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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtacttgtatttttttgtattattatataccatggtttttaaagcggtaaggcgagacaaggcgttggaccaccgcctggatgcctaggcgacgccttaaaaacagtgttatatacatcatttaatgtatatcatatcttactttttacttctataccagGTTTCAGAATATACGTGTTCCTCGTGAGAACTTGCTTAATTTGGTTGCTGATGTTTTGCCAGATGGGCGATATGTTAGCATGATAGATAATCCAGATCAG

Basic information

species Zea mays
transcript GRMZM2G014136_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G014136_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os06g24704.1 (Oryza sativa), 3'ss of exon 4
gtgagtacttgtatttttttgtattattatataccatggtttttaaagcggtaaggcgagacaaggcgttggaccaccgcctggatgcctaggcgacgccttaaaaacagtgttatatacatcatttaatgtatatcatatcttactttttacttctataccagGTTTCAGAATATACGTGTTCCTCGTGAGAACTTGCTTAATTTGGTTGCTGATGTTTTGCCAGATGGGCGATATGTTAGCATGATAGATAATCCAGATCAG
                                                                                  |   |||   |     |  ||||    || || | |   || | | | | | ||  ||  ||| |||  |  | | |  ||||||| | ||||||||||||||||| ||||| ||||| ||| | ||||||||||||||||| ||||||| ||||||||||| ||||||| | || ||||||
----------------------------------------------------------------------------------gtgagcccttgtacttctgtaaa----gttttgtct---tcctatcacgcacattgtaaattaattt--aactgtctgtcagGTTTAACAATATACGTGTTCCTCGAGAGAATTTGCTGAATCTTGTTGCTGATGTTTTGCCGGATGGGCAATATGTTAGCACGATAGATGACCCTGATCAG
















