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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattggttattttaagcaaacttgggcttaatgtgaggtattcatttgtttggtacatgtttcttttatctcagaaatccttgcttcattgtcaatttgtatcttgaccagGGAGCTGTCAACTTTGCATTGATGATGTCACAAATGGAGGGAGGTTGTCCAGTAGACTACAACACTATCACTGATCTCTTCCTTCAG

Basic information

species Zea mays
transcript GRMZM2G057576_T02
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 14
gtaattggttattttaagcaaacttgggcttaatgtgaggtattc--atttgtttggtacatgttt--cttttatctcagaaatccttgcttcattgtcaatttgtatcttgaccagGGAGCTGTCAACTTTGCATTGATGATGTCACAAATGGAGGGAGGTTGTCCAGTAGACTACAACACTATCACTGATCTCTTCCTTCAG
|||||   ||  || |||| |  ||||||| |  ||||  || ||   ||||||  ||   |  ||   |||||| |   ||||   |  || | |||  || | |   || ||||||||||||||||||||||  | |||||||||||||||||||| || |||||||| || ||||| ||||| ||||||||||||||||||
gtaatgtattggtt-aagctattttgggct-agggtgaaatactctgctttgttctgtgggttgttgatttttatttgcaaaattaattatttactgtatatctct---tttaccagGGAGCTGTCAACTTTGCGCTCATGATGTCACAAATGGAGGGGGGCTGTCCAGTTGATTACAATACTATAACTGATCTCTTCCTTCAG

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 14
gtaattggttattttaagcaaacttgggcttaatgtgaggtattc--atttgtttggtacatgttt--cttttatctcagaaatccttgcttcattgtcaatttgtatcttgaccagGGAGCTGTCAACTTTGCATTGATGATGTCACAAATGGAGGGAGGTTGTCCAGTAGACTACAACACTATCACTGATCTCTTCCTTCAG
||||||  ||  || |||| |  ||| ||| |  ||||  |||||   ||||||  ||   |  ||   |||||| |   ||||   |  || | |||  || | |   || ||||||||||||||||||||||  | |||||||||||||||||||| || |||||||| || ||||| ||||| ||||||||||||||||||
gtaatttattggtt-aagctattttgtgct-agggtgaaatattctgctttgttctgtgggttgttgatttttatttgcaaaatttattatttactgtatatctct---tttaccagGGAGCTGTCAACTTTGCGCTCATGATGTCACAAATGGAGGGGGGCTGTCCAGTTGATTACAATACTATAACTGATCTCTTCCTTCAG

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 14
gtaattggttattttaagcaaacttgggcttaatgtgaggtattcatttgtttggta--catgtttcttttatctcagaaatccttgcttcattgtcaatttgtatcttgac--cagGGAGCTGTCAACTTTGCATTGATGATGTCACAAATGGAGGGAGGTTGTCCAGTAGACTACAACACTATCACTGATCTCTTCCTTCAG
          ||| ||  |   ||      | || ||     || |||| ||| | |  || |||  |||| | |  |   |   |    |||  |  | |  | ||||||   ||||| ||||| || |||||  |||||||||| |||||||| ||||| || ||  | ||||||||||| || || |||||||| ||||||
----------attctattc--tctgaaatctgatttgt----ttaatttttttagcatccaagttgatttt-tttttggtttatgtatagcataatttaatactttcttgattgcagGGTGCTGTAAATTTTGCTCTGATGATGTCTCAAATGGAAGGAGGATGCCCCATTGACTACAACACCATAACAGATCTCTTTCTTCAG

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 14
---------------------------gtaattggttattttaagcaaacttgggc--ttaatgtgaggtattcatttgtttggtacatgtttcttttatct--cagaaatccttgctt-cattgtcaatttgtatcttgac---cagGGAGCTGTCAACTTTGCATTGATGATGTCACAAATGGAGGGAGGTTGTCCAGTAGACTACAACACTATCACTGATCTCTTCCTTCAG
                            ||  |  || |||||    ||| ||  |  ||  | ||  |  | |  || ||   |   |  || || |||||      |||   ||||  || |  | ||||  || ||||    ||||| ||||| || |||||||| |||||||| ||||||||||||||| | ||||| || |||||||| || ||||||||||| ||||||
gtgtgagagaaacctctgcagtttatattatataatttttttagttgaacctgaaccatttctttgtagc-tccccttattctctgtctccttgttatatctgttgacaatgtctgctgacagttaccattttcattttgatttgcagGGCGCTGTTAATTTTGCATTAATGATGTCTCAAATGGAGGGAGGTAGCCCAGTTGATTACAACACAATAACTGATCTCTTTCTTCAG

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 14
gtaattggttattttaagcaaacttgggcttaatgtgaggtattcatttgtttggtacatgtttcttttatctcagaaatccttgcttcattgtcaatttgtatcttgaccagGGAGCTGTCAACTTTGCATTGATGATGTCACAAATGGAGGGAGGTTGTCCAGTAGACTACAACACTATCACTGATCTCTTCCTTCAG
  |  |||  ||| ||     | ||    || || | |  | | ||    ||   ||  ||| |    ||  |||  ||       ||| || ||| ||||  |  |    |||| ||||| || |||||||| |||||||| ||||||||||||||||| ||||| || |||||||| || |||||||| || ||||||
--acatggaaattctataactatttttttttcatctcaa-tttgcagaaatt-aatagttgtataaactaattcaagaact-----ttctttttcattttggtttct----agGGTGCTGTTAATTTTGCATTAATGATGTCGCAAATGGAGGGAGGTTGCCCAGTTGATTACAACACCATAACTGATCTGTTTCTTCAG

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 12
gtaattggttattttaagcaaacttgggcttaatgtgaggtattcatttgtttggtacatgtttcttttatctcagaaatccttgcttcattgtcaatttgtatcttgaccagGGAGCTGTCAACTTTGCATTGATGATGTCACAAATGGAGGGAGGTTGTCCAGTAGACTACAACACTATCACTGATCTCTTCCTTCAG
   |||| ||||  |  ||  || | |  |||   | |   | |   |  | |  | |  ||||  | | | |      |  ||  || |||   || | || |  |  | |||| ||||| || |||||  |||||||||| ||||||||||| ||||| || || ||||| ||||| || || |||||||| ||||||
--tattgtttatgat--gcttacctag--ttacctttatacaatatctaatatcttgccagtttactcttttt------ttatttgtttatttagaactcgttttattgc-agGGTGCTGTAAATTTTGCTCTGATGATGTCTCAAATGGAGGGGGGTTGCCCTGTTGACTATAACACAATAACCGATCTCTTTCTTCAG

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 14
gtaattggttattttaagcaaacttgggc-ttaatgtgaggtattcatttgtttggtacatgtttcttttatctcagaaatccttgcttcattgtcaatttgtatcttgaccagGGAGCTGTCAACTTTGCATTGATGATGTCACAAATGGAGGGAGGTTGTCCAGTAGACTACAACACTATCACTGATCTCTTCCTTCAG
 ||  | ||| | | | ||   | | |       | |    |||  |||   ||| ||  |   |||||||| |             || |||   || |||| || |  | |||| ||||| || |||||  |||||||||| ||||||||||| ||||| || || ||||||||||| || ||||||||||| ||||||
ctatattgtt-tatgatgcttgcctagttacctttatacaatatcaattatcttgctagtttactcttttatttg------------tttatttagaacttgtttcattgc-agGGTGCTGTAAATTTTGCTCTGATGATGTCTCAAATGGAGGGGGGTTGCCCTGTTGACTACAACACAATAACTGATCTCTTTCTTCAG

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 14
------------------------------------------------------------gtaattgg--ttattttaagcaaacttgggcttaatgtgaggtattcatttgtttggtaca---tgtttcttttatctcagaaatccttgctt-cattgtcaatttgtatcttgac---cagGGAGCTGTCAACTTTGCATTGATGATGTCACAAATGGAGGGAGGTTGTCCAGTAGACTACAACACTATCACTGATCTCTTCCTTCAG
                                                            |||  |    ||||| |  ||   ||||   |   ||||     |   ||||||| | |||   | | |   |||  |    |||   ||||  || |  | ||||  || ||||    ||||| ||||| || |||||||| |||||||| ||||||||||||||| | ||||| || |||||||| || ||||||||||| ||||||
gtgtgagagaaacctctgcagttcatacaatttttttatttgaacctgaaccatttctttgtagctccccttattgtctgcgtccttgttatatctgtggtaactgtttttgttttgaacagtatatgtacattaagttgacaatgtctgctgacagttaccattttcattttgatttgcagGGCGCTGTTAATTTTGCATTAATGATGTCTCAAATGGAGGGAGGTAGCCCAGTTGATTACAACACAATAACTGATCTCTTTCTTCAG

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 14
gtaattggttattttaagcaaacttgggcttaatgtgaggtattcatttgtttggtacatgtttcttttatctcagaaatccttgcttcattgtcaatttgtatcttgaccagGGAGCTGTCAACTTTGCATTGATGATGTCACAAATGGAGGGAGGTTGTCCAGTAGACTACAACACTATCACTGATCTCTTCCTTCAG
        |   |  || |    |||       | ||  | || ||     ||| |   | |||||||||  | |   ||  |   |  |||   ||  | | | |    ||||||||||| || |||||  |||||||| | |||||||| ||||| || ||  | ||||||||||| || ||||||||||| ||||||
-------atctctgaaatctggtttgtttaagttttgtagcatcca---agttgat---tttttcttttagtttatgtatagtaagtatatttcaaaactttctttattgcagGGAGCTGTAAATTTTGCTCTGATGATGGCTCAAATGGAAGGAGGATGCCCCATTGACTACAACACAATAACTGATCTCTTTCTTCAG

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 14
------------------------------------------------------------------------gtaattggttatt---ttaagca------aacttgggcttaatgtgaggtattcattt-gtttggtacatgtttcttttatctcagaaatccttgcttcattgtcaatttgtatcttga---ccagGGAGCTGTCAACTTTGCATTGATGATGTCACAAATGGAGGGAGGTTGTCCAGTAGACTACAACACTATCACTGATCTCTTCCTTCAG
                                                                         |||||| ||||    |||   |       || |||   |  | | |    ||||| |   || | | |  ||  |  | | | | || |  ||     | | ||  |||  || |||    | |||| ||||| || |||||||| |||||||| ||||||||||||||||| ||||| || |||||||| || |||||||| || ||||||
gtatgagagaatcctctgtagttcatattaactatttctttgtatttctcccattgtctgccacactgttggataattgattatcaaattatatattttctgacatggaaattctataactatttcatctcaatttgcagaaattaatagt-tgtaaaaactaattcaacaactttcttttttcattttggtttctagGGTGCTGTTAATTTTGCATTAATGATGTCGCAAATGGAGGGAGGTTGCCCAGTTGATTACAACACCATAACTGATCTGTTTCTTCAG

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 12
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 14
gtaattggttattttaagcaaacttgggcttaatgtgaggtattcatttgtttggtacatgtttcttttatctcagaaatccttgcttcattgtcaatttgtatcttgaccagGGAGCTGTCAACTTTGCATTGATGATGTCACAAATGGAGGGAGGTTGTCCAGTAGACTACAACACTATCACTGATCTCTTCCTTCAG
     || |  | || | ||| |     || |   |  |   |  |   | |   ||   || | |||| |||   || |   | |||  || ||    ||    |||  |||||||| || || ||||| || |||||||| |||||||| |||||||||||||| ||||||||||||||||||||||| |||||||||
--gcctgctgttgtttatcaagc---aactaagcttttgccctgtaaaagatcaata---gtcttttttttctgctaattatcttcttttttttc---ctgctaattg--cagGGAGCAGTAAATTTTGCTTTAATGATGTCCCAAATGGAAGGAGGTTGTCCAGTTGACTACAACACTATCACTGATCTTTTCCTTCAG

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 12
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 14
------------------------------------------------------------------------------gtaattggttattt-taagcaaacttgg-gcttaatgtga---ggtattcatttgtttggtacatgtttcttttatctcagaaatccttgcttcattgtcaatttgtatcttgaccagGGAGCTGTCAACTTTGCATTGATGATGTCACAAATGGAGGGAGGTTGTCCAGTAGACTACAACACTATCACTGATCTCTTCCTTCAG
                                                                                 |   |||||   | | | ||||||  |  |||| |||   | | ||   | |  ||    || ||| |   | |  |  |||  |   |    | | ||||| ||| |    |||||||| || || |||||||| |||||||| |||||||| ||||||| |||||| ||||||||||| ||||||||||| || ||||||
gttagtgtggtgcactcttgatacttgcaacatactaaactatgaaaggactttactgaatatatgtggcgtaagcactggaagagttatgaatcaactaacttgttgaataatttgacctgatgttatatagaatgaagaatctttttcccaccgtattaata-tcaatagtcttttaatttttattt---gcagGGAGCAGTAAATTTTGCATTAATGATGTCTCAAATGGAAGGAGGTTCTCCAGTTGACTACAACACCATCACTGATCTTTTTCTTCAG

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 12
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 14
--------gtaattggttattttaagcaaacttgggcttaatgtgaggtattcatttgtttggtacatgtttcttttatctcagaaatccttgcttcattgtca-atttgtatcttgac--cagGGAGCTGTCAACTTTGCATTGATGATGTCACAAATGGAGGGAGGTTGTCCAGTAGACTACAACACTATCACTGATCTCTTCCTTCAG
        |   ||   || | |  ||| | ||    || |||  |    | ||           | |   | |   ||   | |||   || ||   | |    |||| | | | |    ||||||||||| || |||||  | |||||||| ||||||||||||||||||||  | || |  || || || ||||||||||| ||||||
gtatgcaagcctttttctagtgtttgcagattttccttttatgaaattgttccagaaaggatcagcttaaatttcaaattggataaaattttcctgagtggaggcatttatttttgggttgcagGGAGCTGTAAATTTTGCGCTAATGATGTCTCAAATGGAGGGAGGTTGTCCCATTGATTTTAATACGATAACTGATCTCTTTCTTCAG

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: 168

GTTGGATACACCCCAGATTATCTCTTCCTCCTGCAAACCATTTTGCGGACAGATCCACAGgtaattggtt ... tcttgaccagGGAGCTGTCAACTTTGCATTGATGATGTCACAAATGGAGGGAGGTTGTCCAGTAGACTACAACACTATCACTGATCTCTTCCTTCAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 121

GTTGGATACACCCCAGATTATCTCTTCCTCCTGCAAACCATTTTGCGGACAGATCCACAGgtaattggtt ... tcttgaccagGGAGCTGTCAACTTTGCATTGATGATGTCACAAATGGAGGGAGGTTGTCCAGTAGACTACAACACTATCACTGATCTCTTCCTTCAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 71

GTTGGATACACCCCAGATTATCTCTTCCTCCTGCAAACCATTTTGCGGACAGATCCACAGgtaattggtt ... tcttgaccagGGAGCTGTCAACTTTGCATTGATGATGTCACAAATGGAGGGAGGTTGTCCAGTAGACTACAACACTATCACTGATCTCTTCCTTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 224

GTTGGATACACCCCAGATTATCTCTTCCTCCTGCAAACCATTTTGCGGACAGATCCACAGgtaattggtt ... tcttgaccagGGAGCTGTCAACTTTGCATTGATGATGTCACAAATGGAGGGAGGTTGTCCAGTAGACTACAACACTATCACTGATCTCTTCCTTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtttcttttatctcagaaatccttgcttcattgtcaatttgtatcttgaccagGGAGCTGTCAACTTTGCATTGATGATGTCACAAATGGAGGGAGGTTGTCCAGTAGACTACAACACTATCACTGATCTCTTCCTTCAG
                                     aatttgtat  TA-rich tract