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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaatttcttaccttgattctgttcgtctactctttctgctgtccaaccttttcactaaccatttgttctgagaaaaagatgtttcctaagtcagctactcctggccttgctcttgccagTCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTACGGACAGAAAGGAGAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTT

Basic information

species Zea mays
transcript GRMZM2G124353_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G124353_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g07570.1 (Oryza sativa), 3'ss of exon 6
--------------------------------------------------------gtaaaatttcttacc-ttgattctgttcgtctactctttctgctgtccaaccttttcact-aaccatttgttctgagaaaaagatgtttcctaagtcagctactcctggccttgctcttgccagTCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTACGGACAGAAAGGAGAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTT
                                                        |    |||    |   ||| ||  |||  |     |||||  |||   ||| |||||||| ||| |||| || |  ||  ||  |||   ||||  |    | |  ||| ||| || ||| ||||||| || ||||||||||| |||||| |||||||||||||||| || ||||| || || ||||||||||| ||||||||| | || |||| |  | ||||
gtaaaatctacaatctttggttatatttgtataacaacatcgccagtttacattctgcttgattcaacattgttgctttagttgatgatgcctttcatctgagtaacattttcactcaactatttattatt-gattaatctgt---ctaatcccatcatt--tggtctttctgttgtcagTCATTGGAGATGTTAGAGGGAGGGGATTGATGCTTGGGGTGGAGCTTGTTACCGATAGGAAGGAGAAGACACCTGCCAAGGCCGAGACCAATTTATTGTT

upper sequence: GRMZM2G124353_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv07s0031g01330.t01 (Vitis vinifera), 3'ss of exon 6
gtaaaatttcttaccttgattctgttcgtctactctttctgctgtccaaccttttcactaaccatttgttctgagaaaaagatgtttcctaagtcagctactcctggccttgctcttgccagTCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTACGGACAGAAAGGAGAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTT
   || ||     | ||||||||| |    | || | ||||   |  | | || |  | |  |||||           | | |||| | ||  ||   ||       ||||| |  |  |||| || || || || ||||||||||| || ||| | ||||||||||| || || |||||||| |||||||||||||||||  |||||||    |   ||||
---aagttcaaacctttgattctgctt-cttcctttctctga-attgagcattatggccagtcattttc---------atggtgtt-cttatatctatta-----aaccttgtttct--cagTTATCGGAGACGTAAGAGGAAGGGGTCTAATGGTGGGGGTGGAACTTGTGACTGACAGAAAAGAGAAGACCCCTGCCAAAGCAGAAACTGCAGTTTTGTT
















