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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgtatatgtagactgttacagtgagattatcccattttttccttctaactcatgtgtcaacgtatgatatgtcaattgtcatttatttatgttaaaacagGAGAAAAGGGATCATTGTTGGAAATGAGCAGGAAGGTGACGACACCATTGTAGTTTGCCAT

Basic information

species Zea mays
transcript GRMZM2G056393_T01
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G056393_T02 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os03g36780.1 (Oryza sativa), 3'ss of exon 17
-cgtatatgtagactgttacagtgagattatcccattttttccttctaactcatgtgtcaacgtatgatatgtcaattgtcattta-tttatgtt-aaaacagGAGAAAAGGGATCATTGTTGGAAATGAGCAGGAAGGTGACGACACCATTGTAGTTTGCCAT
 | | |||   ||   || |  |      |     || |    || |||||    || | ||  |   || ||| | | |  |||  || ||||  ||||||||||||| || ||||||||||||||||| |||||||| ||||||||  |||| |||||||||
tcatctattatgaaaatttccttttagcaacttgtttgtcaagttataact---atgcctactaagtctaagtctaatattgttttcttcatgtggaaaacagGAGAAAGGGTATCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGTGGTTTGCCAT
















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|32933717|gb|CF038529.1|CF038529
EST:     CTCAAATTTCCAACTGAGTTTCAGGGCACAGTAACTGGTGATATGAACAA                         GAGAAAAGGGACCATTGTTGGAAATGAGCAGGAAGGTGACGACACCGTTGT
genomic: CTCAAATTTCCAACTGAGTTTCAGGGCACAGTAACTGGTGATATGAACAAgtaagtgctt ... gttaaaacagGAGAAAAGGGATCATTGTTGGAAATGAGCAGGAAGGTGACGACACCATTGT
EST: gi|84980317|gb|DW530666.1|DW530666
EST:     CTCAAATTTCCAACTGAGTTTCAGGGCACAGTAACTGGTGATATGAACAA                         GAGAAAAGGGATCATTGTTGGAAATGAGCAGGAAGGTGACGACACCATTGT
genomic: CTCAAATTTCCAACTGAGTTTCAGGGCACAGTAACTGGTGATATGAACAAgtaagtgctt ... gttaaaacagGAGAAAAGGGATCATTGTTGGAAATGAGCAGGAAGGTGACGACACCATTGT
EST: gi|32932818|gb|CF037630.1|CF037630
EST:     CTCAAATTTCCAACTGAGTTTCAGGGCACAGTAACTGGTGATATGAACAA                         GAGAAAAGGGATCATTGTTGGAAATGAGCAGGAAGGTGACGACACCGTTGT
genomic: CTCAAATTTCCAACTGAGTTTCAGGGCACAGTAACTGGTGATATGAACAAgtaagtgctt ... gttaaaacagGAGAAAAGGGATCATTGTTGGAAATGAGCAGGAAGGTGACGACACCATTGT
EST: gi|211492457|gb|FL459662.1|FL459662
EST:     CTCAAATTTCCAACTGAGTTTCAGGGCACAGTAACTGGTGATATGAACAA                         GAGAAAAGGGATCATTGTTGGAAATGAGCAGGAAGGTGACGACACCATTGT
genomic: CTCAAATTTCCAACTGAGTTTCAGGGCACAGTAACTGGTGATATGAACAAgtaagtgctt ... gttaaaacagGAGAAAAGGGATCATTGTTGGAAATGAGCAGGAAGGTGACGACACCATTGT
EST: gi|211184463|gb|FL030548.1|FL030548
EST:     CTCAAATTTCCAACTGAGTTTCAGGGCACAGTAACTGGTGATATGAACAA                         GAGAAAAGGGATCATTGTTGGAAATGAGCAGGAAGGTGACGACACCATTGT
genomic: CTCAAATTTCCAACTGAGTTTCAGGGCACAGTAACTGGTGATATGAACAAgtaagtgctt ... gttaaaacagGAGAAAAGGGATCATTGTTGGAAATGAGCAGGAAGGTGACGACACCATTGT
EST: gi|6020648|gb|AW065681.1|AW065681
EST:     CTCAAATTTCCAACTGAGTTTCAGGGCACAGTAACTGGTGATATGAACAA                         GAGAAAAGGGATCATTGNTGGAAATGAGCAGGAAGGTGACGACACCATTGT
genomic: CTCAAATTTCCAACTGAGTTTCAGGGCACAGTAACTGGTGATATGAACAAgtaagtgctt ... gttaaaacagGAGAAAAGGGATCATTGTTGGAAATGAGCAGGAAGGTGACGACACCATTGT
EST: gi|33093919|gb|CF053913.1|CF053913
EST:     CTCAAATTTCCAACTGAGTTTCAGGGCACAGTAACTGGTGATATGAACAA                         GAGAAAAGGGATCATTGTTGGAAATGAGCAGGAAGGTGACGACACCGTTGT
genomic: CTCAAATTTCCAACTGAGTTTCAGGGCACAGTAACTGGTGATATGAACAAgtaagtgctt ... gttaaaacagGAGAAAAGGGATCATTGTTGGAAATGAGCAGGAAGGTGACGACACCATTGT
EST: gi|61119855|gb|DN560816.1|DN560816
EST:     CTCAAATTTCCAACTGAGTTTCAGGGCACAGTAACTGGTGATATGAACAA                         GAGAAAAGGGATCATTGTTGGAAATGAGCAGGAAGGTGACGACACCATTGT
genomic: CTCAAATTTCCAACTGAGTTTCAGGGCACAGTAACTGGTGATATGAACAAgtaagtgctt ... gttaaaacagGAGAAAAGGGATCATTGTTGGAAATGAGCAGGAAGGTGACGACACCATTGT
EST: gi|69351603|gb|DR452190.1|DR452190
EST:     CTCAAATTTCCAACTGAGTTTCAGGGCACAGTAACTGGTGATATGAACAA                         GAGAAAAGGGATCATTGTTGGAAATGGGCAGGAAGGTGACGACACCATTGT
genomic: CTCAAATTTCCAACTGAGTTTCAGGGCACAGTAACTGGTGATATGAACAAgtaagtgctt ... gttaaaacagGAGAAAAGGGATCATTGTTGGAAATGAGCAGGAAGGTGACGACACCATTGT

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: 140

GCTACACTTCTGCCAAACCTGTAATATTAGAACCTGTGATGAAGGTGGAACTCAAATTTCCAACTGAGTTTCAGGGCACAGTAACTGGTGATATGAACAAgtaagtgctt ... gttaaaacagGAGAAAAGGGATCATTGTTGGAAATGAGCAGGAAGGTGACGACACCATTGTAGTTTGCCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 95

GCTACACTTCTGCCAAACCTGTAATATTAGAACCTGTGATGAAGGTGGAACTCAAATTTCCAACTGAGTTTCAGGGCACAGTAACTGGTGATATGAACAAgtaagtgctt ... gttaaaacagGAGAAAAGGGATCATTGTTGGAAATGAGCAGGAAGGTGACGACACCATTGTAGTTTGCCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 78

GCTACACTTCTGCCAAACCTGTAATATTAGAACCTGTGATGAAGGTGGAACTCAAATTTCCAACTGAGTTTCAGGGCACAGTAACTGGTGATATGAACAAgtaagtgctt ... gttaaaacagGAGAAAAGGGATCATTGTTGGAAATGAGCAGGAAGGTGACGACACCATTGTAGTTTGCCAT


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 86

GCTACACTTCTGCCAAACCTGTAATATTAGAACCTGTGATGAAGGTGGAACTCAAATTTCCAACTGAGTTTCAGGGCACAGTAACTGGTGATATGAACAAgtaagtgctt ... gttaaaacagGAGAAAAGGGATCATTGTTGGAAATGAGCAGGAAGGTGACGACACCATTGTAGTTTGCCAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taactcatgtgtcaacgtatgatatgtcaattgtcatttatttatgttaaaacagGAGAAAAGGGATCATTGTTGGAAATGAGCAGGAAGGTGACGACACCATTGTAGTTTGCCAT
 ttctaac  putative branch site (score: 86)
                            aattgtcatttattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgtatatgtagactgttacagtgagattatcccattttttccttctaactcatgtgtcaacgtatgatatgtcaattgtcatttatttatgttaaaacagGAGAAAAGGGATCATTGTTGGAAATGAGCAGGAAGGTGACGACACCATTGTAGTTTGCCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- -atatgta
- - - - - - ctgttac
- - - - - - - - - - - - - - - - - - - - - - - - - catgtgt