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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgttcatgaaggctaccatgctttccatctagcagtatacaacataactacttaataatatactctattgtttctagtgatgtgaggttcttcttgctgctttacagGTCCGATGCTTTAATGCTCCACTCCAGCCTACTGAAATTTCAGGAGTTAAGAGAGTTGTTCAGGAGAAGATGCCTGAAGGCGTAAATGAAAGCGGCCTTA

Basic information

species Zea mays
transcript GRMZM2G004459_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G004459_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g59590.1 (Oryza sativa), 3'ss of exon 4
gtttgtgttcatgaaggctaccatgctttccatctagcagtatacaacataactacttaataatatactctattgtttctagtgatg--tgaggttcttcttgctgctttacagGTCCGATGCTTTAATGCTCCACTCCAGCCTACTGAAATTTCAGGAGTTAAGAGAGTTGTTCAGGAGAAGATGCCTGAAGGCGTAAATGAAAGCGGCCTTA
|||||| ||||   || ||||| |||||||        |||           ||  ||| |   ||  ||| || ||| | ||| ||  |        |  || ||||||| |||||  |||||| |||||||| |||||||||||||||||| |||| || |||||||| ||||| |||||||||||||||||||| ||||| |  |||||||
gtttgtattcacttagtctaccttgctttctgctc--tagtg----------ctttttattgccat--tctgttatttatggtgttgattagaacctcttctggtgctttatagGTCAAATGCTTCAATGCTCCTCTCCAGCCTACTGAAATTGCAGGCGTGAAGAGAGTGGTTCAAGAGAAGATGCCTGAAGGCGTGAATGACAATGGCCTTA

upper sequence: GRMZM2G004459_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g62570.1 (Oryza sativa), 3'ss of exon 4
gtttgtgttcatgaaggctaccatgctttccatctagcagtatacaacata--actactt--aataatatact-ctattgtttctagtgatgtgagg----ttcttcttgctgctttacagGTCCGATGCTTTAATGCTCCACTCCAGCCTACTGAAATTTCAGGAGTTAAGAGAGTTGTTCAGGAGAAGATGCCTGAAGGCGTAAATGAAAGCGGCCTTA
||||||   ||  || ||| || || ||||  |  |  ||| ||   || |  | | |||  | ||  || ||  || |  |||| ||||||| | |    | ||| | |||||||||||||||  |||||| |||||||| ||||| |||| ||||||   ||| || ||||||    | || |||||  || ||||||| ||||||||||  |||||||
gtttgtagccactaaagctgccttggtttct-ttgattagtgtaaggcaaactaatgcttgcactatcattctattaatacttctggtgatgttaagaatctccttttggctgctttacagGTCATATGCTTCAATGCTCCTCTCCAACCTAATGAAATCATAGGCGTGAAGAGAACCATCCAAGAGAAATTGACTGAAGGTGTAAATGAAAATGGCCTTA
















