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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcactcatgtgggagcctccgacattgggtctgtccttttagcctatatgcttagtgatgcaccatgtgctcaataacattgatttaatctcatttcagGAGTATCAGGCCTGATAGTACCTGCAGCAACTGTAGGAGCACTGGGTTACGGTTATATGTGGTGGAAG

Basic information

species Zea mays
transcript GRMZM2G104133_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G104133_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g08980.4 (Oryza sativa), 3'ss of exon 3
ctcactcatgtgggagcct----ccgacattgggtctgtc--cttttagcctatatgcttagtgatgcaccatgtgctcaataacattgatttaatctcatttcagGAGTATCAGGCCTGATAGTACCTGCAGCAACTGTAGGAGCACTGGGTTACGGTTATATGTGGTGGAAG
   | |  ||| | ||| |    | || ||||| |   |   |   |  ||| | || | ||  || ||  ||||    | |    ||||| |  | |  || |||| || |||||  |||||||||||||||||||||| |||||||| ||||| ||||| ||||||||||||
--tatttctgttgtagcttatttcagaaattggcttaattaaccagtgacctctttgatcagacattcatgatgt---tagtgttcttgatcttctttt-ttgcagGGGTGTCAGGTTTGATAGTACCTGCAGCAACTGTTGGAGCACTCGGTTATGGTTACATGTGGTGGAAG
















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|211170332|gb|FK988414.1|FK988414
EST:     TGGTAATTCACGTTCAATAACTGTTCTCAATGGAGGTTCTGCACAATCAG                         GAGTATCAGGCCTGATAGTACCTGCAGCAACTGTAGGAGCACTGGGTTACG
genomic: TGGTAATTCACGTTCAATAACTGTTCTCAATGGAGGTTCTGCACAATCAGgtttgtcttg ... ctcatttcagGAGTATCAGGCCTGATAGTACCTGCAGCAACTGTAGGAGCACTGGGTTACG
EST: gi|211170335|gb|FK988417.1|FK988417
EST:     TGGTAATTCACGTTCAATAACTGTTCTCAATGGAGGTTCTGCACAATCAG                         GAGTATCAGGCCTGATAGTACCTGCAGCAACTGT
genomic: TGGTAATTCACGTTCAATAACTGTTCTCAATGGAGGTTCTGCACAATCAGgtttgtcttg ... ctcatttcagGAGTATCAGGCCTGATAGTACCTGCAGCAACTGT
EST: gi|211170328|gb|FK988410.1|FK988410
EST:     TGGTAATTCACGTTCAATAACTGTTCTCAATGGAGGTTCTGCACAATCAG                         GAGTATCAGGCCTGATAGTACCTGCAGCAACTGTAGGAGCACTGGG
genomic: TGGTAATTCACGTTCAATAACTGTTCTCAATGGAGGTTCTGCACAATCAGgtttgtcttg ... ctcatttcagGAGTATCAGGCCTGATAGTACCTGCAGCAACTGTAGGAGCACTGGG
EST: gi|211170338|gb|FK988420.1|FK988420
EST:     TGGTAATTCACGTTCAATAACTGTTCTCAATGGAGGTTCTGCACAATCAG                         GAGTATCAGGCCTGATAGTACCTGCAGCAACTGTAGGAGCACTGGGTTACG
genomic: TGGTAATTCACGTTCAATAACTGTTCTCAATGGAGGTTCTGCACAATCAGgtttgtcttg ... ctcatttcagGAGTATCAGGCCTGATAGTACCTGCAGCAACTGTAGGAGCACTGGGTTACG
EST: gi|211170331|gb|FK988413.1|FK988413
EST:     GGTAATTCACGTTCAATAACTGTTCCTCAATGGAGGTTCTGCACAATCAG                         GAGTATCAGGCCTGATAGTACCTGCAGCAACTGTAGGAGCACTGGGTTACG
genomic: GGTAATTCACGTTCAATAACTGTTC-TCAATGGAGGTTCTGCACAATCAGgtttgtcttg ... ctcatttcagGAGTATCAGGCCTGATAGTACCTGCAGCAACTGTAGGAGCACTGGGTTACG
EST: gi|211170336|gb|FK988418.1|FK988418
EST:     TGGTAATTCACGTTCAATAACTGTTCTCAATGGAGGTTCTGCACAATCAG                         GAGTATCAGGCCTGATAGTACCTGCAGCAACTGTAGGAGCACTGGGTTACG
genomic: TGGTAATTCACGTTCAATAACTGTTCTCAATGGAGGTTCTGCACAATCAGgtttgtcttg ... ctcatttcagGAGTATCAGGCCTGATAGTACCTGCAGCAACTGTAGGAGCACTGGGTTACG
EST: gi|211170337|gb|FK988419.1|FK988419
EST:     TGGTAATTCACGTTCAATAACTGTTCTCAATGGAGGTTCTGCACAATCAG                         GAGTACCAGGCCTGATAGTA
genomic: TGGTAATTCACGTTCAATAACTGTTCTCAATGGAGGTTCTGCACAATCAGgtttgtcttg ... ctcatttcagGAGTATCAGGCCTGATAGTA
EST: gi|211170340|gb|FK988422.1|FK988422
EST:     TGGTAATTCACGTTCAATAACTGTTCTCAATGGAGGTTCTGCACAATCAG                         GAGTATCAGGCCTGATAGTACCTGCAGCAACTGTAGGAGCACTGGGTTACG
genomic: TGGTAATTCACGTTCAATAACTGTTCTCAATGGAGGTTCTGCACAATCAGgtttgtcttg ... ctcatttcagGAGTATCAGGCCTGATAGTACCTGCAGCAACTGTAGGAGCACTGGGTTACG
EST: gi|211170339|gb|FK988421.1|FK988421
EST:     TGGTAATTCACGTTCAATAACTGTTCTCAATGGAGGTTCTGCACAATCAG                         GAGTATCAGGCCTGATAGTACCTGCAGCAACTGTAGGAGCACTGGGTTACG
genomic: TGGTAATTCACGTTCAATAACTGTTCTCAATGGAGGTTCTGCACAATCAGgtttgtcttg ... ctcatttcagGAGTATCAGGCCTGATAGTACCTGCAGCAACTGTAGGAGCACTGGGTTACG
EST: gi|211170333|gb|FK988415.1|FK988415
EST:     TGGTAATTCACGTTCAATAACTGTTCTCAATGGAGGTTCTGCACAATCAG                         GAGTATCAGGCCTGATAGTACCTGCAGCAACTGTAGGAGCACTGGGTTACG
genomic: TGGTAATTCACGTTCAATAACTGTTCTCAATGGAGGTTCTGCACAATCAGgtttgtcttg ... ctcatttcagGAGTATCAGGCCTGATAGTACCTGCAGCAACTGTAGGAGCACTGGGTTACG

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: 48 (upstream exon), 49 (downstream exon)
Score: 414

GTGCGTCGCCTTGCCATGGAGGTCCGGCAACTTGGTAATTCACGTTCAATAACTGTTCTCAATGGAGGTTCTGCACAATCAGgtttgtcttg ... ctcatttcagGAGTATCAGGCCTGATAGTACCTGCAGCAACTGTAGGAGCACTGGGTTACGGTTATATGTGGTGGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 755

GTGCGTCGCCTTGCCATGGAGGTCCGGCAACTTGGTAATTCACGTTCAATAACTGTTCTCAATGGAGGTTCTGCACAATCAGgtttgtcttg ... ctcatttcagGAGTATCAGGCCTGATAGTACCTGCAGCAACTGTAGGAGCACTGGGTTACGGTTATATGTGGTGGAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 636

GTGCGTCGCCTTGCCATGGAGGTCCGGCAACTTGGTAATTCACGTTCAATAACTGTTCTCAATGGAGGTTCTGCACAATCAGgtttgtcttg ... ctcatttcagGAGTATCAGGCCTGATAGTACCTGCAGCAACTGTAGGAGCACTGGGTTACGGTTATATGTGGTGGAAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 549

GTGCGTCGCCTTGCCATGGAGGTCCGGCAACTTGGTAATTCACGTTCAATAACTGTTCTCAATGGAGGTTCTGCACAATCAGgtttgtcttg ... ctcatttcagGAGTATCAGGCCTGATAGTACCTGCAGCAACTGTAGGAGCACTGGGTTACGGTTATATGTGGTGGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatgcttagtgatgcaccatgtgctcaataacattgatttaatctcatttcagGAGTATCAGGCCTGATAGTACCTGCAGCAACTGTAGGAGCACTGGGTTACGGTTATATGTGGTGGAAG
                                            tctcatttc  CT-rich tract
                            aataacattgatttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctcactcatgtgggagcctccgacattgggtctgtccttttagcctatatgcttagtgatgcaccatgtgctcaataacattgatttaatctcatttcagGAGTATCAGGCCTGATAGTACCTGCAGCAACTGTAGGAGCACTGGGTTACGGTTATATGTGGTGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - catgtgg
- - - - - - - - - - - - - - - - - - - - - - - - atgctta
- - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aataaca