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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaggcccttttgctatacaaagattttatgttgaactttgacataatttcttatttccagaagtttttttggtcacctaatcttatttcatttctgcagGTTCAAGTAGGTAATTCTCCAGAGTACATAACTGACAGGAAGTTAGGTAAAGGTGGTTTTGGTCAGGTCTATGTTGGTCGAAGGGTTTCTGGTGGAGCTG

Basic information

species Zea mays
transcript GRMZM2G164265_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G164265_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 2
agaggcccttttgctatacaaagattttatgttgaactttgacataat--ttcttatttccagaagtttttttgg--tcacctaatcttatttcatttctgcagGTTCAAGTAGGTAATTCTCCAGAGTACATAACTGACAGGAAGTTAGGTAAAGGTGGTTTTGGTCAGGTCTATGTTGGTCGAAGGGTTTCTGGTGGAGCTG
        || | || ||  | | | | || ||| || || || ||||   ||||||||     |   || | ||   || ||||| || | ||||| |||||| |||||||||||||||||||||| || |||||||||||||| ||||||||||||||||||||||| || ||||||||| ||||||| ||||||||| || 
----aaaattcttctctaagatggtgtgatattggacctttacgtaatagatcttatttttgtcatgcttctaggaagcatctaatgttttgtcattgctgcagATTCAAGTAGGTAATTCTCCAGAATATATAACTGACAGGAAATTAGGTAAAGGTGGTTTTGGTCAAGTTTATGTTGGTAGAAGGGTATCTGGTGGAACTA

upper sequence: GRMZM2G164265_T03 (Zea mays), 3'ss of exon 2
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 2
agaggcccttttgctatacaaagattttatgttgaactttgacataatttcttatttcca---gaagtttttttggtcacctaatcttatttcatttctg----cagGTTCAAGTAGGTAATTCTCCAGAGTACATAACTGACAGGAAGTTAGGTAAAGGTGGTTTTGGTCAGGTCTATGTTGGTCGAAGGGTTTCTGGTGGAGCTG
         |  |      |  ||   | |||| || |||  | |    || |  ||| |   | | | |||     || ||| |  | ||   ||| ||     |||| ||||| |||||||||||    ||||  |  || |||||||||||||| |||||||||||||| || ||||||||  |||||||   ||||||  |||
-------tctgaggggctaatggagcatttgttaaaatttttccttcactcgttcttcaacacggattctttcaaagcatctagttgttttctgtttttggttctagGTACAAGTGGGTAATTCTCCTATATACAAGATAGAAAGGAAGTTAGGTAAGGGTGGTTTTGGTCAAGTGTATGTTGGCAGAAGGGTAAGTGGTGGCACTG
















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|148937187|gb|EC881368.2|EC881368
EST:     AGATTATTGGGGCTGAAGATGAATCAACAGCGACACCTGTGCCAGAGAGG                         GTTCAAGTAGGTAATTCTCCAGAGTACATAACTGACAGGAAGTTAGGTAAA
genomic: AGATTATTGGGGCTGAAGATGAATCAACAGCGACACCTGTGCCAGAGAGGgtattacttt ... atttctgcagGTTCAAGTAGGTAATTCTCCAGAGTACATAACTGACAGGAAGTTAGGTAAA
EST: gi|149102516|gb|EE188222.2|EE188222
EST:     AGATTATTGGGGCTGAAGATGAATCAACAGCGACACCTGTGCCAGAGAGG                         GTTCAAGTAGGTAATTCTCCAGAGTACATAACTGACAGGAAGTTAGGTAAA
genomic: AGATTATTGGGGCTGAAGATGAATCAACAGCGACACCTGTGCCAGAGAGGgtattacttt ... atttctgcagGTTCAAGTAGGTAATTCTCCAGAGTACATAACTGACAGGAAGTTAGGTAAA
EST: gi|28909993|gb|CB331203.1|CB331203
EST:     AGATTATTGGGGCTGAAGATGAATCAACAGCGACACCTGTGCCAGAGAGG                         GTTCAAGTAGGTAATTCTCCAGAGTACATAACTGACAGGAAGTTAGGTAAA
genomic: AGATTATTGGGGCTGAAGATGAATCAACAGCGACACCTGTGCCAGAGAGGgtattacttt ... atttctgcagGTTCAAGTAGGTAATTCTCCAGAGTACATAACTGACAGGAAGTTAGGTAAA
EST: gi|18654924|gb|BM499729.1|BM499729
EST:     AGATTATTGGGGCTGAAGATGAATCACCAGCGACACCTGTGCCAGAGAGG                         GTTCAAGTAGGTAATTCTCCAGAGTACATAACTGACAGGAAGTTAGGTAAA
genomic: AGATTATTGGGGCTGAAGATGAATCAACAGCGACACCTGTGCCAGAGAGGgtattacttt ... atttctgcagGTTCAAGTAGGTAATTCTCCAGAGTACATAACTGACAGGAAGTTAGGTAAA
EST: gi|18661950|gb|BM501665.1|BM501665
EST:     AGATTATTGGGGCTGAAGATGAATCAACAGCGACACCTGTGCCAGAGAGG                         GTTCAAGTAGGTAATTCTCCAGAGTACATAACTGACAGGAAGTTAGGTAAA
genomic: AGATTATTGGGGCTGAAGATGAATCAACAGCGACACCTGTGCCAGAGAGGgtattacttt ... atttctgcagGTTCAAGTAGGTAATTCTCCAGAGTACATAACTGACAGGAAGTTAGGTAAA
EST: gi|148950416|gb|EC895983.2|EC895983
EST:     AGATTATTGGGGCTGAAGATGAATCAACAGCGACACCTGTGCCAGAGAGG                         GTTCAAGTAGGTAATTCTCCAGAGTACATAACTGACAGGAAGTTAGGTAAA
genomic: AGATTATTGGGGCTGAAGATGAATCAACAGCGACACCTGTGCCAGAGAGGgtattacttt ... atttctgcagGTTCAAGTAGGTAATTCTCCAGAGTACATAACTGACAGGAAGTTAGGTAAA
EST: gi|87153711|gb|DY398500.1|DY398500
EST:     AGATTATTGGGGCTGAAGATGAATCAACAGCGACACCTGTGCCAGAGAGG                         GTTCAAGTAGGTAATTCTCCAGAGTACATAACTGACAAGAAGTTAGGTAAA
genomic: AGATTATTGGGGCTGAAGATGAATCAACAGCGACACCTGTGCCAGAGAGGgtattacttt ... atttctgcagGTTCAAGTAGGTAATTCTCCAGAGTACATAACTGACAGGAAGTTAGGTAAA
EST: gi|78113587|gb|DV531978.1|DV531978
EST:     AGATTATTGGGGCTGAAGATGAATCAACAGCGACACCTGTGCCAGAGAGG                         GTTCAAGTAGGTAATTCTCCAGAGTACATAACTGACAGGAAGTTAGGTAAA
genomic: AGATTATTGGGGCTGAAGATGAATCAACAGCGACACCTGTGCCAGAGAGGgtattacttt ... atttctgcagGTTCAAGTAGGTAATTCTCCAGAGTACATAACTGACAGGAAGTTAGGTAAA
EST: gi|148950557|gb|EC896134.2|EC896134
EST:     AGATTATTGGGGCTGAAGATGAATCAACAGCGACACCTGTGCCAGAGAGG                         GTTCAAGTAGGTAATTCTCCAGAGTACATAACTGACAGGAAGTTAGGTAAA
genomic: AGATTATTGGGGCTGAAGATGAATCAACAGCGACACCTGTGCCAGAGAGGgtattacttt ... atttctgcagGTTCAAGTAGGTAATTCTCCAGAGTACATAACTGACAGGAAGTTAGGTAAA