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|31361614|gb|CD445971.1|CD445971
EST:     ATAATGACAAGGATGGTGCTCTCAGTGATGTGGAGCTCAATGAATTCCAG                         GTCCGATGCTTTAATGCTCCACTCCAGCCTACTGAAATTTCAGGAGTTAAG
genomic: ATAATGACAAGGATGGTGCTCTCAGTGATGTGGAGCTCAATGAATTCCAGgtttgtgttc ... tgctttacagGTCCGATGCTTTAATGCTCCACTCCAGCCTACTGAAATTTCAGGAGTTAAG
EST: gi|78084949|gb|DV513342.1|DV513342
EST:     ATAATGACAAGGATGGTGCTCTCAGTGATGTGGAGCTCAATGAATTCCAG                         GTCCGATGCTTTAATGCTCCACTCCAGCCTACTGAAATTTCAGGAGTTAAG
genomic: ATAATGACAAGGATGGTGCTCTCAGTGATGTGGAGCTCAATGAATTCCAGgtttgtgttc ... tgctttacagGTCCGATGCTTTAATGCTCCACTCCAGCCTACTGAAATTTCAGGAGTTAAG
EST: gi|211289495|gb|FL459844.1|FL459844
EST:     ATAATGACAAGGATGGTGCTCTCAGTGATGTGGAGCTCAATGAATTCCAG                         GTCCGATGCTTTAATGCTCCACTCCAGCCTACTGAAATTTCAGGAGTTAA
genomic: ATAATGACAAGGATGGTGCTCTCAGTGATGTGGAGCTCAATGAATTCCAGgtttgtgttc ... tgctttacagGTCCGATGCTTTAATGCTCCACTCCAGCCTACTGAAATTTCAGGAGTTAA
EST: gi|211153232|gb|FL160597.1|FL160597
EST:     ATAATGACAAGGATGGTGCTCTCAGTGATGTGGAGCTCAATGAATTCCAG                         GTCCGATGCTTTAATGCTCCACTCCAGCCTACTGAAATTTCAGGAG
genomic: ATAATGACAAGGATGGTGCTCTCAGTGATGTGGAGCTCAATGAATTCCAGgtttgtgttc ... tgctttacagGTCCGATGCTTTAATGCTCCACTCCAGCCTACTGAAATTTCAGGAG
EST: gi|211289494|gb|FL459843.1|FL459843
EST:     ATAATGACAAGGATGGTGCTCTCAGTGATGTGGAGCTCAATGAATTCCAG                         GTCCGATGCTTTAATGCTCCACTCCAGCCTACTGAAATT-CAGGAGTTAA
genomic: ATAATGACAAGGATGGTGCTCTCAGTGATGTGGAGCTCAATGAATTCCAGgtttgtgttc ... tgctttacagGTCCGATGCTTTAATGCTCCACTCCAGCCTACTGAAATTTCAGGAGTTAA
EST: gi|91053299|gb|EB163717.1|EB163717
EST:     ATAATGACAAGGATGGTGCTCTCAGTGATGTGGAGCTCAATGAATTCCAG                         GTCCGATGCTTTAATGCTCCACTCCAGCCTACTGAAATTTCAGGAGTTAAG
genomic: ATAATGACAAGGATGGTGCTCTCAGTGATGTGGAGCTCAATGAATTCCAGgtttgtgttc ... tgctttacagGTCCGATGCTTTAATGCTCCACTCCAGCCTACTGAAATTTCAGGAGTTAAG
EST: gi|60339673|gb|DN206646.1|DN206646
EST:     ATAATGACAAGGATGGTGCTCTCAGTGATGTGGAGCTCAATGAATTCCAG                         GTCCGATGCTTTAATGCTCCACTCCAGCCTACTGAAATTTCAGGAGTTAAG
genomic: ATAATGACAAGGATGGTGCTCTCAGTGATGTGGAGCTCAATGAATTCCAGgtttgtgttc ... tgctttacagGTCCGATGCTTTAATGCTCCACTCCAGCCTACTGAAATTTCAGGAGTTAAG
EST: gi|211153243|gb|FL160608.1|FL160608
EST:     ATAATGACAAGGATGGTGCTCTCAGTGATGTGGAGCTCAATGAATTCCAG                         GTCCGATGCTTTAATGCTCCACTCCAGCCTACTGAAATTTCAGGAGTTAAG
genomic: ATAATGACAAGGATGGTGCTCTCAGTGATGTGGAGCTCAATGAATTCCAGgtttgtgttc ... tgctttacagGTCCGATGCTTTAATGCTCCACTCCAGCCTACTGAAATTTCAGGAGTTAAG
EST: gi|60340644|gb|DN207617.1|DN207617
EST:     ATAATGACAAGGATGGTGCTCTCAGTGATGTGGAGCTCAATGAATTCCAG                         GTCCGATGCTTTAATGCTCCACTCCAGCCTACTGAAATTTCAGGAGTTAAG
genomic: ATAATGACAAGGATGGTGCTCTCAGTGATGTGGAGCTCAATGAATTCCAGgtttgtgttc ... tgctttacagGTCCGATGCTTTAATGCTCCACTCCAGCCTACTGAAATTTCAGGAGTTAAG
EST: gi|60354705|gb|DN221678.1|DN221678
EST:     ATAATGACAAGGATGGTGCTCTCAGTGATGTGGAGCTCAATGAATTCCAG                         GTCCGATGCTTTAATGCTCCACTCCAGCCTACTGAAATTTCAGGAGTTAAG
genomic: ATAATGACAAGGATGGTGCTCTCAGTGATGTGGAGCTCAATGAATTCCAGgtttgtgttc ... tgctttacagGTCCGATGCTTTAATGCTCCACTCCAGCCTACTGAAATTTCAGGAGTTAAG
EST: gi|31358133|gb|CD442490.1|CD442490
EST:     ATAATGACAAGGATGGTGCTCTCAGTGATGTGGAGCTCAATGAATTCCAG                         GTCCGATGCTTTAATGCTCCACTCCAGCCTACTGAAATTTCAGGAGTTAAG
genomic: ATAATGACAAGGATGGTGCTCTCAGTGATGTGGAGCTCAATGAATTCCAGgtttgtgttc ... tgctttacagGTCCGATGCTTTAATGCTCCACTCCAGCCTACTGAAATTTCAGGAGTTAAG

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: 169

TCTGAAGCCTCGATGTGTGAGAGCGTTGAAGCGGATATTTATTATATGTGATAATGACAAGGATGGTGCTCTCAGTGATGTGGAGCTCAATGAATTCCAGgtttgtgttc ... tgctttacagGTCCGATGCTTTAATGCTCCACTCCAGCCTACTGAAATTTCAGGAGTTAAGAGAGTTGTTCAGGAGAAGATGCCTGAAGGCGTAAATGAAAGCGGCCTTA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 82

TCTGAAGCCTCGATGTGTGAGAGCGTTGAAGCGGATATTTATTATATGTGATAATGACAAGGATGGTGCTCTCAGTGATGTGGAGCTCAATGAATTCCAGgtttgtgttc ... tgctttacagGTCCGATGCTTTAATGCTCCACTCCAGCCTACTGAAATTTCAGGAGTTAAGAGAGTTGTTCAGGAGAAGATGCCTGAAGGCGTAAATGAAAGCGGCCTTA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 94

TCTGAAGCCTCGATGTGTGAGAGCGTTGAAGCGGATATTTATTATATGTGATAATGACAAGGATGGTGCTCTCAGTGATGTGGAGCTCAATGAATTCCAGgtttgtgttc ... tgctttacagGTCCGATGCTTTAATGCTCCACTCCAGCCTACTGAAATTTCAGGAGTTAAGAGAGTTGTTCAGGAGAAGATGCCTGAAGGCGTAAATGAAAGCGGCCTTA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 118

TCTGAAGCCTCGATGTGTGAGAGCGTTGAAGCGGATATTTATTATATGTGATAATGACAAGGATGGTGCTCTCAGTGATGTGGAGCTCAATGAATTCCAGgtttgtgttc ... tgctttacagGTCCGATGCTTTAATGCTCCACTCCAGCCTACTGAAATTTCAGGAGTTAAGAGAGTTGTTCAGGAGAAGATGCCTGAAGGCGTAAATGAAAGCGGCCTTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taataatatactctattgtttctagtgatgtgaggttcttcttgctgctttacagGTCCGATGCTTTAATGCTCCACTCCAGCCTACTGAAATTTCAGGAGTTAAGAGAGTTGTTCAGGAGAAGATGCCTGAAGGCGTAAATGAAAGCGGCCTTA
 acttaat  putative branch site (score: 118)
                                   ttcttcttgctgcttt  putative PPT
             tattgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtgttcatgaaggctaccatgctttccatctagcagtatacaacataactacttaataatatactctattgtttctagtgatgtgaggttcttcttgctgctttacagGTCCGATGCTTTAATGCTCCACTCCAGCCTACTGAAATTTCAGGAGTTAAGAGAGTTGTTCAGGAGAAGATGCCTGAAGGCGTAAATGAAAGCGGCCTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG