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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgagatgtagcctttcatttgtacttggatgttagcggtccagatattgctctgtcctgactcgaccctctgcagCTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAG

Basic information

species Zea mays
transcript GRMZM2G303431_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G303431_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os11g38800.1 (Oryza sativa), 3'ss of exon 6
-----------------------------------------------gtgagtgagatgtagcctttcatttgtacttggatgttagcggtccagatattgctctgtcctgactcgaccctctgcagCTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAG
                                                ||||    |||| | |||  |  | |  ||  |  | |    |  | || |     ||| ||   || |    |  ||||| ||||| |||||||||||||| ||||||||||| ||||| |||||||| |||||||||||||||||||||||||| ||||||||||||
gttagtcttgtgttccttccccactttttttatcttattggttctttctgagctcaatgttgacttaaaaatctttttttacatgac---ttaaaatctattaatgttct---tcaatgtccaacagCTCTTTCTACTTCGAGCTGCTGGATTTCTGCTGCCATGCTATATCATGGCTTGGATATTCAGTATTTTGCATCGCCGGCGACAAAGACAG

upper sequence: GRMZM2G303431_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA20G04870.1 (Glycine max), 3'ss of exon 5
--------------------gtgagtgagatgt-agcctttcatttgtacttggatgttag--cggtccagatattgctctgtcctgactcgaccctctgcagCTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAG
                     ||  | ||  || | |     ||||||| ||| ||   |   |  |   |   |  |    |       | |  |||||||||||||  ||||||| |||||||| |||||  | || ||||| |||||||| |||  | ||||||||||||| ||||| ||||||||||| 
gtgagtgactttagttcattttggataagtggttaacacagtatttgta-ttgcattcaaatacattgtcggcctaacctaattacacaaccaaactctgcagCTTTTCTTGCTTCGTGCTGCTGGTTTTCTTTTACCTTGCTATATCATGGCTTGGGCAATCAGTATTTTGCAACGCCGGCGACAAAGACAA

upper sequence: GRMZM2G303431_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA07G35750.2 (Glycine max), 3'ss of exon 5
-------------gtgagtgagatgta-gcctttcattt-gtacttggat-gttagcggtccagatattgctctgtcctgact------cgaccctctgcagCTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAG
             ||   | ||   || |   ||||| | ||| ||| || | |  |         ||||  ||  ||| |        | |  |||||||||||||  |||||||||||||||| |||||  | || ||||| |||||||| |||  | ||||||||||||| ||||| ||||||||||| 
gtgagtgactttagttcattagggataagtggttcatatagtagttgtattgctttcaaatacatcattgggctaacctcatcacatggccattctctgcagCTTTTCTTGCTTCGAGCTGCTGGTTTTCTTTTACCTTGCTATATCATGGCTTGGGCAATCAGTATTTTGCAACGCCGGCGACAAAGACAA

upper sequence: GRMZM2G303431_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA01G05800.1 (Glycine max), 3'ss of exon 6
------------------gtgagtgagatgtagcctttcatttgtacttggatgtta----gcggtccagatattgctctgtcctga---ctcgaccctctgcagCTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAG
                       | ||    |  ||| || |  |   | ||| | |    ||  |  |||     |    || | |   ||| |   ||||||||||||  ||||||| |||||||| |||||  | || |||||||||||||| |||  | |||||||| |||| || || ||||||||||| 
gtgagtgatttgagtttttctttttagtcaaattcttccaatgttttattgatttcaaaatgcaatttagagccaacctaatcgtcagctctctattttctgcagCTTTTCTTGCTTCGTGCTGCTGGATTTCTATTACCTTGCTACATCATGGCTTGGGCAATCAGTATTCTGCAGCGTCGGCGACAAAGACAA

