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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagcatacagtaaatctcctttgatttatctatattatgctccaagttttttggtgatttgccatgcactattaaccactctatttacactaccttacagGTACCGACAATCCTGTGTAGAGTCCAGAAAAGATGCAAGGAATTTTGTGAGATCCAGAACTAATAGGAGATGGAAGTATTACGAATAATAATACTAGACT

Basic information

species Zea mays
transcript GRMZM5G845878_T01
intron # 2
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|18165281|gb|BM335120.1|BM335120
EST:     ACCACTCGAAACTATTCAAAAAGGATAAATATTTTTTCATTTCAAATACG                         GTACCGACAATCCTGTGTAGAGTCCAGAAAAGATGCAAGGAATTTTGTGAG
genomic: ACCACTCGAAACTATTCAAAAAGGATAAATATTTTTTCATTTCAAATACGgtatgttatc ... taccttacagGTACCGACAATCCTGTGTAGAGTCCAGAAAAGATGCAAGGAATTTTGTGAG
EST: gi|60341451|gb|DN208424.1|DN208424
EST:     ACCACTCGAAACTATTCAAAAAGGATAAATATTTTTTCATTTCAAATACG                         GTACCGACAATCCTGTGTAGAGTCCAGAAAAGATGCAAGGAATTTTGTGAG
genomic: ACCACTCGAAACTATTCAAAAAGGATAAATATTTTTTCATTTCAAATACGgtatgttatc ... taccttacagGTACCGACAATCCTGTGTAGAGTCCAGAAAAGATGCAAGGAATTTTGTGAG
EST: gi|8367149|gb|BE050094.1|BE050094
EST:     ATTCAAAAAGGATAAATATTTTTTCATTTCAAATACG                         GTACCGACAATCCTGTGTAGAGTCCAGAAAAGATGCAAGGAATTTTGTGAG
genomic: ATTCAAAAAGGATAAATATTTTTTCATTTCAAATACGgtatgttatc ... taccttacagGTACCGACAATCCTGTGTAGAGTCCAGAAAAGATGCAAGGAATTTTGTGAG
EST: gi|18166666|gb|BM336505.1|BM336505
EST:     ACCACTCGAAACTATTCAAAAAGGATAAATATTTTTTCATTTCAAATACG                         GTACCGACAATCCTGTGTAGAGTCCAGAAAAGATGCAAGGAATTTTGTGAG
genomic: ACCACTCGAAACTATTCAAAAAGGATAAATATTTTTTCATTTCAAATACGgtatgttatc ... taccttacagGTACCGACAATCCTGTGTAGAGTCCAGAAAAGATGCAAGGAATTTTGTGAG
EST: gi|4680869|gb|AI629539.1|AI629539
EST:     CTCGAAACTATTCAAAAAGGATAAATATTTTTTCATTTCAAATACG                         GTACCGACAATCCTGTGTAGAGTCCAGAAAAGATGCAAGGAATTTTGTGAG
genomic: CTCGAAACTATTCAAAAAGGATAAATATTTTTTCATTTCAAATACGgtatgttatc ... taccttacagGTACCGACAATCCTGTGTAGAGTCCAGAAAAGATGCAAGGAATTTTGTGAG
EST: gi|16379085|gb|BI992744.1|BI992744
EST:     ACCACTCGGAACTATTCAAAAAGGATAAATATTTTTTCATTTCAAATACG                         GTACCGACAATCCTGTGTAGAGTCCAGAAAAGATGCAAGGAATTTTGTGAG
genomic: ACCACTCGAAACTATTCAAAAAGGATAAATATTTTTTCATTTCAAATACGgtatgttatc ... taccttacagGTACCGACAATCCTGTGTAGAGTCCAGAAAAGATGCAAGGAATTTTGTGAG
EST: gi|8367150|gb|BE050095.1|BE050095
EST:     ACCACTCGAAACTATTCAAAAAGGATAAATATTTTTTCATTTCAAATACG                         GTACCGACAATCCTGTGTAGAGTCCAGAAAAGATGCAAGGAATTTTGTGAG
genomic: ACCACTCGAAACTATTCAAAAAGGATAAATATTTTTTCATTTCAAATACGgtatgttatc ... taccttacagGTACCGACAATCCTGTGTAGAGTCCAGAAAAGATGCAAGGAATTTTGTGAG
EST: gi|7162323|gb|AW519930.1|AW519930
EST:     CCACTCGAAACTATTCAAAAAGGATAAATANNNNNNNCATTTCAAATACG                         GTACCGACAATCCTGTGTAGAGTCCAGAAAAGATGCAAGGAATTTTGTGAG
genomic: CCACTCGAAACTATTCAAAAAGGATAAATATTTTTT-CATTTCAAATACGgtatgttatc ... taccttacagGTACCGACAATCCTGTGTAGAGTCCAGAAAAGATGCAAGGAATTTTGTGAG
EST: gi|13381999|gb|BG458674.1|BG458674
EST:     ACCACTCGGGACTATTCAAAAAGGATAAATATTTTTTCATTTCAAATACG                         GTACCGAGCAATGCCTGTGTAGAGTCCAGAAAAGATGCAAGGAATTTTGTG
genomic: ACCACTCGAAACTATTCAAAAAGGATAAATATTTTTTCATTTCAAATACGgtatgttatc ... taccttacagGTACCGA-CAAT-CCTGTGTAGAGTCCAGAAAAGATGCAAGGAATTTTGTG

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 3 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 27

ATATGAAATCCCACCACTCGAAACTATTCAAAAAGGATAAATATTTTTTCATTTCAAATACGgtatgttatc ... taccttacagGTACCGACAATCCTGTGTAGAGTCCAGAAAAGATGCAAGGAATTTTGTGAGATCCAGAACTAATAGGAGATGGAAGTATTACGAATAATAATACTAGACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 139

ATATGAAATCCCACCACTCGAAACTATTCAAAAAGGATAAATATTTTTTCATTTCAAATACGgtatgttatc ... taccttacagGTACCGACAATCCTGTGTAGAGTCCAGAAAAGATGCAAGGAATTTTGTGAGATCCAGAACTAATAGGAGATGGAAGTATTACGAATAATAATACTAGACT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 57

ATATGAAATCCCACCACTCGAAACTATTCAAAAAGGATAAATATTTTTTCATTTCAAATACGgtatgttatc ... taccttacagGTACCGACAATCCTGTGTAGAGTCCAGAAAAGATGCAAGGAATTTTGTGAGATCCAGAACTAATAGGAGATGGAAGTATTACGAATAATAATACTAGACT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttttggtgatttgccatgcactattaaccactctatttacactaccttacagGTACCGACAATCCTGTGTAGAGTCCAGAAAAGATGCAAGGAATTTTGTGAGATCCAGAACTAATAGGAGATGGAAGTATTACGAATAATAATACTAGACT
                        tattaac  putative branch site (score: 57)
                                            ctacctt  putative PPT
                      actattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagcatacagtaaatctcctttgatttatctatattatgctccaagttttttggtgatttgccatgcactattaaccactctatttacactaccttacagGTACCGACAATCCTGTGTAGAGTCCAGAAAAGATGCAAGGAATTTTGTGAGATCCAGAACTAATAGGAGATGGAAGTATTACGAATAATAATACTAGACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- gcataca
- - - - - - - - - - - - - - - - - - -tgctcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - tgatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccatgca