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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acgccttgtgttttgtttatcggttattttgagacaccgcgtgttaatgtgcagtatactgataaatgtttatttgaatgataattatttttttgtgcagGATAAATACATGCAAAACAGACTTGTGAGACTAGTTTGTGTTTTTCTGCAGAGTCTTATCCGAAACAAGATTATAAACG

Basic information

species Zea mays
transcript GRMZM2G098815_T04
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G098815_T04 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os12g09610.1 (Oryza sativa), 3'ss of exon 9
acgccttgtgttttgtttatcggttattttgagaca---ccgcgtgttaatgtgcagtatactgataaatgtttatttgaatgataattatttttttgtgcagGATAAATACATGCAAAACAGACTTGTGAGACTAGTTTGTGTTTTTCTGCAGAGTCTTATCCGAAACAAGATTATAAACG
 | | ||| ||  ||  ||      |||||| | |     | | ||||||  |||  ||   |  | ||  |   |  | ||||| ||| || || ||||||||||||||||||||| |||||  | |||||||||||||||||||| || |||  ||| |||||||||||||| |||||||
-ctcattgggtgatgggtaatttgcattttgtggctgcctcacttgttaa-atgcgttactttcttgaagttccttcagtatgattatt-ttattatgtgcagGATAAATACATGCAGAACAGGTTGGTGAGACTAGTTTGTGTTTTCCTTCAGTCTCTCATCCGAAACAAGATCATAAACG

upper sequence: GRMZM2G098815_T04 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA02G00750.2 (Glycine max), 3'ss of exon 10
acgccttgtgttttgtttatcggttattttgagac-accgcgtgttaatgtgcagtatactgataaatgtttatttgaatgataattatttttttgtgcagGATAAATACATGCAAAACAGACTTGTGAGACTAGTTTGTGTTTTTCTGCAGAGTCTTATCCGAAACAAGATTATAAACG---------------------
          |||   |  | |  | |  | |||  ||   |   |    | |      |     |   || |  |   || |   || ||||||   ||||||||||||||||| ||||| ||||||||||| || |||||||||||||| || || || || ||||| ||||| || |                     
-tagtaaccatttctctccttgcatttcataagatgactatgctattgcttccccccctccccccataattaacatctctgctttctactttttttctcagGATAAATACATGCAGAACAGGCTTGTGAGACTTGTCTGTGTTTTTCTGCAAAGCCTCATTCGGAACAATATTATTAATGGTGAGTTTACCCAGTTGGACA

upper sequence: GRMZM2G098815_T04 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA10G00610.1 (Glycine max), 3'ss of exon 10
-acgccttgtgttttgtttatcggttattttgagacaccgc-gtgttaatgtgcagtatactgataaatgtttatttgaatgataattatttttttgtgcagGATAAATACATGCAAAACAGACTTGTGAGACTAGTTTGTGTTTTTCTGCAGAGTCTTATCCGAAACAAGATTATAAACG
 |     |     ||  |        ||||    | |   |  || || ||     |   |  |||| |      |   ||    | | ||||||| | ||||||||||||||||| ||| | ||||||||||| || |||||||||||||| || || || || ||||| ||||| || |
aatttagtaaccatttctctctttgcatttcataatatgactatgctattgcttt-tccccccataattaacatctctgatttctactttttttttct-cagGATAAATACATGCAGAACCGGCTTGTGAGACTTGTCTGTGTTTTTCTGCAAAGCCTCATTCGGAACAACATTATTAATG

upper sequence: GRMZM2G098815_T04 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA02G00750.1 (Glycine max), 3'ss of exon 10
acgccttgtgttttgtttatcggttattttgagac-accgcgtgttaatgtgcagtatactgataaatgtttatttgaatgataattatttttttgtgcagGATAAATACATGCAAAACAGACTTGTGAGACTAGTTTGTGTTTTTCTGCAGAGTCTTATCCGAAACAAGATTATAAACG
          |||   |  | |  | |  | |||  ||   |   |    | |      |     |   || |  |   || |   || ||||||   ||||||||||||||||| ||||| ||||||||||| || |||||||||||||| || || || || ||||| ||||| || |
-tagtaaccatttctctccttgcatttcataagatgactatgctattgcttccccccctccccccataattaacatctctgctttctactttttttctcagGATAAATACATGCAGAACAGGCTTGTGAGACTTGTCTGTGTTTTTCTGCAAAGCCTCATTCGGAACAATATTATTAATG

upper sequence: GRMZM2G098815_T04 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA10G00610.2 (Glycine max), 3'ss of exon 10
-acgccttgtgttttgtttatcggttattttgagacaccgc-gtgttaatgtgcagtatactgataaatgtttatttgaatgataattatttttttgtgcagGATAAATACATGCAAAACAGACTTGTGAGACTAGTTTGTGTTTTTCTGCAGAGTCTTATCCGAAACAAGATTATAAACG---------------------
 |     |     ||  |        ||||    | |   |  || || ||     |   |  |||| |      |   ||    | | ||||||| | ||||||||||||||||| ||| | ||||||||||| || |||||||||||||| || || || || ||||| ||||| || |                     
aatttagtaaccatttctctctttgcatttcataatatgactatgctattgcttt-tccccccataattaacatctctgatttctactttttttttct-cagGATAAATACATGCAGAACCGGCTTGTGAGACTTGTCTGTGTTTTTCTGCAAAGCCTCATTCGGAACAACATTATTAATGGTGAGTTTACCCAGTTGGGAC

upper sequence: GRMZM2G098815_T04 (Zea mays), 3'ss of exon 10
lower sequence: Vv07s0130g00310.t01 (Vitis vinifera), 3'ss of exon 10
acgccttgtgttttgtttatcggttat--tttgagacaccgcgtgttaatgtgcagtatactgataaatgtttatttgaatgataattatttt-tttgtgcagGATAAATACATGCAAAACAGACTTGTGAGACTAGTTTGTGTTTTTCTGCAGAGTCTTATCCGAAACAAGATTATAAACG
   | |  |||| |  |    ||||||  ||   |      | | | |     |    |   | || |    | |     |  |  ||  ||| | | | |||||||  |||||||| ||||||||||||||||| || ||||| ||  ||||||| || || ||||| || ||||| ||||
---cttcctgttgtagtgggtggttatgtttctggtttgttcatatcagcaaacccagttagggtagaaacatctcaatcttcttcttcctttatctttccagGATAGGTACATGCAGAACAGACTTGTGAGACTTGTATGTGTATTCTTGCAGAGCCTAATTCGAAATAAAATTATTAACG

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|94474580|gb|EB703538.1|EB703538
EST:     TTGTCCATGAGTACATCACAAATTGTATCCAATCATGTCAAAACATAAAG                         GATAAATACATGCAAAACAGACTTGTGAGAGTAGTTTGTGNNNNNNNGCAG
genomic: TTGTCCATGAGTACATCACAAATTGTATCCAATCATGTCAAAACATAAAGgtttgttctt ... ttttgtgcagGATAAATACATGCAAAACAGACTTGTGAGACTAGTTTGTGTTTTTCTGCAG
EST: gi|71759264|gb|DR957201.1|DR957201
EST:     TTGTCCATGAGTACATCACAAATTGTATCCAATCATGTCAAAACATAAAG                         GATAAATACATGCAAAACAGACTTGTGAGACTAGTTTGTGTTTTTCTGCAG
genomic: TTGTCCATGAGTACATCACAAATTGTATCCAATCATGTCAAAACATAAAGgtttgttctt ... ttttgtgcagGATAAATACATGCAAAACAGACTTGTGAGACTAGTTTGTGTTTTTCTGCAG
EST: gi|5740633|gb|AI948323.1|AI948323
EST:     TTGTCCATGAGTACATCGCAAATTGTATCCAATCATGTCAAAACATAAAG                         GATAAATACATGCAAAACAGACTTGTGAGACTAGTTTGTGTTTTTCTGCAG
genomic: TTGTCCATGAGTACATCACAAATTGTATCCAATCATGTCAAAACATAAAGgtttgttctt ... ttttgtgcagGATAAATACATGCAAAACAGACTTGTGAGACTAGTTTGTGTTTTTCTGCAG
EST: gi|71433708|gb|DR814758.1|DR814758
EST:     TTGTCCATGAGTACATCACAAATTGTATCCAATCATGTCAAAACATAAAG                         GATAAATACATGCAAAACAGACTTGTGAGACTAGTTTGTGTTTTTCTGCAG
genomic: TTGTCCATGAGTACATCACAAATTGTATCCAATCATGTCAAAACATAAAGgtttgttctt ... ttttgtgcagGATAAATACATGCAAAACAGACTTGTGAGACTAGTTTGTGTTTTTCTGCAG
EST: gi|76014272|gb|DT941442.1|DT941442
EST:     TTGTCCATGAGTACATCACAAATTGTATCCAATCATGTCAAAACATAAAG                         GATAAATACATGCAAAACAGACTTGTGAGACTAGTTTGTGTTTTTCTGCAG
genomic: TTGTCCATGAGTACATCACAAATTGTATCCAATCATGTCAAAACATAAAGgtttgttctt ... ttttgtgcagGATAAATACATGCAAAACAGACTTGTGAGACTAGTTTGTGTTTTTCTGCAG
EST: gi|211480513|gb|FL444430.1|FL444430
EST:     TTGTCCATGAGTACATCACAAATTGTATCCAATCATGTCAAAACATAAAG                         GATAAATACATGCAAAACAGACTTGTGAGACTAGTTTGTGTTTTTCTGCAG
genomic: TTGTCCATGAGTACATCACAAATTGTATCCAATCATGTCAAAACATAAAGgtttgttctt ... ttttgtgcagGATAAATACATGCAAAACAGACTTGTGAGACTAGTTTGTGTTTTTCTGCAG
EST: gi|110944532|gb|EE164689.1|EE164689
EST:     TTGTCCATGAGTACATCACAAATTGTATCCAATCATGTCAAAACATAAAG                         GATAAATACATGCAAAACAGACTTGTGAGACTAGTTTGTGTTTTTCTGCAG
genomic: TTGTCCATGAGTACATCACAAATTGTATCCAATCATGTCAAAACATAAAGgtttgttctt ... ttttgtgcagGATAAATACATGCAAAACAGACTTGTGAGACTAGTTTGTGTTTTTCTGCAG
EST: gi|71449727|gb|DR830777.1|DR830777
EST:     TTGTCCATGAGTACATCACAAATTGTATCCAATCATGTCAAAACATAAAG                         GATAAATACATGCAAAACAGACTTGTGAGACTAGTTTGTGTTTTTCTGCAG
genomic: TTGTCCATGAGTACATCACAAATTGTATCCAATCATGTCAAAACATAAAGgtttgttctt ... ttttgtgcagGATAAATACATGCAAAACAGACTTGTGAGACTAGTTTGTGTTTTTCTGCAG
EST: gi|84969904|gb|DW468307.1|DW468307
EST:     TTGTCCATGAGTACATCACAAATTGTATCCAATCATGTCAAAACATAAAG                         GATAAATACATGCAAAACAGACTTGTGAGACTAGTTTGTGTTTTTCTGCAG
genomic: TTGTCCATGAGTACATCACAAATTGTATCCAATCATGTCAAAACATAAAGgtttgttctt ... ttttgtgcagGATAAATACATGCAAAACAGACTTGTGAGACTAGTTTGTGTTTTTCTGCAG
EST: gi|149082608|gb|EE171807.2|EE171807
EST:     TTGTCCATGAGTACATCACAAATTGTATCCAATCATGTCAAAACATAAAG                         GATAAATACATGCAAAACAGACTTGTGAGACTAGTTTGTGTTTTTCTGCAG
genomic: TTGTCCATGAGTACATCACAAATTGTATCCAATCATGTCAAAACATAAAGgtttgttctt ... ttttgtgcagGATAAATACATGCAAAACAGACTTGTGAGACTAGTTTGTGTTTTTCTGCAG
EST: gi|148952744|gb|EC898725.2|EC898725
EST:     TTGTCCATGAGTACATCACAAATTGTATCCAATCATGTCAAAACATAAAG                         GATAAATACATGCAAAACAGACTTGTGAGACTAGTTTGTGTTTTTCTGCAG
genomic: TTGTCCATGAGTACATCACAAATTGTATCCAATCATGTCAAAACATAAAGgtttgttctt ... ttttgtgcagGATAAATACATGCAAAACAGACTTGTGAGACTAGTTTGTGTTTTTCTGCAG
EST: gi|86472031|gb|DY238401.1|DY238401
EST:     TTGTCCATGAGTACATCACAAATTGTATCCAATCATGTCAAAACATAAAG                         GATAAATACATGCAAAACAGACTTGTGAGACTAGTTTGTGTTTTTCTGCAG
genomic: TTGTCCATGAGTACATCACAAATTGTATCCAATCATGTCAAAACATAAAGgtttgttctt ... ttttgtgcagGATAAATACATGCAAAACAGACTTGTGAGACTAGTTTGTGTTTTTCTGCAG
EST: gi|60336775|gb|DN203748.1|DN203748
EST:     TTGTCCATGAGTACATCACAAATTGTATCCAATCATGTCAAAACATAAAG                         GATAAATACATGCAAAACAGACTTGTGAGACTAGTTTGTGTTTTTCTGCAG
genomic: TTGTCCATGAGTACATCACAAATTGTATCCAATCATGTCAAAACATAAAGgtttgttctt ... ttttgtgcagGATAAATACATGCAAAACAGACTTGTGAGACTAGTTTGTGTTTTTCTGCAG
EST: gi|78022525|gb|DV490912.1|DV490912
EST:     TTGTCCATGAGTACATCACAAATTGTATCCAATCATGTCAAAACATAAAG                         GATAAATACATGCAAAACAGACTTGTGAGACTAGTTTGTGTTTTTCTGCAG
genomic: TTGTCCATGAGTACATCACAAATTGTATCCAATCATGTCAAAACATAAAGgtttgttctt ... ttttgtgcagGATAAATACATGCAAAACAGACTTGTGAGACTAGTTTGTGTTTTTCTGCAG

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), 48 (downstream exon)
Score: 141

TATGGAAGTTGTGAACAGACTCACTACTGCCGTTGACCTTCCAACAGAATTTGTCCATGAGTACATCACAAATTGTATCCAATCATGTCAAAACATAAAGgtttgttctt ... ttttgtgcagGATAAATACATGCAAAACAGACTTGTGAGACTAGTTTGTGTTTTTCTGCAGAGTCTTATCCGAAACAAGATTATAAACG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 110

TATGGAAGTTGTGAACAGACTCACTACTGCCGTTGACCTTCCAACAGAATTTGTCCATGAGTACATCACAAATTGTATCCAATCATGTCAAAACATAAAGgtttgttctt ... ttttgtgcagGATAAATACATGCAAAACAGACTTGTGAGACTAGTTTGTGTTTTTCTGCAGAGTCTTATCCGAAACAAGATTATAAACG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 156

TATGGAAGTTGTGAACAGACTCACTACTGCCGTTGACCTTCCAACAGAATTTGTCCATGAGTACATCACAAATTGTATCCAATCATGTCAAAACATAAAGgtttgttctt ... ttttgtgcagGATAAATACATGCAAAACAGACTTGTGAGACTAGTTTGTGTTTTTCTGCAGAGTCTTATCCGAAACAAGATTATAAACG


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 72

TATGGAAGTTGTGAACAGACTCACTACTGCCGTTGACCTTCCAACAGAATTTGTCCATGAGTACATCACAAATTGTATCCAATCATGTCAAAACATAAAGgtttgttctt ... ttttgtgcagGATAAATACATGCAAAACAGACTTGTGAGACTAGTTTGTGTTTTTCTGCAGAGTCTTATCCGAAACAAGATTATAAACG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgtgcagtatactgataaatgtttatttgaatgataattatttttttgtgcagGATAAATACATGCAAAACAGACTTGTGAGACTAGTTTGTGTTTTTCTGCAGAGTCTTATCCGAAACAAGATTATAAACG
           tactgat  putative branch site (score: 72)
                                       ttattttttt  putative PPT
         tatactgataaatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acgccttgtgttttgtttatcggttattttgagacaccgcgtgttaatgtgcagtatactgataaatgtttatttgaatgataattatttttttgtgcagGATAAATACATGCAAAACAGACTTGTGAGACTAGTTTGTGTTTTTCTGCAGAGTCTTATCCGAAACAAGATTATAAACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - tgtgttt
- - - - - - - - - - - - - - - - - - - - - - - -tgtgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tactgat