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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcttccccattgcaatacattatcccttttcggaagatacagttgtctttccatatgctataatatgtgcagtctttctgattctaaatgcctttgcagATTCATCCTGTCGTTTCTCGTCTGTGTGCTTCCATTCAGGGCACTAGTCCAGCTCGTCTGGCTGAATGTCTGGGCCTTGATTCGGCTAAG

Basic information

species Zea mays
transcript GRMZM2G149802_T02
intron # 24
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149802_T02 (Zea mays), 3'ss of exon 24
lower sequence: LOC_Os01g64820.1 (Oryza sativa), 3'ss of exon 24
gttcttccccattgcaatacattatcccttttcggaagatacagttgtctttccatatgctataatatgtgcagtctttctgattctaaatgcc-tttgcagATTCATCCTGTCGTTTCTCGTCTGTGTGCTTCCATTCAGGGCACTAGTCCAGCTCGTCTGGCTGAATGTCTGGGCCTTGATTCGGCTAAG
                     ||  |  |     ||| |   | |      |   |  | |||  |||||  |   | ||| |||||  || || ||| |||||||||||||| ||||| |||||||||||||| || |||||||| || |||||||| ||||||||||| || || ||||||||  | |||
--------------------gttccctttgcatagaaaaagaaatataagcttatttcgttatgctatgtctatattctcttattctggattccgtttacagATTCATCCTGTAGTTTCCCGTCTGTGTGCTTCGATCCAGGGCACCAGCCCAGCTCGCCTGGCTGAATGCCTTGGGCTTGATTCATCCAAG

upper sequence: GRMZM2G149802_T02 (Zea mays), 3'ss of exon 24
lower sequence: Vv07s0031g00470.t01 (Vitis vinifera), 3'ss of exon 23
---gttcttccccattg-caatacattatcccttttcggaagatacagttgtctttccatatgctataatatgtgcagtctttctgattctaaatgccttt--gcagATTCATCCTGTCGTTTCTCGTCTGTGTGCTTCCATTCAGGGCACTAGTCCAGCTCGTCTGGCTGAATGTCTGGGCCTTGATTCGGCTAAG
    | |||    ||||   || | | ||    ||   | |  ||  ||||  ||   ||  |||  | | |   |||  |   ||||  | |||  || |  ||||||||||||||| || |||||||| |||||||| |||||||| || || ||||| ||| |||| || ||| | || ||||| ||  | |||
gttttgcttatgtattgatgatgcttaattaaattgtagtaactaatgttggtttgtgattagcttcattctc--cagcttgcttgatggttaatatctctatgcagATTCATCCTGTGGTCTCTCGTCTATGTGCTTCAATTCAGGGTACAAGCCCAGCACGTTTGGCCGATTGTTTAGGGCTTGACTCATCCAAG
















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|32939296|gb|CF044115.1|CF044115
EST:     GAGACCCTGACAAGTGGATGATTGACATTGACTATTATTTATCACAACAG                         ATTCATCCTGTTGTTTCTCGTCTGTGTGCTTCCATTCAGGGCACTAGTCCA
genomic: GAGACCCTGACAAGTGGATGATTGACATTGACTATTATTTATCACAACAGgttcttcccc ... gcctttgcagATTCATCCTGTCGTTTCTCGTCTGTGTGCTTCCATTCAGGGCACTAGTCCA
EST: gi|211402399|gb|FL354720.1|FL354720
EST:     GAGACCCTGACAAGTGGATGATTGACATTGACTATTATTTATCACAACAG                         ATTCATCCTGTTGTTTCTCGTCTGTGTGCTTCCATTCAGGGCACTAGTCCA
genomic: GAGACCCTGACAAGTGGATGATTGACATTGACTATTATTTATCACAACAGgttcttcccc ... gcctttgcagATTCATCCTGTCGTTTCTCGTCTGTGTGCTTCCATTCAGGGCACTAGTCCA
EST: gi|32938785|gb|CF043604.1|CF043604
EST:     GAGACCCTGACAAGTGGATGATTGACATTGACTATTATTTATCACAACAG                         ATTCATCCTGTTGTTTCTCGTCTGTGTGCTTCCATTCAGGGCACTAGTCCA
genomic: GAGACCCTGACAAGTGGATGATTGACATTGACTATTATTTATCACAACAGgttcttcccc ... gcctttgcagATTCATCCTGTCGTTTCTCGTCTGTGTGCTTCCATTCAGGGCACTAGTCCA
EST: gi|32938920|gb|CF043739.1|CF043739
EST:     GAGACCCTGACAAGTGGATGATTGACATTGACTATTATTTATCACAACAG                         ATTCATCCTGTTGTTTCTCGTCTGTGTGCTTCCATTCAGGGCACTAGTCCA
genomic: GAGACCCTGACAAGTGGATGATTGACATTGACTATTATTTATCACAACAGgttcttcccc ... gcctttgcagATTCATCCTGTCGTTTCTCGTCTGTGTGCTTCCATTCAGGGCACTAGTCCA
EST: gi|74242013|gb|DT649927.1|DT649927
EST:     GAGACCCTGACAAGTGGATGATTGACATTGACTATTATTTATCACAACAG                         ATTCATCCTGTCGTTTCTCGTCTGTGTGCTTCCATTCAGGGCACTAGTCCA
genomic: GAGACCCTGACAAGTGGATGATTGACATTGACTATTATTTATCACAACAGgttcttcccc ... gcctttgcagATTCATCCTGTCGTTTCTCGTCTGTGTGCTTCCATTCAGGGCACTAGTCCA

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: 47 (upstream exon), 47 (downstream exon)
Score: 59

ACATTCTGTGGGAATAGCTCAGAGAGCTAGACATCCCGAGGAGTTAAAAAGAGACCCTGACAAGTGGATGATTGACATTGACTATTATTTATCACAACAGgttcttcccc ... gcctttgcagATTCATCCTGTCGTTTCTCGTCTGTGTGCTTCCATTCAGGGCACTAGTCCAGCTCGTCTGGCTGAATGTCTGGGCCTTGATTCGGCTAAG


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 16

ACATTCTGTGGGAATAGCTCAGAGAGCTAGACATCCCGAGGAGTTAAAAAGAGACCCTGACAAGTGGATGATTGACATTGACTATTATTTATCACAACAGgttcttcccc ... gcctttgcagATTCATCCTGTCGTTTCTCGTCTGTGTGCTTCCATTCAGGGCACTAGTCCAGCTCGTCTGGCTGAATGTCTGGGCCTTGATTCGGCTAAG


Block sizes: 35 (upstream exon), 47 (downstream exon)
Score: 22

ACATTCTGTGGGAATAGCTCAGAGAGCTAGACATCCCGAGGAGTTAAAAAGAGACCCTGACAAGTGGATGATTGACATTGACTATTATTTATCACAACAGgttcttcccc ... gcctttgcagATTCATCCTGTCGTTTCTCGTCTGTGTGCTTCCATTCAGGGCACTAGTCCAGCTCGTCTGGCTGAATGTCTGGGCCTTGATTCGGCTAAG


Block sizes: 44 (upstream exon), 44 (downstream exon)
Score: 10

ACATTCTGTGGGAATAGCTCAGAGAGCTAGACATCCCGAGGAGTTAAAAAGAGACCCTGACAAGTGGATGATTGACATTGACTATTATTTATCACAACAGgttcttcccc ... gcctttgcagATTCATCCTGTCGTTTCTCGTCTGTGTGCTTCCATTCAGGGCACTAGTCCAGCTCGTCTGGCTGAATGTCTGGGCCTTGATTCGGCTAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctttccatatgctataatatgtgcagtctttctgattctaaatgcctttgcagATTCATCCTGTCGTTTCTCGTCTGTGTGCTTCCATTCAGGGCACTAGTCCAGCTCGTCTGGCTGAATGTCTGGGCCTTGATTCGGCTAAG
                                     ttctaaa  putative branch site (score: 10)
                                            tgccttt  CT-rich tract
        atatgctataatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcttccccattgcaatacattatcccttttcggaagatacagttgtctttccatatgctataatatgtgcagtctttctgattctaaatgcctttgcagATTCATCCTGTCGTTTCTCGTCTGTGTGCTTCCATTCAGGGCACTAGTCCAGCTCGTCTGGCTGAATGTCTGGGCCTTGATTCGGCTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC