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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgccatataattatgttattattgtctcacttgaatggaatcttttgatcggctatgtaccagataattttttacttgtttttttggccctcgtctctaactgctccaaaaattgcagCGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAG

Basic information

species Zea mays
transcript GRMZM2G158021_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158021_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os07g43470.1 (Oryza sativa), 3'ss of exon 8
gtgagtgccatataattatgttattattgtctcacttgaatggaatcttttgatcggctatgtaccagataattttttacttgtttttttggccctcgtctctaactgctc-caaaaattgcagCGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAG
                                        ||      ||   | |  | |   |   ||| |||| | | |||| |      |   ||  |||||||||| |||||  ||||| ||  |||| |||||||| || ||||| ||||||||||||||||||||||||
---------------------------------------gtgagtatcttcatttgtatcttgtctgaatatttttgtccctgttatcc--atctgtgtggctaactgctcacaaaacctgcagTGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAG

upper sequence: GRMZM2G158021_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA06G15180.2 (Glycine max), 3'ss of exon 8
gtgagtgccatataattatgttattattgtctcacttgaatggaatcttttgatcggctatgtaccagataattttttacttgtttttttggccctcgtct---ctaactgctccaaaaattgcagCGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAG
                      |  |  || | | |  |    ||||| |    |          || | ||  | ||  ||  |||  || |  || | |     |  |   |||||   ||||| ||| |||| |||||||| |||| |||||| |||||||| ||||||||||||
----------------------aaaaaagtttgagtcaat--aaatctctctccccttagcccttcaaaaaaaatgtt--tttctttcctgacattcatttaattcacatttaccaaatgatgcagTGCTTTGGTCTGGGGTTCAAGTGCGAAACACAAGCCTCAAAGAGTTGGCAAG

upper sequence: GRMZM2G158021_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA04G39690.1 (Glycine max), 3'ss of exon 8
gtgagtgccatataattatgttattattgtctcacttgaatggaatcttttgatcggctatgtaccagataattttttacttgtttttttggccctcgtct---ctaactgctccaaaaattgcagCGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAG
                                 | |||| |  ||   | | | |  ||  || |   ||||    |   ||  |||  || |  || | |     |  |   || ||   ||||| ||| |||| |||||||| ||||  ||||| |||||||| ||||||||||||
-------------------------gagaaaaaagttgagtaaaaaaatctcaccc-ctcggtcctccataaaaaatgtttttctttcctgacattcatttaattcacatttaccgaatgatgcagTGCTTTGGTCTGGGGTTCAAGTGCAAAACACAAGCCTCAAAGAGTTGGCAAG

upper sequence: GRMZM2G158021_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA06G15180.1 (Glycine max), 3'ss of exon 8
gtgagtgccatataattatgttattattgtctcacttgaatggaatcttttgatcggctatgtaccagataattttttacttgtttttttggccctcgtct---ctaactgctccaaaaattgcagCGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAG------------------------------------------------
                      |  |  || | | |  |    ||||| |    |          || | ||  | ||  ||  |||  || |  || | |     |  |   |||||   ||||| ||| |||| |||||||| |||| |||||| |||||||| ||||||||||||                                                
----------------------aaaaaagtttgagtcaat--aaatctctctccccttagcccttcaaaaaaaatgtt--tttctttcctgacattcatttaattcacatttaccaaatgatgcagTGCTTTGGTCTGGGGTTCAAGTGCGAAACACAAGCCTCAAAGAGTTGGCAAGGTTGATACTGTACTTAATTTACATTATTTTTTGCTTCATCCTCTTTTC

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|78025510|gb|DV493897.1|DV493897
EST:     GAAGATTTCTGCGACAGAATCCACAAGGACATGGTCAAACAATTTAAATA                         CGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAA
genomic: GAAGATTTCTGCGACAGAATCCACAAGGACATGGTCAAACAATTTAAATAgtgagtgcca ... aaaattgcagCGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAA
EST: gi|60398886|gb|DN231702.1|DN231702
EST:     GAAGATTTCTGCGACAGAATCCACAAGGACATGGTCAAACAATTTAAATA                         CGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAA
genomic: GAAGATTTCTGCGACAGAATCCACAAGGACATGGTCAAACAATTTAAATAgtgagtgcca ... aaaattgcagCGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAA
EST: gi|29544633|gb|CB605013.1|CB605013
EST:     GAAGATTTCTGCGACAGAATCCACAAGGACATGGTCAAACAATTTAAATA                         CGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAA
genomic: GAAGATTTCTGCGACAGAATCCACAAGGACATGGTCAAACAATTTAAATAgtgagtgcca ... aaaattgcagCGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAA
EST: gi|32934872|gb|CF039684.1|CF039684
EST:     GAAGATTTCTGCGACAGAATCCACAAGGACATGGTCAAACAATTTAAATA                         CGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAA
genomic: GAAGATTTCTGCGACAGAATCCACAAGGACATGGTCAAACAATTTAAATAgtgagtgcca ... aaaattgcagCGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAA
EST: gi|29543482|gb|CB605568.1|CB605568
EST:     GAAGATTTCTGCGACAGAATCCACAAGGACATGGTCAAACAATTTAAATA                         CGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAA
genomic: GAAGATTTCTGCGACAGAATCCACAAGGACATGGTCAAACAATTTAAATAgtgagtgcca ... aaaattgcagCGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAA
EST: gi|60358587|gb|DN225560.1|DN225560
EST:     GAAGATTTCTGCGACAGAATCCACAAGGACATGGTCAAACAATTTAAATA                         CGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAA
genomic: GAAGATTTCTGCGACAGAATCCACAAGGACATGGTCAAACAATTTAAATAgtgagtgcca ... aaaattgcagCGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAA
EST: gi|4886224|gb|AI677344.1|AI677344
EST:     GAAGATTTTTGCGCCAGAATCCCCAAGGACATGGTCAAACAATTTAAATA                         CGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAA
genomic: GAAGATTTCTGCGACAGAATCCACAAGGACATGGTCAAACAATTTAAATAgtgagtgcca ... aaaattgcagCGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAA
EST: gi|74240037|gb|DT647951.1|DT647951
EST:     GAAGATTTCTGCGACAGAATCCACAAGGACATGGTCAAACAATTTAAATA                         CGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAA
genomic: GAAGATTTCTGCGACAGAATCCACAAGGACATGGTCAAACAATTTAAATAgtgagtgcca ... aaaattgcagCGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAA
EST: gi|14203739|gb|BG837416.1|BG837416
EST:     GAAGATTTCTGCGACAGAATCCACAAGGACATGGTCAAACAATTTAAATA                         CGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAA
genomic: GAAGATTTCTGCGACAGAATCCACAAGGACATGGTCAAACAATTTAAATAgtgagtgcca ... aaaattgcagCGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAA
EST: gi|211345618|gb|FL479628.1|FL479628
EST:     GAAGATTTCTGCGACAGAATCCACAAGGACATGGTCAAACAATTTAAATA                         CGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAA
genomic: GAAGATTTCTGCGACAGAATCCACAAGGACATGGTCAAACAATTTAAATAgtgagtgcca ... aaaattgcagCGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAA
EST: gi|211493768|gb|FL172984.1|FL172984
EST:     GAAGATTTCTGCGACAGAATCCACAAGGACATGGTCAAACAATTTAAATA                         CGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAA
genomic: GAAGATTTCTGCGACAGAATCCACAAGGACATGGTCAAACAATTTAAATAgtgagtgcca ... aaaattgcagCGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAA
EST: gi|32932341|gb|CF037153.1|CF037153
EST:     GAAGATTTCTGCGACAGAATCCACAAGGACATGGTCAAACAATTTAAATA                         CGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAA
genomic: GAAGATTTCTGCGACAGAATCCACAAGGACATGGTCAAACAATTTAAATAgtgagtgcca ... aaaattgcagCGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAA
EST: gi|71758265|gb|DR956202.1|DR956202
EST:     GAAGATTTCTGCGACAGAATCCACAAGGACATGGTCAAACAATTTAAATA                         CGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAA
genomic: GAAGATTTCTGCGACAGAATCCACAAGGACATGGTCAAACAATTTAAATAgtgagtgcca ... aaaattgcagCGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAA
EST: gi|86472109|gb|DY238479.1|DY238479
EST:     GAAGATTTCTGCGACAGAATCCACAAGGACATGGTCAAACAATTTAAATA                         CGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAA
genomic: GAAGATTTCTGCGACAGAATCCACAAGGACATGGTCAAACAATTTAAATAgtgagtgcca ... aaaattgcagCGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAA
EST: gi|32933065|gb|CF037877.1|CF037877
EST:     GAAGATTTCTGCGACAGAATCCACAAGGACATGGTCAAACAATTTAAATA                         CGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAA
genomic: GAAGATTTCTGCGACAGAATCCACAAGGACATGGTCAAACAATTTAAATAgtgagtgcca ... aaaattgcagCGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAA
EST: gi|211493769|gb|FL172985.1|FL172985
EST:     GAAGATTTCTGCGACAGAATCCACAAGGACATGGTCAAACAATTTAAATA                         CGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAA
genomic: GAAGATTTCTGCGACAGAATCCACAAGGACATGGTCAAACAATTTAAATAgtgagtgcca ... aaaattgcagCGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAA
EST: gi|30088250|gb|CB886455.1|CB886455
EST:     GAAGATTTCTGCGACAGAATCCACAAGGACATGGTCAAACAATTTAAATA                         CGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAA
genomic: GAAGATTTCTGCGACAGAATCCACAAGGACATGGTCAAACAATTTAAATAgtgagtgcca ... aaaattgcagCGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAA
EST: gi|22542064|gb|BU092502.1|BU092502
EST:     GAAGATTTCTGCGACAGAATCCACAAGGACATGGTCAAACAATTTAAATA                         CGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAA
genomic: GAAGATTTCTGCGACAGAATCCACAAGGACATGGTCAAACAATTTAAATAgtgagtgcca ... aaaattgcagCGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAA
EST: gi|71418754|gb|DR804530.1|DR804530
EST:     GAAGATTTCTGCGACAGAATCCACAAGGACATGGTCAAACAATTTAAATA                         CGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAA
genomic: GAAGATTTCTGCGACAGAATCCACAAGGACATGGTCAAACAATTTAAATAgtgagtgcca ... aaaattgcagCGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAA
EST: gi|29544505|gb|CB604885.1|CB604885
EST:     GAAGATTTCTGCGACAGAATCCACAAGGACATGGTCAAACAATTTAAATA                         CGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAA
genomic: GAAGATTTCTGCGACAGAATCCACAAGGACATGGTCAAACAATTTAAATAgtgagtgcca ... aaaattgcagCGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAA
EST: gi|5108308|gb|AI740021.1|AI740021
EST:     GAAGATTTCTGCGACAGAATCCACAAGGACATGGTCAAACAATTTAAATA                         CGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAA
genomic: GAAGATTTCTGCGACAGAATCCACAAGGACATGGTCAAACAATTTAAATAgtgagtgcca ... aaaattgcagCGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAA
EST: gi|32916029|gb|CF020841.1|CF020841
EST:     AAGGACATGGTCAAACAATTTAAATA                         CGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAA
genomic: AAGGACATGGTCAAACAATTTAAATAgtgagtgcca ... aaaattgcagCGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAA

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: 257

ACCCAGATTATGAGGATCCTGTTATCGTATCATCTAAGAAGAAAACCGTGGAAGATTTCTGCGACAGAATCCACAAGGACATGGTCAAACAATTTAAATAgtgagtgcca ... aaaattgcagCGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 249

ACCCAGATTATGAGGATCCTGTTATCGTATCATCTAAGAAGAAAACCGTGGAAGATTTCTGCGACAGAATCCACAAGGACATGGTCAAACAATTTAAATAgtgagtgcca ... aaaattgcagCGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 231

ACCCAGATTATGAGGATCCTGTTATCGTATCATCTAAGAAGAAAACCGTGGAAGATTTCTGCGACAGAATCCACAAGGACATGGTCAAACAATTTAAATAgtgagtgcca ... aaaattgcagCGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 214

ACCCAGATTATGAGGATCCTGTTATCGTATCATCTAAGAAGAAAACCGTGGAAGATTTCTGCGACAGAATCCACAAGGACATGGTCAAACAATTTAAATAgtgagtgcca ... aaaattgcagCGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataattttttacttgtttttttggccctcgtctctaactgctccaaaaattgcagCGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAG
                               ctctaac  putative branch site (score: 214)
     tttttacttgtttttt  TA-rich tract