upper sequence: GRMZM2G303431_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA02G11960.1 (Glycine max), 3'ss of exon 6
-----------------------gtgagtgagatgtagcct---ttcatttgtacttggatgtta----gcggtccagatattgctctgtcctgactcgaccctctgcagCTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAG
                        | ||| |  |    ||    | || |  |   | ||| | |    ||  | ||||     |    ||    | | |   ||||||||||||  ||||||| || ||||| |||||  | || |||||||||||||| |||  | |||||||| |||| || || ||||||||||| 
gtaagtgatttgagttttttctttttagtcaagttcttcccatgtccaatgttttattgatttcaaaatgcaatgcagagcccacctaatctgctcactattttctgcagCTTTTCTTGCTTCGTGCCGCTGGATTTCTATTACCTTGCTACATCATGGCTTGGGCAATCAGTATTCTGCAGCGTCGGCGACAAAGACAA

upper sequence: GRMZM2G303431_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv01s0026g02470.t01 (Vitis vinifera), 3'ss of exon 8
-------------gtgagtgagatgtagcctttcatttgtacttggatgttagcggtccagatattgctctgtcctgact-------cgaccctctgcagCTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAG
                  ||| ||||    || |||   |       | |  |   |     | |||  |   | | |||        ||  || ||||||||||  ||||||| |||||||||||| | ||||| |||||||| ||||| |||    | ||||| ||||| || ||  |||| || |||
accctttattttatcacatgaaatgtgtatttccatagtttgccaattttgggtcattttattgttgaaccaacttcactaactggttgatgctttgcagCTTTTCTTGCTTCGGGCTGCTGGGTTTTTACTGCCCTGCTACATTATGGCCTGGGCCATTAGTATCTTGCAGCGTCGAAGACAGAGGCAG

upper sequence: GRMZM2G303431_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv17s0000g06230.t01 (Vitis vinifera), 3'ss of exon 6
---------------------------------------gtgagtgag-atgtagcctttcatttgtacttggatgttagcggtccagatattgctctgtcctgactc-----gaccctctgcagCTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAG
                                       ||| |   | ||||  |  | | | | ||  |  ||| | ||     ||   || | |  |    |  |     ||  ||   |||||||| ||||||||||||||||| || || || || |||||||| ||||| |||    ||||||| ||||| || ||  |||||||||||
gtgagtgagatatgtgtactattcatttgataataatttgtgtgcttgtatgtgtctatacttgtatatatccatggttgcatggaagtggtttcaccattaaaatacatatggatgcttgacagCTTTTCCTGCTTCGAGCTGCTGGTTTCCTTCTCCCTTGCTACATTATGGCCTGGGCTATCAGTATATTGCAGCGTCGAAGACAAAGACAG

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|32868616|gb|CF008298.1|CF008298
EST:     CTATGTCAGACAACGAAGGAAACGATGATGACGCTTCTACCATATTCTCG                         CTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCA
genomic: CTATGTCAGACAACGAAGGAAACGATGATGACGCTTCTACCATATTCTCGgtgagtgaga ... ccctctgcagCTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCA
EST: gi|71761787|gb|DR959724.1|DR959724
EST:     CTATGTCAGACAACGAAGGAAACGATGATGACGCTTCTACCATATTCTCG                         CTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCA
genomic: CTATGTCAGACAACGAAGGAAACGATGATGACGCTTCTACCATATTCTCGgtgagtgaga ... ccctctgcagCTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCA
EST: gi|149074740|gb|EE163170.2|EE163170
EST:     CTATGTCAGACAACGAAGGAAACGATGATGACGCTTCTACCATATTCTCG                         CTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCA
genomic: CTATGTCAGACAACGAAGGAAACGATGATGACGCTTCTACCATATTCTCGgtgagtgaga ... ccctctgcagCTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCA
EST: gi|37374573|gb|CF623659.1|CF623659
EST:     CAACGAAGGAAACGATGATGACGCTTCTACCATATTCTCG                         CTTTTTCTGCTTCGAGCTGCTGTGTTTCTGCTGCCGTGCTACATCATGGCA
genomic: CAACGAAGGAAACGATGATGACGCTTCTACCATATTCTCGgtgagtgaga ... ccctctgcagCTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCA
EST: gi|211322224|gb|FL096771.1|FL096771
EST:     CTATGTCAGACAACGAAGGAAACGATGATGACGCTTCTACCATATTCTCG                         CTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCA
genomic: CTATGTCAGACAACGAAGGAAACGATGATGACGCTTCTACCATATTCTCGgtgagtgaga ... ccctctgcagCTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCA
EST: gi|32858443|gb|CD998124.1|CD998124
EST:     CTATGGCAAACCACCAAGGAAACCATGATTACCCTTTTACCATATTCTCG                         CTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCA
genomic: CTATGTCAGACAACGAAGGAAACGATGATGACGCTTCTACCATATTCTCGgtgagtgaga ... ccctctgcagCTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCA
EST: gi|61118260|gb|DN559221.1|DN559221
EST:     GTCAGACAACGAAGGAAACCGATGATGACGCTTCTACCATATTCTCG                         CTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCA
genomic: GTCAGACAACGAAGGAAA-CGATGATGACGCTTCTACCATATTCTCGgtgagtgaga ... ccctctgcagCTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCA
EST: gi|32919905|gb|CF024717.1|CF024717
EST:     CTATGTCAGACAACGAAGGAAACGATGATGACGCTTCTACCATATTCTCG                         CTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCA
genomic: CTATGTCAGACAACGAAGGAAACGATGATGACGCTTCTACCATATTCTCGgtgagtgaga ... ccctctgcagCTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCA
EST: gi|211322223|gb|FL096770.1|FL096770
EST:     CTATGTCAGACAACGAAGGAAACGATGATGACGCTTCTACCATATTCTCG                         CTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCA
genomic: CTATGTCAGACAACGAAGGAAACGATGATGACGCTTCTACCATATTCTCGgtgagtgaga ... ccctctgcagCTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCA
EST: gi|22546481|gb|BU098792.1|BU098792
EST:     TCTACCATATTCTCG                         CTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCA
genomic: TCTACCATATTCTCGgtgagtgaga ... ccctctgcagCTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCA
EST: gi|60401280|gb|DN234087.1|DN234087
EST:     CTGTGTCAGACAACGAAGGAAACGATGATGACGCTTCTACCATATTCTCG                         CTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCA
genomic: CTATGTCAGACAACGAAGGAAACGATGATGACGCTTCTACCATATTCTCGgtgagtgaga ... ccctctgcagCTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCA
EST: gi|24934168|gb|CA452386.1|CA452386
EST:     CTATGTCAGNCANCGAAGGAAACGATGATGACGCTTCTACCATATTCTCG                         CTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCA
genomic: CTATGTCAGACAACGAAGGAAACGATGATGACGCTTCTACCATATTCTCGgtgagtgaga ... ccctctgcagCTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCA

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: 48 (upstream exon), 48 (downstream exon)
Score: 226

TTAATGGCACTGTTGCTTCTAAGGCATGCATTGTCTATGTCAGACAACGAAGGAAACGATGATGACGCTTCTACCATATTCTCGgtgagtgaga ... ccctctgcagCTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 336

TTAATGGCACTGTTGCTTCTAAGGCATGCATTGTCTATGTCAGACAACGAAGGAAACGATGATGACGCTTCTACCATATTCTCGgtgagtgaga ... ccctctgcagCTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 421

TTAATGGCACTGTTGCTTCTAAGGCATGCATTGTCTATGTCAGACAACGAAGGAAACGATGATGACGCTTCTACCATATTCTCGgtgagtgaga ... ccctctgcagCTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 227

TTAATGGCACTGTTGCTTCTAAGGCATGCATTGTCTATGTCAGACAACGAAGGAAACGATGATGACGCTTCTACCATATTCTCGgtgagtgaga ... ccctctgcagCTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtacttggatgttagcggtccagatattgctctgtcctgactcgaccctctgcagCTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAG
                                  tcctgac  putative branch site (score: 227)
                                             ccctctgc  putative PPT
                     agatatt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgagatgtagcctttcatttgtacttggatgttagcggtccagatattgctctgtcctgactcgaccctctgcagCTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA