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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagctactaaacatttatcagttgcaacacatttgtagcatgcagatgtttatattgatctgaaacatgatctatgtgaaatgcagTCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAATGGTGACATTCTCGCAAGGCCAATGATGTTCCTTGCGCTGACATATGACC

Basic information

species Zea mays
transcript GRMZM5G807639_T03
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G807639_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os04g32330.1 (Oryza sativa), 3'ss of exon 12
gtagctactaaacatttatcagttgcaaca--catttgtagcatgcagatgtttatattgatctgaaaca-tg-atctatgtgaaatgcagTCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAATGGTGACATTCTCGCAAGGCCAATGATGTTCCTTGCGCTGACATATGACC
||  ||  |  |  |||  || |||||| |         |  | |  ||| || ||  | |||||| ||| || || ||| |  |||||||||  | ||||| || ||||| |||||||| |||||||||||||| ||| | ||  |||||||||| ||||||||||||| ||||||||||||||||||||
gtc-ctttttcatttttgccacttgcaaaaattgccctcactaggttgatattcat--tcatctgacacaatgtatatatatctaatgcagTCTGCTATTCTTGGAATGCACTCCATTGTACAACGCCCTGTGGTCGTGGACGGCAACATTCTCGCGAGGCCAATGATGTACCTTGCGCTGACATATGACC
















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|211354774|gb|FL462364.1|FL462364
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAG                         TCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAGgtagctacta ... tgaaatgcagTCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|93017174|gb|EB642694.1|EB642694
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAG                         TCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAGgtagctacta ... tgaaatgcagTCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|6918669|gb|AW400199.1|AW400199
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAG                         TCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAGgtagctacta ... tgaaatgcagTCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|16925492|gb|BM078560.1|BM078560
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAG                         TCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAGgtagctacta ... tgaaatgcagTCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|32935625|gb|CF040437.1|CF040437
EST:     GTAGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAG                         TCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAGgtagctacta ... tgaaatgcagTCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|16919656|gb|BM074297.1|BM074297
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAG                         TCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAGgtagctacta ... tgaaatgcagTCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|5871687|gb|AW018158.1|AW018158
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAG                         TCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAGgtagctacta ... tgaaatgcagTCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|60343714|gb|DN210687.1|DN210687
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAG                         TCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAGgtagctacta ... tgaaatgcagTCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|32866729|gb|CF006411.1|CF006411
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAG                         TCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAGgtagctacta ... tgaaatgcagTCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|16926010|gb|BM079078.1|BM079078
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAG                         TCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAGgtagctacta ... tgaaatgcagTCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|30306816|gb|CD001489.1|CD001489
EST:     CTCCTCAGCACACCTATCATCAACCCCCCACAG                         TCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: CTCCTCAGCACACCTATCATCAACCCCCCACAGgtagctacta ... tgaaatgcagTCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|60349623|gb|DN216596.1|DN216596
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAG                         TCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAGgtagctacta ... tgaaatgcagTCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|6918383|gb|AW399913.1|AW399913
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAG                         TCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAGgtagctacta ... tgaaatgcagTCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|211104574|gb|FL031920.1|FL031920
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAG                         TCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAGgtagctacta ... tgaaatgcagTCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|6020821|gb|AW065749.1|AW065749
EST:     GTGGTGTCTATGGAAGCCTNCTCAGCACACCTATCATCAACCCCCCACAG                         TCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGNTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAGgtagctacta ... tgaaatgcagTCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|60399105|gb|DN231919.1|DN231919
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAG                         TCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAGgtagctacta ... tgaaatgcagTCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT

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), 46 (downstream exon)
Score: 68

GGCGCTCTCGATTGATGACATGGCAGGAGGAACATTCACTATCTCCAATGGTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAGgtagctacta ... tgaaatgcagTCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAATGGTGACATTCTCGCAAGGCCAATGATGTTCCTTGCGCTGACATATGACC


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 71

GGCGCTCTCGATTGATGACATGGCAGGAGGAACATTCACTATCTCCAATGGTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAGgtagctacta ... tgaaatgcagTCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAATGGTGACATTCTCGCAAGGCCAATGATGTTCCTTGCGCTGACATATGACC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 41

GGCGCTCTCGATTGATGACATGGCAGGAGGAACATTCACTATCTCCAATGGTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAGgtagctacta ... tgaaatgcagTCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAATGGTGACATTCTCGCAAGGCCAATGATGTTCCTTGCGCTGACATATGACC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 110

GGCGCTCTCGATTGATGACATGGCAGGAGGAACATTCACTATCTCCAATGGTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAGgtagctacta ... tgaaatgcagTCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAATGGTGACATTCTCGCAAGGCCAATGATGTTCCTTGCGCTGACATATGACC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtagcatgcagatgtttatattgatctgaaacatgatctatgtgaaatgcagTCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAATGGTGACATTCTCGCAAGGCCAATGATGTTCCTTGCGCTGACATATGACC
                     tattgat  putative branch site (score: 110)
              atgtttatattgat  TA-rich tract