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: 249

GGAGGTAGCCGAGGTTGGTGTTCTGAAAATGAATGGTGTGAGTGCAGAGAAGATTATTGGGGCTGAAGATGAATCAACAGCGACACCTGTGCCAGAGAGGgtattacttt ... atttctgcagGTTCAAGTAGGTAATTCTCCAGAGTACATAACTGACAGGAAGTTAGGTAAAGGTGGTTTTGGTCAGGTCTATGTTGGTCGAAGGGTTTCTGGTGGAGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 148

GGAGGTAGCCGAGGTTGGTGTTCTGAAAATGAATGGTGTGAGTGCAGAGAAGATTATTGGGGCTGAAGATGAATCAACAGCGACACCTGTGCCAGAGAGGgtattacttt ... atttctgcagGTTCAAGTAGGTAATTCTCCAGAGTACATAACTGACAGGAAGTTAGGTAAAGGTGGTTTTGGTCAGGTCTATGTTGGTCGAAGGGTTTCTGGTGGAGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 110

GGAGGTAGCCGAGGTTGGTGTTCTGAAAATGAATGGTGTGAGTGCAGAGAAGATTATTGGGGCTGAAGATGAATCAACAGCGACACCTGTGCCAGAGAGGgtattacttt ... atttctgcagGTTCAAGTAGGTAATTCTCCAGAGTACATAACTGACAGGAAGTTAGGTAAAGGTGGTTTTGGTCAGGTCTATGTTGGTCGAAGGGTTTCTGGTGGAGCTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 114

GGAGGTAGCCGAGGTTGGTGTTCTGAAAATGAATGGTGTGAGTGCAGAGAAGATTATTGGGGCTGAAGATGAATCAACAGCGACACCTGTGCCAGAGAGGgtattacttt ... atttctgcagGTTCAAGTAGGTAATTCTCCAGAGTACATAACTGACAGGAAGTTAGGTAAAGGTGGTTTTGGTCAGGTCTATGTTGGTCGAAGGGTTTCTGGTGGAGCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttcttatttccagaagtttttttggtcacctaatcttatttcatttctgcagGTTCAAGTAGGTAATTCTCCAGAGTACATAACTGACAGGAAGTTAGGTAAAGGTGGTTTTGGTCAGGTCTATGTTGGTCGAAGGGTTTCTGGTGGAGCTG
                              acctaat  putative branch site (score: 114)
                                    tcttatttcatttct  CT-rich tract
                                 taatcttatttcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaggcccttttgctatacaaagattttatgttgaactttgacataatttcttatttccagaagtttttttggtcacctaatcttatttcatttctgcagGTTCAAGTAGGTAATTCTCCAGAGTACATAACTGACAGGAAGTTAGGTAAAGGTGGTTTTGGTCAGGTCTATGTTGGTCGAAGGGTTTCTGGTGGAGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT