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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctctgtgtagttcagtagttgtgtatatactattgcatcattccccttttaccctgatgactctgaatcaccgtctgtctgtgacttgcatttgaacagGGTGAGGCTAAGAGCGCTGAGTTGATTGGCCAAGCCATTGCCAACAACCCCGCCTTCCTGGCTCTGAGACAGATTGAAGCTGCCAGGGAGATCTCCCACA

Basic information

species Zea mays
transcript AC217358.3_FGT005
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC217358.3_FGT005 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g60000.1 (Oryza sativa), 3'ss of exon 4
tctctgtgtagttcagtagttgtgtatatactattgc-atcattccccttttaccctgatgactctgaatcaccgtctgtctgtgacttgca-tttgaacagGGTGAGGCTAAGAGCGCTGAGTTGATTGGCCAAGCCATTGCCAACAACCCCGCCTTCCTGGCTCTGAGACAGATTGAAGCTGCCAGGGAGATCTCCCACA
  |      |  ||| | |   |||  ||   ||     |  |     ||| |   || |   | ||  |    ||||| ||||||  |    ||||||||||||||||||||||| ||  || |||||||  | || |||  ||||||||| |||||||| |||||  |||||||||||||||||||||||||||| ||||
-gttaagacatatcaatggcactgttcatttcatcattgttttatatatttcattgtgtttggtgtgggttga-gtctgactgtgaggtctgctttgaacagGGTGAGGCTAAGAGTGCACAGCTGATTGGTGAGGCGATTAACAACAACCCTGCCTTCCTCGCTCTCCGACAGATTGAAGCTGCCAGGGAGATCTCTCACA

upper sequence: AC217358.3_FGT005 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g62490.1 (Oryza sativa), 3'ss of exon 4
-----------------------------------------------------------------------------------------tctctgtgtagttcagtagttgtgtatatactattgcatcattcc---ccttttaccctgatgactctgaatcaccgtctgtctgtgacttgcatttgaacagGGTGAGGCTAAGAGCGCTGAGTTGATTGGCCAAGCCATTGCCAACAACCCCGCCTTCCTGGCTCTGAGACAGATTGAAGCTGCCAGGGAGATCTCCCACA
                                                                                         | |      |  ||| | |   ||| |||  |  | |||  || |     ||| |   |  |   | ||  |    ||||| ||||||       |||||||||||||||||||||| ||  || |||||||  | || |||  ||||||||| |||||||| |||||  |||||||||||||||||||||||||||| ||||
gtaagcaaagatgcaatggattatttctggtttagatggctttcaccatattccttgataagtttactacctgtagttttagtgacaattgttaagacatatcaatggcactgtttat--ttcttcattgtttcatatatttcatttttgttggtgtgggttga-gtctgactgtgaggcctgcttgaacagGGTGAGGCTAAGAGTGCACAGCTGATTGGTGAGGCGATTAACAACAACCCTGCCTTCCTCGCTCTCCGACAGATTGAAGCTGCCAGGGAGATCTCTCACA

upper sequence: AC217358.3_FGT005 (Zea mays), 3'ss of exon 4
lower sequence: Vv15s0048g02350.t01 (Vitis vinifera), 3'ss of exon 6
---tctctgtg-tagttcagtagttgtgtatatactattgcatcattccccttttaccctgatgactctgaatcaccgtctgtctgtgacttgcatttgaacagGGTGAGGCTAAGAGCGCTGAGTTGATTGGCCAAGCCATTGCCAACAACCCCGCCTTCCTGGCTCTGAGACAGATTGAAGCTGCCAGGGAGATCTCCCACA
   |     |  |||||   |  |||      |  |   |  |  ||| |||| |   | | |     | |||       |        ||  |   ||||||||||||||||||||| ||  || |||| || ||||| ||||||||||| || || ||| |  | || ||| | ||||||||| || | || ||  | || |
aatttcaaatactagtttgat--ttggacccctgattgagggtggttcaccttcttttcagtta--cataaattttaaagtaagcaaatctctctggtgaacagGGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCAGCATTCATCACGCTCAGAAAAATTGAAGCTTCCCGAGAAATTGCACATA

upper sequence: AC217358.3_FGT005 (Zea mays), 3'ss of exon 4
lower sequence: Vv19s0085g00730.t01 (Vitis vinifera), 3'ss of exon 6
tctctgtgtagttcagtagttgtgta--tatactattgcatcattccccttttaccctg----atgactctgaatcaccgtctgtctgtgacttgcatttgaacagGGTGAGGCTAAGAGCGCTGAGTTGATTGGCCAAGCCATTGCCAACAACCCCGCCTTCCTGGCTCTGAGACAGATTGAAGCTGCCAGGGAGATCTCCCACA
  |  | || |||||         ||  || |||     ||  | |||||| |   | |    || | | | ||  |  |    |||||  || |    ||||||||||||||||||||| ||  || |||| || ||||| ||||||||||| || || ||| |  | || ||| | ||||||||| || | || ||  | || |
-ttgagggtggttcaccttcctcttagttacactcaaatattgtgccccttcttttcagtttcataaattttaagtaa-gcaaatctgtctctgg----tgaacagGGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCAGCATTCATCACGCTCAGAAAAATTGAAGCTTCCCGAGAAATTGCACATA