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|32922586|gb|CF027398.1|CF027398
EST:     GACTGTGGCCATAAGATTGGACTGAATGGCGTTGATAATGGGCGGATTTG                         GTTTCAGAATATACGTGTTCCTCGTGAGAACTTGCTTAATTTGGTTGGTGA
genomic: GACTGTGGCCATAAGATTGGACTGAATGGCGTTGATAATGGGCGGATTTGgtgagtactt ... tctataccagGTTTCAGAATATACGTGTTCCTCGTGAGAACTTGCTTAATTTGGTTGCTGA
EST: gi|32922930|gb|CF027742.1|CF027742
EST:     GACTGTGGCCATAAGATTGGACTGAATGGCGTTGATAATGGGCGGATTTG                         GTTTCAGAATATACGTGTTCCTCGTGAGAACTTGCTTAATTTGGTTGGTGA
genomic: GACTGTGGCCATAAGATTGGACTGAATGGCGTTGATAATGGGCGGATTTGgtgagtactt ... tctataccagGTTTCAGAATATACGTGTTCCTCGTGAGAACTTGCTTAATTTGGTTGCTGA
EST: gi|32922923|gb|CF027735.1|CF027735
EST:     GACTGTGGCCATAAGATTGGACTGAATGGCGTTGATAATGGGCGGATTTG                         GTTTCAGAATATACGTGTTCCTCGTGAGAACTTGCTTAATTTGGTTGGTGA
genomic: GACTGTGGCCATAAGATTGGACTGAATGGCGTTGATAATGGGCGGATTTGgtgagtactt ... tctataccagGTTTCAGAATATACGTGTTCCTCGTGAGAACTTGCTTAATTTGGTTGCTGA
EST: gi|50322995|gb|CO518121.1|CO518121
EST:     GACTGTGGCCATAAGATTGGACTGAATGGCGTTGATAATGGGCGGATTTG                         GTTTCAGAATATACGTGTTCCTCGTGAGAACTTGCTTAATTTGGTTGCTGA
genomic: GACTGTGGCCATAAGATTGGACTGAATGGCGTTGATAATGGGCGGATTTGgtgagtactt ... tctataccagGTTTCAGAATATACGTGTTCCTCGTGAGAACTTGCTTAATTTGGTTGCTGA
EST: gi|78118417|gb|DV536803.1|DV536803
EST:     GACTGTGGCCATAAGATTGGACTGAATGGCGTTGATAATGGGCGGATTTG                         GTTTCAGAATATACGTGTTCCTCGTGAGAACTTGCTTAATTTGGTTGCTGA
genomic: GACTGTGGCCATAAGATTGGACTGAATGGCGTTGATAATGGGCGGATTTGgtgagtactt ... tctataccagGTTTCAGAATATACGTGTTCCTCGTGAGAACTTGCTTAATTTGGTTGCTGA
EST: gi|32923030|gb|CF027842.1|CF027842
EST:     GACTGTGGCCATAAGATTGGACTGAATGGCGTTGATAATGGGCGGATTTG                         GTTTCAGAATATACGTGTTCCTCGTGAGAACTTGCTTAATTTGGTTGGTGA
genomic: GACTGTGGCCATAAGATTGGACTGAATGGCGTTGATAATGGGCGGATTTGgtgagtactt ... tctataccagGTTTCAGAATATACGTGTTCCTCGTGAGAACTTGCTTAATTTGGTTGCTGA
EST: gi|32923258|gb|CF028070.1|CF028070
EST:     GACTGTGGCCATAAGATTGGACTGAATGGCGTTGATAATGGGCGGATTTG                         GTTTCAGAATATACGTGTTCCTCGTGAGAACTTGCTTAATTTGGTTGGTGA
genomic: GACTGTGGCCATAAGATTGGACTGAATGGCGTTGATAATGGGCGGATTTGgtgagtactt ... tctataccagGTTTCAGAATATACGTGTTCCTCGTGAGAACTTGCTTAATTTGGTTGCTGA
EST: gi|78122592|gb|DV540976.1|DV540976
EST:     GACTGTGGCCATAAGATTGGACTGAATGGCGTTGATAATGGGCGGATTTG                         GTTTCAGAATATACGTGTTCCTCGTGAGAACTTGCTTAATTTGGTTGCTGA
genomic: GACTGTGGCCATAAGATTGGACTGAATGGCGTTGATAATGGGCGGATTTGgtgagtactt ... tctataccagGTTTCAGAATATACGTGTTCCTCGTGAGAACTTGCTTAATTTGGTTGCTGA
EST: gi|32921855|gb|CF026667.1|CF026667
EST:     GACTGTGGCCATAAGATTGGACTGAATGGCGTTGATAATGGGCGGATTTG                         GTTTCAGAATATACGTGTTCCTCGTGAGAACTTGCTTAATTTGGTTGGTGA
genomic: GACTGTGGCCATAAGATTGGACTGAATGGCGTTGATAATGGGCGGATTTGgtgagtactt ... tctataccagGTTTCAGAATATACGTGTTCCTCGTGAGAACTTGCTTAATTTGGTTGCTGA
EST: gi|61119686|gb|DN560647.1|DN560647
EST:     CGTTGATAATGGGCGGATTTG                         GTTTCAGAATATACGTGTTCCTCGTGAGAACTTGCTTAATTTGGTTGCTGA
genomic: CGTTGATAATGGGCGGATTTGgtgagtactt ... tctataccagGTTTCAGAATATACGTGTTCCTCGTGAGAACTTGCTTAATTTGGTTGCTGA
EST: gi|32923274|gb|CF028086.1|CF028086
EST:     GACTGTGGCCATAAGATTGGACTGAATGGCGTTGATAATGGGCGGATTTG                         GTTTCAGAATATACGTGTTCCTCGTGAGAACTTGCTTAATTTGGTTGGTGA
genomic: GACTGTGGCCATAAGATTGGACTGAATGGCGTTGATAATGGGCGGATTTGgtgagtactt ... tctataccagGTTTCAGAATATACGTGTTCCTCGTGAGAACTTGCTTAATTTGGTTGCTGA
EST: gi|32921928|gb|CF026740.1|CF026740
EST:     GACTGTGGCCATAAGATTGGACTGAATGGCGTTGATAATGGGCGGATTTG                         GTTTCAGAATATACGTGTTCCTCGTGAGAACTTGCTTAATTTGGTTGGTGA
genomic: GACTGTGGCCATAAGATTGGACTGAATGGCGTTGATAATGGGCGGATTTGgtgagtactt ... tctataccagGTTTCAGAATATACGTGTTCCTCGTGAGAACTTGCTTAATTTGGTTGCTGA
EST: gi|32922650|gb|CF027462.1|CF027462
EST:     GACTGTGGCCATAAGATTGGACTGAATGGCGTTGATAATGGGCGGATTTG                         GTTTCAGAATATACGTGTTCCTCGTGAGAACTTGCTTAATTTGGTTGGTGA
genomic: GACTGTGGCCATAAGATTGGACTGAATGGCGTTGATAATGGGCGGATTTGgtgagtactt ... tctataccagGTTTCAGAATATACGTGTTCCTCGTGAGAACTTGCTTAATTTGGTTGCTGA
EST: gi|32920277|gb|CF025089.1|CF025089
EST:     GACTGTGGCCATAAGATTGGACTGAATGGCGTTGATAATGGGCGGATTTG                         GTTTCAGAATATACGTGTTCCTCGTGAGAACTTGCTTAATTTGGTTGGTGA
genomic: GACTGTGGCCATAAGATTGGACTGAATGGCGTTGATAATGGGCGGATTTGgtgagtactt ... tctataccagGTTTCAGAATATACGTGTTCCTCGTGAGAACTTGCTTAATTTGGTTGCTGA
EST: gi|211534371|gb|FL093851.1|FL093851
EST:     GACTGTGGCCATAAGATTGGACTGAATGGCGTTGATAATGGGCGGATTTG                         GTTTCAGAATATACGTGTTCC
genomic: GACTGTGGCCATAAGATTGGACTGAATGGCGTTGATAATGGGCGGATTTGgtgagtactt ... tctataccagGTTTCAGAATATACGTGTTCC

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), 41 (downstream exon)
Score: 78

CTCAAATTAGGGATGAAGATGGAACTGTGTTGCCTAATATCCATATAGCTGACTGTGGCCATAAGATTGGACTGAATGGCGTTGATAATGGGCGGATTTGgtgagtactt ... tctataccagGTTTCAGAATATACGTGTTCCTCGTGAGAACTTGCTTAATTTGGTTGCTGATGTTTTGCCAGATGGGCGATATGTTAGCATGATAGATAATCCAGATCAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 234

CTCAAATTAGGGATGAAGATGGAACTGTGTTGCCTAATATCCATATAGCTGACTGTGGCCATAAGATTGGACTGAATGGCGTTGATAATGGGCGGATTTGgtgagtactt ... tctataccagGTTTCAGAATATACGTGTTCCTCGTGAGAACTTGCTTAATTTGGTTGCTGATGTTTTGCCAGATGGGCGATATGTTAGCATGATAGATAATCCAGATCAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 307

CTCAAATTAGGGATGAAGATGGAACTGTGTTGCCTAATATCCATATAGCTGACTGTGGCCATAAGATTGGACTGAATGGCGTTGATAATGGGCGGATTTGgtgagtactt ... tctataccagGTTTCAGAATATACGTGTTCCTCGTGAGAACTTGCTTAATTTGGTTGCTGATGTTTTGCCAGATGGGCGATATGTTAGCATGATAGATAATCCAGATCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 143

CTCAAATTAGGGATGAAGATGGAACTGTGTTGCCTAATATCCATATAGCTGACTGTGGCCATAAGATTGGACTGAATGGCGTTGATAATGGGCGGATTTGgtgagtactt ... tctataccagGTTTCAGAATATACGTGTTCCTCGTGAGAACTTGCTTAATTTGGTTGCTGATGTTTTGCCAGATGGGCGATATGTTAGCATGATAGATAATCCAGATCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgttatatacatcatttaatgtatatcatatcttactttttacttctataccagGTTTCAGAATATACGTGTTCCTCGTGAGAACTTGCTTAATTTGGTTGCTGATGTTTTGCCAGATGGGCGATATGTTAGCATGATAGATAATCCAGATCAG
                              atcttac  putative branch site (score: 143)
                               tcttactttttacttc  CT-rich tract
              atttaatgtatatcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtacttgtatttttttgtattattatataccatggtttttaaagcggtaaggcgagacaaggcgttggaccaccgcctggatgcctaggcgacgccttaaaaacagtgttatatacatcatttaatgtatatcatatcttactttttacttctataccagGTTTCAGAATATACGTGTTCCTCGTGAGAACTTGCTTAATTTGGTTGCTGATGTTTTGCCAGATGGGCGATATGTTAGCATGATAGATAATCCAGATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA