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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttccaatggaaaataaactaattttctttgcgaagatgaaaatctcttgtgaaaatggtgtttccaaactagccctaaatggatatttggttccctgcagGTGATTTTTTCCGGTCATTTTTAGTGGAGGACAAGGCGCCTGGCGTCTTCTCCTACGTCGAGTTCCTTGTGCATGTCCACAGGCAAATCCAAAGCAAGAT

Basic information

species Zea mays
transcript GRMZM2G142697_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G142697_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os11g29200.1 (Oryza sativa), 3'ss of exon 23
ttccaatggaaaataaactaattttctttgcgaagatgaaaatctcttgtgaaaatggtgtttccaaactagccctaaatggatatttggttc-cctgcagGTGATTTTTTCCGGTCATTTTTAGTGGAGGACAAGGCGCCTGGCGTCTTCTCCTACGTCGAGTTCCTTGTGCATGTCCACAGGCAAATCCAAAGCAAGAT
        |  | |   || |      ||| || | |   |||  ||  | |  ||||  |||      || |  || |   | ||||| |||  ||||||||||||| ||||| ||||||||    ||||||||||| ||||| | | | ||||| || ||||||||||||||||| |||||||||||||| ||||||||
--------gttagtcttctgacaacacttgtgatgttcccaattgctgtttaccatggaattttattgttaacaataca--aacatttgattcatctgcagGTGATTTCTTCCGCTCATTTTTGACAGAGGACAAGGCACCTGGTGGCCTTTCCTATGTGGAGTTCCTTGTGCATGTGCACAGGCAAATCCAGAGCAAGAT
















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|5005943|gb|AI712005.1|AI712005
EST:     GAGGTGCTCATACTTGAGGTTAAGACAATGCAGAAGGGGTGACCCATCTG                         GTGATTTTTTCCGGTCATTTTTAGTGGAGGACAAGGCGCCTGGCGTCTTCT
genomic: GAGGTGCTCATACTTGAGGTTAAGACAATGCAGAAGGGGTGAACCATCTGgttagttttc ... ttccctgcagGTGATTTTTTCCGGTCATTTTTAGTGGAGGACAAGGCGCCTGGCGTCTTCT
EST: gi|31361258|gb|CD445615.1|CD445615
EST:     GAGGTGCTCATACTTGAGGTTAAGACAATGCAGAAGGGGTGAACCATCTG                         GTGATTTTTTCCGGTCATTTTTAGTGGAGGACAAGGCGCCTGGCGTCTTCT
genomic: GAGGTGCTCATACTTGAGGTTAAGACAATGCAGAAGGGGTGAACCATCTGgttagttttc ... ttccctgcagGTGATTTTTTCCGGTCATTTTTAGTGGAGGACAAGGCGCCTGGCGTCTTCT
EST: gi|31351902|gb|CD436259.1|CD436259
EST:     GAGGTGCTCATACTTGAGGTTAAGACAATGCAGAAGGGGTGAACCATCTG                         GTGATTTTTTCCGGTCATTTTTAGTGGAGGACAAGGCGCCTGGCGTCTTCT
genomic: GAGGTGCTCATACTTGAGGTTAAGACAATGCAGAAGGGGTGAACCATCTGgttagttttc ... ttccctgcagGTGATTTTTTCCGGTCATTTTTAGTGGAGGACAAGGCGCCTGGCGTCTTCT
EST: gi|5597113|gb|AI891316.1|AI891316
EST:     GGGGTGAACCATCTG                         GTGATTTTTTCCGGTCATTTTTAGTGGAGGACAAGGCGCCTGGCGTCTTCT
genomic: GGGGTGAACCATCTGgttagttttc ... ttccctgcagGTGATTTTTTCCGGTCATTTTTAGTGGAGGACAAGGCGCCTGGCGTCTTCT
EST: gi|32826257|gb|CD965935.1|CD965935
EST:     TAAGGCAATGCAGAAGGGGTGAACCATCTG                         GTGATTTTTTCCGGTCATTTTTAGTGGAGGACAAGGCGCCTGGCGTCTTCT
genomic: TAAGACAATGCAGAAGGGGTGAACCATCTGgttagttttc ... ttccctgcagGTGATTTTTTCCGGTCATTTTTAGTGGAGGACAAGGCGCCTGGCGTCTTCT
EST: gi|211457248|gb|FL096403.1|FL096403
EST:     GAGGTGCTCATACTTGAGGTTAAGACAATGCAGAAGGGGTGAACCATCTG                         GTGATTTTTTCCGGTCATTTTTAGTGGAGGACAAGGCGCCTGGCGTCTTCT
genomic: GAGGTGCTCATACTTGAGGTTAAGACAATGCAGAAGGGGTGAACCATCTGgttagttttc ... ttccctgcagGTGATTTTTTCCGGTCATTTTTAGTGGAGGACAAGGCGCCTGGCGTCTTCT
EST: gi|211457249|gb|FL096404.1|FL096404
EST:     GAGGTGCTCATACTTGAGGTTAAGACAATGCAGAAGGGGTGAACCATCTG                         GTGATTTTTTCCGGTCATTTTTAGTGGAGGACAAGGCGCCTGGCGTCTTCT
genomic: GAGGTGCTCATACTTGAGGTTAAGACAATGCAGAAGGGGTGAACCATCTGgttagttttc ... ttccctgcagGTGATTTTTTCCGGTCATTTTTAGTGGAGGACAAGGCGCCTGGCGTCTTCT
EST: gi|31351412|gb|CD435769.1|CD435769
EST:     GAGGTGCTCATACTTGAGGTTAAGACAATGCAGAAGGGGTGAACCATCTG                         GTGATTTTTTCCGGTCATTTTTAGTGGAGGACAAGGCGCCTGGCGTCTTCT
genomic: GAGGTGCTCATACTTGAGGTTAAGACAATGCAGAAGGGGTGAACCATCTGgttagttttc ... ttccctgcagGTGATTTTTTCCGGTCATTTTTAGTGGAGGACAAGGCGCCTGGCGTCTTCT
EST: gi|12968391|gb|BG265337.1|BG265337
EST:     GAGGTGCTCATACTTGAGGTTAAGACAATGCAGAAGGGGTGAACCATCTG                         GTGATTTTTTCCGGTCATTTTTAGTGGAGGACAAGGCGCCTGGCGTCTTCT
genomic: GAGGTGCTCATACTTGAGGTTAAGACAATGCAGAAGGGGTGAACCATCTGgttagttttc ... ttccctgcagGTGATTTTTTCCGGTCATTTTTAGTGGAGGACAAGGCGCCTGGCGTCTTCT
EST: gi|24770055|gb|CA405184.1|CA405184
EST:     GTGCTCATACTTGAGGTTAAGACAATGCAGAAGGGGTGACCCATCTG                         GTGATTTTTTCCGGTCATTTTTAGTGGAGGACAAGGCGCCTGGCGTCTTCT
genomic: GTGCTCATACTTGAGGTTAAGACAATGCAGAAGGGGTGAACCATCTGgttagttttc ... ttccctgcagGTGATTTTTTCCGGTCATTTTTAGTGGAGGACAAGGCGCCTGGCGTCTTCT

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: 240

AACGAACTCTCGAGGAAGGTTAACGAAGTTGTAAATGAAATAAGACGCCAGAGGTGCTCATACTTGAGGTTAAGACAATGCAGAAGGGGTGAACCATCTGgttagttttc ... ttccctgcagGTGATTTTTTCCGGTCATTTTTAGTGGAGGACAAGGCGCCTGGCGTCTTCTCCTACGTCGAGTTCCTTGTGCATGTCCACAGGCAAATCCAAAGCAAGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 220

AACGAACTCTCGAGGAAGGTTAACGAAGTTGTAAATGAAATAAGACGCCAGAGGTGCTCATACTTGAGGTTAAGACAATGCAGAAGGGGTGAACCATCTGgttagttttc ... ttccctgcagGTGATTTTTTCCGGTCATTTTTAGTGGAGGACAAGGCGCCTGGCGTCTTCTCCTACGTCGAGTTCCTTGTGCATGTCCACAGGCAAATCCAAAGCAAGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 181

AACGAACTCTCGAGGAAGGTTAACGAAGTTGTAAATGAAATAAGACGCCAGAGGTGCTCATACTTGAGGTTAAGACAATGCAGAAGGGGTGAACCATCTGgttagttttc ... ttccctgcagGTGATTTTTTCCGGTCATTTTTAGTGGAGGACAAGGCGCCTGGCGTCTTCTCCTACGTCGAGTTCCTTGTGCATGTCCACAGGCAAATCCAAAGCAAGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 250

AACGAACTCTCGAGGAAGGTTAACGAAGTTGTAAATGAAATAAGACGCCAGAGGTGCTCATACTTGAGGTTAAGACAATGCAGAAGGGGTGAACCATCTGgttagttttc ... ttccctgcagGTGATTTTTTCCGGTCATTTTTAGTGGAGGACAAGGCGCCTGGCGTCTTCTCCTACGTCGAGTTCCTTGTGCATGTCCACAGGCAAATCCAAAGCAAGAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgtgaaaatggtgtttccaaactagccctaaatggatatttggttccctgcagGTGATTTTTTCCGGTCATTTTTAGTGGAGGACAAGGCGCCTGGCGTCTTCTCCTACGTCGAGTTCCTTGTGCATGTCCACAGGCAAATCCAAAGCAAGAT
                           ccctaaa  putative branch site (score: 250)
                                             ttccctgc  putative PPT
                                     atattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttccaatggaaaataaactaattttctttgcgaagatgaaaatctcttgtgaaaatggtgtttccaaactagccctaaatggatatttggttccctgcagGTGATTTTTTCCGGTCATTTTTAGTGGAGGACAAGGCGCCTGGCGTCTTCTCCTACGTCGAGTTCCTTGTGCATGTCCACAGGCAAATCCAAAGCAAGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - aaataaa
- - - - - - - - - - - - - - - - - gatgaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tggtgtt