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|5005748|gb|AI711810.1|AI711810
EST:     TTGTTGAGAAGGCTGAGCAGGACAAGCGCAGTGCAGTTATCAGGGCACAG                         GGTGAGGCTAAGAGCGCGGAGTTGATTGGCCAAGCCATTGCCAACAACCCC
genomic: TTGTTGAGAAGGCTGAGCAGGACAAGCGCAGTGCAGTTATCAGGGCACAGgttagtggcc ... atttgaacagGGTGAGGCTAAGAGCGCTGAGTTGATTGGCCAAGCCATTGCCAACAACCCC
EST: gi|9733307|gb|BE512059.1|BE512059
EST:     TTGTTGAGAAGGCTGAGCAGGACAAGCGCAGTGCAGTTATCAGGGCACAG                         GGTGAGGCTAAGAGCGCGGAGTTGATTGGCCAAGCCATTGCCAACAACCCC
genomic: TTGTTGAGAAGGCTGAGCAGGACAAGCGCAGTGCAGTTATCAGGGCACAGgttagtggcc ... atttgaacagGGTGAGGCTAAGAGCGCTGAGTTGATTGGCCAAGCCATTGCCAACAACCCC
EST: gi|78081933|gb|DV510345.1|DV510345
EST:     TTGTTGAGAAGGCTGAGCAGGACAAGCGCAGTGCAGTTATCAGGGCACAG                         GGTGAGGCTAAGAGCGCTGAGTTGATTGGCCAAGCCATTTGCCA-CAACCC
genomic: TTGTTGAGAAGGCTGAGCAGGACAAGCGCAGTGCAGTTATCAGGGCACAGgttagtggcc ... atttgaacagGGTGAGGCTAAGAGCGCTGAGTTGATTGGCCAAGCCATT-GCCAACAACCC
EST: gi|148982739|gb|EE028558.2|EE028558
EST:     TTGTTGAGAAGGCTGAGCAGGACAAGCGCAGTGCAGTTATCANGGCACAG                         GGTGAGGCTAAGAGCGCTGAGTTGATTGGCCAAGCCATTTGCCA-CA-CCC
genomic: TTGTTGAGAAGGCTGAGCAGGACAAGCGCAGTGCAGTTATCAGGGCACAGgttagtggcc ... atttgaacagGGTGAGGCTAAGAGCGCTGAGTTGATTGGCCAAGCCATT-GCCAACAACCC
EST: gi|71308360|gb|DR790410.1|DR790410
EST:     TTGTTGAGAAGGCTGAGCAGGACAAGCGCAGTGCAGTTATCAGGGCACAG                         GGTGAGGCTAAGAGCGCTGAGTTGATTGGCCAAGCCATTGCCAACAACCCC
genomic: TTGTTGAGAAGGCTGAGCAGGACAAGCGCAGTGCAGTTATCAGGGCACAGgttagtggcc ... atttgaacagGGTGAGGCTAAGAGCGCTGAGTTGATTGGCCAAGCCATTGCCAACAACCCC
EST: gi|149112958|gb|EE295743.2|EE295743
EST:     TTGTTGAGAAGGCTGAGCAGGACAAGCGCAGTGCAGTTATCAGGGCACAG                         GGTGAGGCTAAGAGCGCTGAGTTGATTGGCCAAGCCATTGCCCACAACCCC
genomic: TTGTTGAGAAGGCTGAGCAGGACAAGCGCAGTGCAGTTATCAGGGCACAGgttagtggcc ... atttgaacagGGTGAGGCTAAGAGCGCTGAGTTGATTGGCCAAGCCATTGCCAACAACCCC
EST: gi|18654880|gb|BM499685.1|BM499685
EST:     TTGTTGAGAAGGCTGAGCAGGACAAGCGCAGTGCAGTTATCAGGGCACAG                         GGTGAGGCTAAGAGCGCGGAGCTGATTGGCCAAGCCATTGCCAACAACCCC
genomic: TTGTTGAGAAGGCTGAGCAGGACAAGCGCAGTGCAGTTATCAGGGCACAGgttagtggcc ... atttgaacagGGTGAGGCTAAGAGCGCTGAGTTGATTGGCCAAGCCATTGCCAACAACCCC
EST: gi|78084473|gb|DV512866.1|DV512866
EST:     TTGTTGAGAAGGCTGAGCAGGACAAGCGCAGTGCAGTTATCAGGGCACAG                         GGTGAGGCTAAGAGCGCTGAGTTGATTGG
genomic: TTGTTGAGAAGGCTGAGCAGGACAAGCGCAGTGCAGTTATCAGGGCACAGgttagtggcc ... atttgaacagGGTGAGGCTAAGAGCGCTGAGTTGATTGG
EST: gi|19437062|gb|BM953472.1|BM953472
EST:     TTGNTGAGAAGGCTGAGCAGGACAAGCGCAGTGCAGTTATCAGGGCACAG                         GGTGAGGCTAAGAGCGCGGAGCTGATTGGCCAAGCCATTGCCAACAACCCC
genomic: TTGTTGAGAAGGCTGAGCAGGACAAGCGCAGTGCAGTTATCAGGGCACAGgttagtggcc ... atttgaacagGGTGAGGCTAAGAGCGCTGAGTTGATTGGCCAAGCCATTGCCAACAACCCC
EST: gi|31355780|gb|CD440137.1|CD440137
EST:     TTGTTGAGAAGGCTGAGCAGGACAAGCGCAGTGCAGTTATCAGGGCACAG                         GGTGAGGCTAAGAGCGCTGAGTTGATTGGCCAAGCCATTGCCAACAACCCC
genomic: TTGTTGAGAAGGCTGAGCAGGACAAGCGCAGTGCAGTTATCAGGGCACAGgttagtggcc ... atttgaacagGGTGAGGCTAAGAGCGCTGAGTTGATTGGCCAAGCCATTGCCAACAACCCC
EST: gi|60398117|gb|DN230933.1|DN230933
EST:     TTGTTGAGAAGGCTGAGCAGGACAAGCGCAGTGCAGTTATCAGGGCACAG                         GGTGAGGCTAAGAGCGCTGAGTTGATTGGCCAAGCCATTGCCAACAACCCC
genomic: TTGTTGAGAAGGCTGAGCAGGACAAGCGCAGTGCAGTTATCAGGGCACAGgttagtggcc ... atttgaacagGGTGAGGCTAAGAGCGCTGAGTTGATTGGCCAAGCCATTGCCAACAACCCC
EST: gi|211504558|gb|FK951745.1|FK951745
EST:     TTGTTGAGAAGGCTGAGCAGGACAAGCGCAGTGCAGTTATCAGGGCACAG                         GGTGAGGCTAAGAGCGCTGAGTTGATTGGCCAAGCCATTGCCAACAACCCC
genomic: TTGTTGAGAAGGCTGAGCAGGACAAGCGCAGTGCAGTTATCAGGGCACAGgttagtggcc ... atttgaacagGGTGAGGCTAAGAGCGCTGAGTTGATTGGCCAAGCCATTGCCAACAACCCC
EST: gi|148987626|gb|EE031500.2|EE031500
EST:     TTGTTGAGAAGGCTGAGCAGGACAAGCGCAGTGCAGTTATCAGGGCACAG                         GGTGAGGCTAAGAGCGCTGAGTTGATTGGCCAAGCCATTGCCAACAACCCC
genomic: TTGTTGAGAAGGCTGAGCAGGACAAGCGCAGTGCAGTTATCAGGGCACAGgttagtggcc ... atttgaacagGGTGAGGCTAAGAGCGCTGAGTTGATTGGCCAAGCCATTGCCAACAACCCC
EST: gi|76011854|gb|DT939024.1|DT939024
EST:     TTGTTGAGAAGGCTGAGCAGGACAAGCGCAGTGCAGTTATCAGGGCACAG                         GGTGAGGCTAAGAG
genomic: TTGTTGAGAAGGCTGAGCAGGACAAGCGCAGTGCAGTTATCAGGGCACAGgttagtggcc ... atttgaacagGGTGAGGCTAAGAG
EST: gi|78079465|gb|DV507877.1|DV507877
EST:     TTGTTGAGAAGGCTGAGCAGGACAAGCGCAGTGCAGTTATCAGGGCACAG                         GGTGAGGCTAAGAGCGCTGAGTTGATTGGCCAAGCCATTGCCAACAACCCC
genomic: TTGTTGAGAAGGCTGAGCAGGACAAGCGCAGTGCAGTTATCAGGGCACAGgttagtggcc ... atttgaacagGGTGAGGCTAAGAGCGCTGAGTTGATTGGCCAAGCCATTGCCAACAACCCC
EST: gi|18654881|gb|BM499686.1|BM499686
EST:     TTGTTGAGAAGGCTGAGCAGGACAAGCGCAGTGCAGTTATCAGGGCACAG                         GGTGAGGCTAAGAGCGCGGAGCTGATTGGCCAAGCCATTGCCAACAACCCC
genomic: TTGTTGAGAAGGCTGAGCAGGACAAGCGCAGTGCAGTTATCAGGGCACAGgttagtggcc ... atttgaacagGGTGAGGCTAAGAGCGCTGAGTTGATTGGCCAAGCCATTGCCAACAACCCC
EST: gi|211504561|gb|FK951748.1|FK951748
EST:     TTGTTGAGAAGGCTGAGCAGGACAAGCGCAGTGCAGTTATCAGGGCACAG                         GGTGAGGCTAAGAGCGCTGAGTTGATTGGNCAAGCCATTGGCAACAACCCC
genomic: TTGTTGAGAAGGCTGAGCAGGACAAGCGCAGTGCAGTTATCAGGGCACAGgttagtggcc ... atttgaacagGGTGAGGCTAAGAGCGCTGAGTTGATTGGCCAAGCCATTGCCAACAACCCC
EST: gi|31356533|gb|CD440890.1|CD440890
EST:     --GTTGAGAAGGCTGAGCAGGACAAGCGCAGTGCAGTTATCAGGGCACAG                         GGTGAGGCTAAGAGCGCTGAGTTGATTGGCCAAGCCATTGCCAACAACCCC
genomic: TTGTTGAGAAGGCTGAGCAGGACAAGCGCAGTGCAGTTATCAGGGCACAGgttagtggcc ... atttgaacagGGTGAGGCTAAGAGCGCTGAGTTGATTGGCCAAGCCATTGCCAACAACCCC

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: 408

CATTGAAGCCAAGCAGGTTGCTGCACAAGAAGCTGAGCGTGCCAAGTTCATTGTTGAGAAGGCTGAGCAGGACAAGCGCAGTGCAGTTATCAGGGCACAGgttagtggcc ... atttgaacagGGTGAGGCTAAGAGCGCTGAGTTGATTGGCCAAGCCATTGCCAACAACCCCGCCTTCCTGGCTCTGAGACAGATTGAAGCTGCCAGGGAGATCTCCCACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 158

CATTGAAGCCAAGCAGGTTGCTGCACAAGAAGCTGAGCGTGCCAAGTTCATTGTTGAGAAGGCTGAGCAGGACAAGCGCAGTGCAGTTATCAGGGCACAGgttagtggcc ... atttgaacagGGTGAGGCTAAGAGCGCTGAGTTGATTGGCCAAGCCATTGCCAACAACCCCGCCTTCCTGGCTCTGAGACAGATTGAAGCTGCCAGGGAGATCTCCCACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 119

CATTGAAGCCAAGCAGGTTGCTGCACAAGAAGCTGAGCGTGCCAAGTTCATTGTTGAGAAGGCTGAGCAGGACAAGCGCAGTGCAGTTATCAGGGCACAGgttagtggcc ... atttgaacagGGTGAGGCTAAGAGCGCTGAGTTGATTGGCCAAGCCATTGCCAACAACCCCGCCTTCCTGGCTCTGAGACAGATTGAAGCTGCCAGGGAGATCTCCCACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 291

CATTGAAGCCAAGCAGGTTGCTGCACAAGAAGCTGAGCGTGCCAAGTTCATTGTTGAGAAGGCTGAGCAGGACAAGCGCAGTGCAGTTATCAGGGCACAGgttagtggcc ... atttgaacagGGTGAGGCTAAGAGCGCTGAGTTGATTGGCCAAGCCATTGCCAACAACCCCGCCTTCCTGGCTCTGAGACAGATTGAAGCTGCCAGGGAGATCTCCCACA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttttaccctgatgactctgaatcaccgtctgtctgtgacttgcatttgaacagGGTGAGGCTAAGAGCGCTGAGTTGATTGGCCAAGCCATTGCCAACAACCCCGCCTTCCTGGCTCTGAGACAGATTGAAGCTGCCAGGGAGATCTCCCACA
       ccctgat  putative branch site (score: 291)
                                             atttgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctctgtgtagttcagtagttgtgtatatactattgcatcattccccttttaccctgatgactctgaatcaccgtctgtctgtgacttgcatttgaacagGGTGAGGCTAAGAGCGCTGAGTTGATTGGCCAAGCCATTGCCAACAACCCCGCCTTCCTGGCTCTGAGACAGATTGAAGCTGCCAGGGAGATCTCCCACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - -ttgcatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgaatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgtctg