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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgaaaatttacatttggcaaggcaagtgcaacagatataggtcgaaaccgatgttctgttttcgtcaaatactaattgtcacattatgtgctctgcagTGCCATTTCTCGCCTCGGCATGACAAGGCATGTATTGCTTCACCGGTGAGGAACATTGGGGCAGCTTACCATGGTCCTGCTCGTACTACATACAGATCAT

Basic information

species Zea mays
transcript GRMZM2G112782_T01
intron # 4
splice site 3'
intron type U2

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|60359241|gb|DN226214.1|DN226214
EST:     CCGTTCTATTCGGATCACCCTCTTACTGGTGCTGAGTATCTTTCTGATTG                         TGCCATTTCTCGCCTCGGCATGACAAGGCATGTATTGCTTCACCGGTGAGG
genomic: CCGTTCTATTCGGATCACCCTCTTACTGGTGCTGAGTATCTTTCTGATTGgtcagtgccc ... tgctctgcagTGCCATTTCTCGCCTCGGCATGACAAGGCATGTATTGCTTCACCGGTGAGG
EST: gi|110194413|gb|EC876311.1|EC876311
EST:     CCGTTCTATTCGGATCACCCTCTTACTGGTGCTGAGTATCTTTCTGATTG                         TGCCATTTCTCGCCTCGGCATGACAAGGCATGTATTGCTTCACCGGTGAGG
genomic: CCGTTCTATTCGGATCACCCTCTTACTGGTGCTGAGTATCTTTCTGATTGgtcagtgccc ... tgctctgcagTGCCATTTCTCGCCTCGGCATGACAAGGCATGTATTGCTTCACCGGTGAGG
EST: gi|149070488|gb|EE158891.2|EE158891
EST:     CCGTTCTATTCGGATCACCCTCTTACTGGTGCTGAGTATCTTTCTGATTG                         TGCCATTTCTCGCCTCGGCATGACAAGGCATGTATTGCTTCACCGGTGAGG
genomic: CCGTTCTATTCGGATCACCCTCTTACTGGTGCTGAGTATCTTTCTGATTGgtcagtgccc ... tgctctgcagTGCCATTTCTCGCCTCGGCATGACAAGGCATGTATTGCTTCACCGGTGAGG
EST: gi|93016783|gb|EB642303.1|EB642303
EST:     CCGTTCTATTCGGATCACCCTCTTACTGGTGCTGAGTATCTTTCTGATTG                         TGCCATTTCTCGCCTCGGCATGACAAGGCATGTATTGCTTCACCGGTGAGG
genomic: CCGTTCTATTCGGATCACCCTCTTACTGGTGCTGAGTATCTTTCTGATTGgtcagtgccc ... tgctctgcagTGCCATTTCTCGCCTCGGCATGACAAGGCATGTATTGCTTCACCGGTGAGG
EST: gi|71442014|gb|DR823064.1|DR823064
EST:     CCGTTCTATTCGGATCACCCTCTTACTGGTGCTGAGTATCTTTCTGATTG                         TGCCATTTCTCGCCTCGGCATGACAAGGCATGTATTGCTTCACCGGTGAGG
genomic: CCGTTCTATTCGGATCACCCTCTTACTGGTGCTGAGTATCTTTCTGATTGgtcagtgccc ... tgctctgcagTGCCATTTCTCGCCTCGGCATGACAAGGCATGTATTGCTTCACCGGTGAGG
EST: gi|14204198|gb|BG837875.1|BG837875
EST:     CCGTTCTATTCGGATCACCCTCTTACTGGTGCTGAGTATCTTTCTGATTG                         TGCCATTTCTCGCCTCGGCATGACAAGGCATGTATTGCTTCACCGGTGAGG
genomic: CCGTTCTATTCGGATCACCCTCTTACTGGTGCTGAGTATCTTTCTGATTGgtcagtgccc ... tgctctgcagTGCCATTTCTCGCCTCGGCATGACAAGGCATGTATTGCTTCACCGGTGAGG
EST: gi|211457523|gb|FL445969.1|FL445969
EST:     GCTGAGGTATCTTTCTGATTG                         TGCCATTTTTCGCCTCGGCATGACAAGGCATGTATTGCTTCACGGGTGAGG
genomic: GCTGA-GTATCTTTCTGATTGgtcagtgccc ... tgctctgcagTGCCATTTCTCGCCTCGGCATGACAAGGCATGTATTGCTTCACCGGTGAGG
EST: gi|110193128|gb|EC875026.1|EC875026
EST:     CCGTTCTATTCGGATCACCCTCTTACTGGTGCTGAGTATCTTTCTGATTG                         TGCCATTTCTCGCCTCGGCATGACAAGGCATGTATTGCTTCACCGGTGAGG
genomic: CCGTTCTATTCGGATCACCCTCTTACTGGTGCTGAGTATCTTTCTGATTGgtcagtgccc ... tgctctgcagTGCCATTTCTCGCCTCGGCATGACAAGGCATGTATTGCTTCACCGGTGAGG
EST: gi|60337811|gb|DN204784.1|DN204784
EST:     CCGTTCTATTCGGATCACCCTCTTACTGGTGCTGAGTATCTTTCTGATTG                         TGCCATTTCTCGCCTCGGCATGACAAGGCATGTATTGCTTCACCGGTGAGG
genomic: CCGTTCTATTCGGATCACCCTCTTACTGGTGCTGAGTATCTTTCTGATTGgtcagtgccc ... tgctctgcagTGCCATTTCTCGCCTCGGCATGACAAGGCATGTATTGCTTCACCGGTGAGG
EST: gi|211054682|gb|FL184554.1|FL184554
EST:     CCGTTCTATTCGGATCACCCTCTTACTGGTGCTGAGTATCTTTCTGATTG                         TGCCATTTCTCGCCTCGGCATGACAAGGCATGTATTGCTTCACCGGTGAGG
genomic: CCGTTCTATTCGGATCACCCTCTTACTGGTGCTGAGTATCTTTCTGATTGgtcagtgccc ... tgctctgcagTGCCATTTCTCGCCTCGGCATGACAAGGCATGTATTGCTTCACCGGTGAGG
EST: gi|94477558|gb|EB706516.1|EB706516
EST:     CCGTTCTATTCGGATCACCCTCTTACTGGTGCTGAGTATCTTTCTGATTG                         TGCCATTTCTCGCCTCGGCATGACAAGGCATGTATTGCTTCACCGGTGAGG
genomic: CCGTTCTATTCGGATCACCCTCTTACTGGTGCTGAGTATCTTTCTGATTGgtcagtgccc ... tgctctgcagTGCCATTTCTCGCCTCGGCATGACAAGGCATGTATTGCTTCACCGGTGAGG

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), 49 (downstream exon)
Score: 97

AGGACGGGTGGGCTTCATATACAAGGCCAACAACAGAACATTCAGTTTGGCCGTTCTATTCGGATCACCCTCTTACTGGTGCTGAGTATCTTTCTGATTGgtcagtgccc ... tgctctgcagTGCCATTTCTCGCCTCGGCATGACAAGGCATGTATTGCTTCACCGGTGAGGAACATTGGGGCAGCTTACCATGGTCCTGCTCGTACTACATACAGATCAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 88

AGGACGGGTGGGCTTCATATACAAGGCCAACAACAGAACATTCAGTTTGGCCGTTCTATTCGGATCACCCTCTTACTGGTGCTGAGTATCTTTCTGATTGgtcagtgccc ... tgctctgcagTGCCATTTCTCGCCTCGGCATGACAAGGCATGTATTGCTTCACCGGTGAGGAACATTGGGGCAGCTTACCATGGTCCTGCTCGTACTACATACAGATCAT


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 66

AGGACGGGTGGGCTTCATATACAAGGCCAACAACAGAACATTCAGTTTGGCCGTTCTATTCGGATCACCCTCTTACTGGTGCTGAGTATCTTTCTGATTGgtcagtgccc ... tgctctgcagTGCCATTTCTCGCCTCGGCATGACAAGGCATGTATTGCTTCACCGGTGAGGAACATTGGGGCAGCTTACCATGGTCCTGCTCGTACTACATACAGATCAT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 216

AGGACGGGTGGGCTTCATATACAAGGCCAACAACAGAACATTCAGTTTGGCCGTTCTATTCGGATCACCCTCTTACTGGTGCTGAGTATCTTTCTGATTGgtcagtgccc ... tgctctgcagTGCCATTTCTCGCCTCGGCATGACAAGGCATGTATTGCTTCACCGGTGAGGAACATTGGGGCAGCTTACCATGGTCCTGCTCGTACTACATACAGATCAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaaccgatgttctgttttcgtcaaatactaattgtcacattatgtgctctgcagTGCCATTTCTCGCCTCGGCATGACAAGGCATGTATTGCTTCACCGGTGAGGAACATTGGGGCAGCTTACCATGGTCCTGCTCGTACTACATACAGATCAT
                          tactaat  putative branch site (score: 216)
                       aaatactaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgaaaatttacatttggcaaggcaagtgcaacagatataggtcgaaaccgatgttctgttttcgtcaaatactaattgtcacattatgtgctctgcagTGCCATTTCTCGCCTCGGCATGACAAGGCATGTATTGCTTCACCGGTGAGGAACATTGGGGCAGCTTACCATGGTCCTGCTCGTACTACATACAGATCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - tacattt
- - - - - - - - - - - - - - -gcaacag