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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catggtgatggtgcttgattgttttattactcgatttgtagttgggtgttgtaattatcacatgatagatactgacatacttctctcacccctgttttagGTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCCTAT

Basic information

species Zea mays
transcript GRMZM2G135132_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G135132_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g41590.1 (Oryza sativa), 3'ss of exon 1
---------catggtgatggtgcttgattgttttattactcgatttgtagttgggtgttgtaattatcacatgatagatactgacatacttctctcacccctgttttagGTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCCTAT
           |  ||||  |||| || |   | |||| |     ||| | |   | | ||  | |||||       |   |||| | ||||||  |    ||||||||||||||| |||||||||||||||| |||||||||||||| ||||||| ||||||
gtttactgctttaatgata-tgctggagtacatgattattta---tgttgcttattatggtg-tcatcacggttggcaatttgacgtgcttctccaa----tgttttagGTATGACGTCAAGCTGAACAATGCAATTCTCGCTGAGGAAAAGCACTTGCCTAT
















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|211433554|gb|FL254730.1|FL254730
EST:     AACCCCCTCCTCGACATCTCCGCCGTTGTCGATGACGCCTTCCTGGCAAA                         GTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCC
genomic: AACCCCCTCCTCGACATCTCCGCCGTTGTCGATGACGCCTTCCTGGCAAAgtaagtcggt ... cctgttttagGTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCC
EST: gi|211433558|gb|FL254734.1|FL254734
EST:     AACCCCCTCCTCGACATCTCCGCCGTTGTCGATGACGCCTTCCTGGCAAA                         GTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCC
genomic: AACCCCCTCCTCGACATCTCCGCCGTTGTCGATGACGCCTTCCTGGCAAAgtaagtcggt ... cctgttttagGTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCC
EST: gi|211436159|gb|FL254742.1|FL254742
EST:     AACCCCCTCCTCGACATCTCCGCCGTTGTCGATGACGCCTTCCTGGCAAA                         GTATGACATCAAGCTGAA-AATGCCATTCTCGCTGAGGAGAAGCACTTGCC
genomic: AACCCCCTCCTCGACATCTCCGCCGTTGTCGATGACGCCTTCCTGGCAAAgtaagtcggt ... cctgttttagGTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCC
EST: gi|211430963|gb|FL254725.1|FL254725
EST:     AACCCCCTCCTCGACATCTCCGCCGTTGTCGATGACGCCTTCCTGGCAAA                         GTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCC
genomic: AACCCCCTCCTCGACATCTCCGCCGTTGTCGATGACGCCTTCCTGGCAAAgtaagtcggt ... cctgttttagGTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCC
EST: gi|87155643|gb|DY400432.1|DY400432
EST:     AACCCCCTCCTCGACATCTCCGCCGTTGTCGATGACGCCTTCCTGGCAAA                         GTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTTGCC
genomic: AACCCCCTCCTCGACATCTCCGCCGTTGTCGATGACGCCTTCCTGGCAAAgtaagtcggt ... cctgttttagGTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCC
EST: gi|211430959|gb|FL254721.1|FL254721
EST:     AACCCCCTCCTCGACATCTCCGCCGTTGTCGATGACGCCTTCCTGGCAAA                         GTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCC
genomic: AACCCCCTCCTCGACATCTCCGCCGTTGTCGATGACGCCTTCCTGGCAAAgtaagtcggt ... cctgttttagGTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCC
EST: gi|211535005|gb|FL000874.1|FL000874
EST:     AACCCCCTCCTCGACATCTCCGCCGTTGTCGATGACGCCTTCCTGGCAAA                         GTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTTGCC
genomic: AACCCCCTCCTCGACATCTCCGCCGTTGTCGATGACGCCTTCCTGGCAAAgtaagtcggt ... cctgttttagGTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCC
EST: gi|211430960|gb|FL254722.1|FL254722
EST:     AACCCCCTCCTCGACATCTCCGCCGTTGTCGATGACGCCTTCCTGGCAAA                         GTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCC
genomic: AACCCCCTCCTCGACATCTCCGCCGTTGTCGATGACGCCTTCCTGGCAAAgtaagtcggt ... cctgttttagGTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCC
EST: gi|211433562|gb|FL254738.1|FL254738
EST:     AACCCCCTCCTCGACATCTCCGCCGTTGTCGATGACGCCTTCCTGGCAAA                         GTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCC
genomic: AACCCCCTCCTCGACATCTCCGCCGTTGTCGATGACGCCTTCCTGGCAAAgtaagtcggt ... cctgttttagGTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCC
EST: gi|211430956|gb|FL254718.1|FL254718
EST:     AACCCCCTCCTCGACATCTCCGCCGTTGTCGATGACGCCTTCCTGGCAAA                         GTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCC
genomic: AACCCCCTCCTCGACATCTCCGCCGTTGTCGATGACGCCTTCCTGGCAAAgtaagtcggt ... cctgttttagGTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCC
EST: gi|211433550|gb|FL254726.1|FL254726
EST:     AACCCCCTCCTCGACATCTCCGCCGTTGTCGATGACGCCTTCCTGGCAAA                         GTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCC
genomic: AACCCCCTCCTCGACATCTCCGCCGTTGTCGATGACGCCTTCCTGGCAAAgtaagtcggt ... cctgttttagGTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCC
EST: gi|211430955|gb|FL254717.1|FL254717
EST:     AACCCCCTCCTCGACATCTCCGCCGTTGTCGATGACGCCTTCCTGGCAAA                         GTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCC
genomic: AACCCCCTCCTCGACATCTCCGCCGTTGTCGATGACGCCTTCCTGGCAAAgtaagtcggt ... cctgttttagGTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCC
EST: gi|26559465|gb|CA831700.1|CA831700
EST:     AACCCCCTCCTCGACATCTCCGCCGTTGTCGATGACGCCTTCCTGGCAAA                         GTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTTGCC
genomic: AACCCCCTCCTCGACATCTCCGCCGTTGTCGATGACGCCTTCCTGGCAAAgtaagtcggt ... cctgttttagGTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCC
EST: gi|32916313|gb|CF021125.1|CF021125
EST:     AACCCCCTCCTCGACATCTCCGCCGTTGTCGATGACGCCTTCCTAGCAAA                         GTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTTGCC
genomic: AACCCCCTCCTCGACATCTCCGCCGTTGTCGATGACGCCTTCCTGGCAAAgtaagtcggt ... cctgttttagGTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCC
EST: gi|211433561|gb|FL254737.1|FL254737
EST:     AACCCCCTCCTCGACATCTCCGCCGTTGTCGATGACGCCTTCCTGGCAAA                         GTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCC
genomic: AACCCCCTCCTCGACATCTCCGCCGTTGTCGATGACGCCTTCCTGGCAAAgtaagtcggt ... cctgttttagGTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCC
EST: gi|211430957|gb|FL254719.1|FL254719
EST:     AACCCCCTCCTCGACATCTCCGCCGTTGTCGATGACGCCTTCCTGGCAAA                         GTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCC
genomic: AACCCCCTCCTCGACATCTCCGCCGTTGTCGATGACGCCTTCCTGGCAAAgtaagtcggt ... cctgttttagGTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCC
EST: gi|22546548|gb|BU098859.1|BU098859
EST:     AACCCCCTCCTCGACATCTCCGCCGTTGTCGATGACGCCTTCCTGGCAAA                         GTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTTGCC
genomic: AACCCCCTCCTCGACATCTCCGCCGTTGTCGATGACGCCTTCCTGGCAAAgtaagtcggt ... cctgttttagGTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCC
EST: gi|211433560|gb|FL254736.1|FL254736
EST:     AACCCCCTCCTCGACATCTCCGCCGTTGTCGATGACGCCTTCCTGGCAAA                         GTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCC
genomic: AACCCCCTCCTCGACATCTCCGCCGTTGTCGATGACGCCTTCCTGGCAAAgtaagtcggt ... cctgttttagGTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCC
EST: gi|211430954|gb|FL254716.1|FL254716
EST:     AACCCCCTCCTCGACATCTCCGCCGTTGTCGATGACGCCTTCCTGGCAAA                         GTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCC
genomic: AACCCCCTCCTCGACATCTCCGCCGTTGTCGATGACGCCTTCCTGGCAAAgtaagtcggt ... cctgttttagGTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCC
EST: gi|211433557|gb|FL254733.1|FL254733
EST:     AACCCCCTCCTCGACATCTCCGCCGTTGTCGATGACGCCTTCCTGGCAAA                         GTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCC
genomic: AACCCCCTCCTCGACATCTCCGCCGTTGTCGATGACGCCTTCCTGGCAAAgtaagtcggt ... cctgttttagGTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCC
EST: gi|31353988|gb|CD438345.1|CD438345
EST:     AACCCCCTCCTCGACATCTCCGCCGTTGTCGATGACGCCTTCCTGGCAAA                         GTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTTGCC
genomic: AACCCCCTCCTCGACATCTCCGCCGTTGTCGATGACGCCTTCCTGGCAAAgtaagtcggt ... cctgttttagGTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCC
EST: gi|211538002|gb|FL000876.1|FL000876
EST:     AACCCCCTCCTCGACATCTCCGCCGTTGTCGATGACGCCTTCCTGGCAAA                         GTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTTGCC
genomic: AACCCCCTCCTCGACATCTCCGCCGTTGTCGATGACGCCTTCCTGGCAAAgtaagtcggt ... cctgttttagGTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCC

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), 48 (downstream exon)
Score: 87

AGAGAAGAGAGGAAATGGCGGCGAGCGAGGGCGTGCTCCTGGGGATGGGCAACCCCCTCCTCGACATCTCCGCCGTTGTCGATGACGCCTTCCTGGCAAAgtaagtcggt ... cctgttttagGTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCCTAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 108

AGAGAAGAGAGGAAATGGCGGCGAGCGAGGGCGTGCTCCTGGGGATGGGCAACCCCCTCCTCGACATCTCCGCCGTTGTCGATGACGCCTTCCTGGCAAAgtaagtcggt ... cctgttttagGTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCCTAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 184

AGAGAAGAGAGGAAATGGCGGCGAGCGAGGGCGTGCTCCTGGGGATGGGCAACCCCCTCCTCGACATCTCCGCCGTTGTCGATGACGCCTTCCTGGCAAAgtaagtcggt ... cctgttttagGTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCCTAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 91

AGAGAAGAGAGGAAATGGCGGCGAGCGAGGGCGTGCTCCTGGGGATGGGCAACCCCCTCCTCGACATCTCCGCCGTTGTCGATGACGCCTTCCTGGCAAAgtaagtcggt ... cctgttttagGTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCCTAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgttgtaattatcacatgatagatactgacatacttctctcacccctgttttagGTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCCTAT
                                tacttctctcacccct  CT-rich tract
      taattatca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catggtgatggtgcttgattgttttattactcgatttgtagttgggtgttgtaattatcacatgatagatactgacatacttctctcacccctgttttagGTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCCTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- -ggtgatg
- - - - - -tgcttga
- - - - - - - - - - - - - - - - - - - - - - ggtgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatactg