCATTGTTGCTAAAGAAGGATTTAAAGGACTGTACGCTgtatgtgtat ... tggtttgtagGGTTATGGTTCCTTTCTACTTCGAGATCTACCATTTGATGCCATCCAGTTC
EST: gi|67018887|gb|CO447636.1|CO447636
EST:     ATGCTGTTCGTCTCATTGTTGCTAAAGAAGGATTTAAAGGACTGTACGCT                         GGTTATGGTTCCTTTCTACTTCGAGATCTACCATTTGATGCCATCCAGTTC
genomic: ATGCTGTTCGTCTCATTGTTGCTAAAGAAGGATTTAAAGGACTGTACGCTgtatgtgtat ... tggtttgtagGGTTATGGTTCCTTTCTACTTCGAGATCTACCATTTGATGCCATCCAGTTC
EST: gi|78083391|gb|DV511784.1|DV511784
EST:     ATGCTGTTCGTCTCATTGTTGCTAAAGAAGGATTTAAAGGACTGTACGCT                         GGTTATGGTTCCTTTCTACTTCGAGATCTACCATTTGATGCCATCCAGTTC
genomic: ATGCTGTTCGTCTCATTGTTGCTAAAGAAGGATTTAAAGGACTGTACGCTgtatgtgtat ... tggtttgtagGGTTATGGTTCCTTTCTACTTCGAGATCTACCATTTGATGCCATCCAGTTC

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: 43 (upstream exon), 48 (downstream exon)
Score: 98

GTGGTCAAACAAAGGATGCAAACTGGTCAATTCAAGTCTGCACCTGATGCTGTTCGTCTCATTGTTGCTAAAGAAGGATTTAAAGGACTGTACGCTgtatgtgtat ... tggtttgtagGGTTATGGTTCCTTTCTACTTCGAGATCTACCATTTGATGCCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 155

GTGGTCAAACAAAGGATGCAAACTGGTCAATTCAAGTCTGCACCTGATGCTGTTCGTCTCATTGTTGCTAAAGAAGGATTTAAAGGACTGTACGCTgtatgtgtat ... tggtttgtagGGTTATGGTTCCTTTCTACTTCGAGATCTACCATTTGATGCCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 84

GTGGTCAAACAAAGGATGCAAACTGGTCAATTCAAGTCTGCACCTGATGCTGTTCGTCTCATTGTTGCTAAAGAAGGATTTAAAGGACTGTACGCTgtatgtgtat ... tggtttgtagGGTTATGGTTCCTTTCTACTTCGAGATCTACCATTTGATGCCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 38

GTGGTCAAACAAAGGATGCAAACTGGTCAATTCAAGTCTGCACCTGATGCTGTTCGTCTCATTGTTGCTAAAGAAGGATTTAAAGGACTGTACGCTgtatgtgtat ... tggtttgtagGGTTATGGTTCCTTTCTACTTCGAGATCTACCATTTGATGCCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaatatatcttgtgataatatccattatatcaccggtttcttttggtttgtagGGTTATGGTTCCTTTCTACTTCGAGATCTACCATTTGATGCCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTG
                                      tttctttt  CT-rich tract
                ataatatccattatat  TA-rich tract