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|6540601|gb|AW225263.1|AW225263
EST:     TGGATCTCCCTTGTTGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAA                         TCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTA
genomic: TGGATCTCACTTGTTGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAAgtaaaatttc ... ctcttgccagTCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTA
EST: gi|6194732|gb|AW146836.1|AW146836
EST:     TGTATCTCACTTGTTGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAA                         TCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTA
genomic: TGGATCTCACTTGTTGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAAgtaaaatttc ... ctcttgccagTCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTA
EST: gi|31910695|gb|CD651553.1|CD651553
EST:     TGGATCTCACTTGTTGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAA                         TCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTA
genomic: TGGATCTCACTTGTTGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAAgtaaaatttc ... ctcttgccagTCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTA
EST: gi|60350662|gb|DN217635.1|DN217635
EST:     TGGATCTCACTTGTTGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAA                         TCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTA
genomic: TGGATCTCACTTGTTGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAAgtaaaatttc ... ctcttgccagTCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTA
EST: gi|30031576|gb|CB833427.1|CB833427
EST:     TGGATCTCACTTGTTGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAA                         TCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTA
genomic: TGGATCTCACTTGTTGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAAgtaaaatttc ... ctcttgccagTCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTA
EST: gi|32942110|gb|CF046929.1|CF046929
EST:     TGGATCTCACTTGTTGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAA                         TCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTA
genomic: TGGATCTCACTTGTTGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAAgtaaaatttc ... ctcttgccagTCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTA
EST: gi|30031577|gb|CB833428.1|CB833428
EST:     TGGATCTCACTTGTTGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAA                         TCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGG
genomic: TGGATCTCACTTGTTGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAAgtaaaatttc ... ctcttgccagTCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGG
EST: gi|32943504|gb|CF048323.1|CF048323
EST:     TGGATCTCACTTGTTGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAA                         TCATAGGTGATGTTAGAGGAAGGGGACTAAAAAATAGGGTGGAACTCGTTA
genomic: TGGATCTCACTTGTTGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAAgtaaaatttc ... ctcttgccagTCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTA
EST: gi|148955021|gb|EC900524.2|EC900524
EST:     TGGATCTCACTTGTTGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAA                         TCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTA
genomic: TGGATCTCACTTGTTGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAAgtaaaatttc ... ctcttgccagTCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTA
EST: gi|60338215|gb|DN205188.1|DN205188
EST:     TGGATCTCACTTGTTGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAA                         TCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTA
genomic: TGGATCTCACTTGTTGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAAgtaaaatttc ... ctcttgccagTCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTA
EST: gi|60349531|gb|DN216504.1|DN216504
EST:     TGGATCTCACTTGTTGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAA                         TCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTA
genomic: TGGATCTCACTTGTTGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAAgtaaaatttc ... ctcttgccagTCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTA
EST: gi|211311886|gb|FK975957.1|FK975957
EST:     TGGATCTCACTTGTTGGAGCGTCTAAAATCGCTTCAGGACAAGCACGAAA                         TTATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTA
genomic: TGGATCTCACTTGTTGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAAgtaaaatttc ... ctcttgccagTCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTA
EST: gi|60398309|gb|DN231125.1|DN231125
EST:     TGGATCTCACTTGTTGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAA                         TCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTA
genomic: TGGATCTCACTTGTTGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAAgtaaaatttc ... ctcttgccagTCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTA
EST: gi|5871627|gb|AW018098.1|AW018098
EST:     TGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAA                         TCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTA
genomic: TGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAAgtaaaatttc ... ctcttgccagTCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTA
EST: gi|8318607|gb|BE025352.1|BE025352
EST:     TGGATCTCACTTGTTGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAA                         TCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTA
genomic: TGGATCTCACTTGTTGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAAgtaaaatttc ... ctcttgccagTCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTA
EST: gi|67014041|gb|CO442790.1|CO442790
EST:     TGGATCTCACTTGTTGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAA                         TCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTA
genomic: TGGATCTCACTTGTTGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAAgtaaaatttc ... ctcttgccagTCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTA
EST: gi|113701983|gb|EE679487.1|EE679487
EST:     TGGATCTCACTTGTTGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAA                         TTATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTA
genomic: TGGATCTCACTTGTTGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAAgtaaaatttc ... ctcttgccagTCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTA
EST: gi|78025401|gb|DV493788.1|DV493788
EST:     TGGATCTCACTTGTTGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAA                         TCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTA
genomic: TGGATCTCACTTGTTGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAAgtaaaatttc ... ctcttgccagTCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTA
EST: gi|60356418|gb|DN223391.1|DN223391
EST:     TGGATCTCACTTGTTGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAA                         TCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTA
genomic: TGGATCTCACTTGTTGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAAgtaaaatttc ... ctcttgccagTCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTA
EST: gi|6564029|gb|AW231651.1|AW231651
EST:     TGGATCTCACTTGTTGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAA                         TCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTA
genomic: TGGATCTCACTTGTTGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAAgtaaaatttc ... ctcttgccagTCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTA
EST: gi|4776049|gb|AI665052.1|AI665052
EST:     TGGATCTCACTTGTTGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAA                         TCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTA
genomic: TGGATCTCACTTGTTGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAAgtaaaatttc ... ctcttgccagTCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTA
EST: gi|148931506|gb|EC874539.2|EC874539
EST:     TGGATCTCACTTGTTGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAA                         TCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTA
genomic: TGGATCTCACTTGTTGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAAgtaaaatttc ... ctcttgccagTCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTA
EST: gi|5439282|gb|AI820203.1|AI820203
EST:     TGGATCTCACTTGTTGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAA                         TCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTA
genomic: TGGATCTCACTTGTTGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAAgtaaaatttc ... ctcttgccagTCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTA
EST: gi|37390746|gb|CF632607.1|CF632607
EST:     TGGATCTCACTTGTTGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAA                         TTATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTA
genomic: TGGATCTCACTTGTTGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAAgtaaaatttc ... ctcttgccagTCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTA

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: 357

GTGCTTAAGGTTCTTGACAAGGAGAAACGCCAGGCACATTGTGCTGATGTTGGATCTCACTTGTTGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAAgtaaaatttc ... ctcttgccagTCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTACGGACAGAAAGGAGAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 725

GTGCTTAAGGTTCTTGACAAGGAGAAACGCCAGGCACATTGTGCTGATGTTGGATCTCACTTGTTGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAAgtaaaatttc ... ctcttgccagTCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTACGGACAGAAAGGAGAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 834

GTGCTTAAGGTTCTTGACAAGGAGAAACGCCAGGCACATTGTGCTGATGTTGGATCTCACTTGTTGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAAgtaaaatttc ... ctcttgccagTCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTACGGACAGAAAGGAGAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 371

GTGCTTAAGGTTCTTGACAAGGAGAAACGCCAGGCACATTGTGCTGATGTTGGATCTCACTTGTTGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAAgtaaaatttc ... ctcttgccagTCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTACGGACAGAAAGGAGAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttctgagaaaaagatgtttcctaagtcagctactcctggccttgctcttgccagTCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTACGGACAGAAAGGAGAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTT
                                        ccttgctctt  CT-rich tract
        aaaaagat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaatttcttaccttgattctgttcgtctactctttctgctgtccaaccttttcactaaccatttgttctgagaaaaagatgtttcctaagtcagctactcctggccttgctcttgccagTCATAGGTGATGTTAGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTACGGACAGAAAGGAGAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA