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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATCTTATCGCGAAAAGTTTAGCCACATCAGATCAACAAGATGCGTCTGGAAATAAGCTGCTTCTTGATATTGGTCTTTGGCTGACTCACAAGATAAAGgtacataactatataactaaaatattcttgctgctggatttgagccacttatcttatgttgtagtttggtattcactgtctcgggtattgcaaatgagctaaatggctccactatactgtatgtggttcttgaaagttttgcttaataggccttgtgctaattcctcgtag

Basic information

species Zea mays
transcript GRMZM2G004932_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G004932_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os05g44922.1 (Oryza sativa), 5'ss of exon 11
GGATCTTATCGCGAAAAGTTTAGCCACATCAGATCAACAAGATGCGTCTGGAAATAAGCTGCTTCTTGATATTGGTCTTTGGCTGACTCACAAGATAAAGgtacataactatataactaaaatattcttgctgctggatttgagccacttatcttatgttgtagtttggtattcactgtctcgggtattgcaaatgagctaaatggctccactatactgtatgtggttcttgaaagttttgcttaataggccttgtgctaattcctcgtag
||||||||| || ||||||||| | || || || || |||||||| || ||||||||||| || ||||||||||||||||||||||||||||||||||||||||| ||    | |  |||     | ||||| ||| |||   | |   |    | ||||    |  |  | | |    ||  |  ||| | | |||      ||                                                                  
GGATCTTATAGCCAAAAGTTTATCTACTTCTGAGCAGCAAGATGCATCAGGAAATAAGCTACTGCTTGATATTGGTCTTTGGCTGACTCACAAGATAAAGgtacacaaa---acacttaa-----ttttgcttctgaattcaggtctgctgctct-tgttaatataggtaactaaaacactaagcaattcccactgaaaactgtgatga--------------------------------------------------------------
















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|32932754|gb|CF037566.1|CF037566
EST:     GAAATAAGCTGCTTCTTGATATTGGTCTTTGGCTGACTCACAAGATAAAG                         GACTACTTCAAAAGCAAAAAGATGGAGATGACGATTAAATACATAG
genomic: GAAATAAGCTGCTTCTTGATATTGGTCTTTGGCTGACTCACAAGATAAAGgtacataact ... ttcctcgtagGACTACTTCAAAAGCAAAAAGATGGAGATGACGATTAAATACATAG
EST: gi|211119332|gb|FL065967.1|FL065967
EST:     AAATAAGCTGCTTCTTGATATTGGTCTTTGGCTGACTCAACAAGATAAAG                         GACTACTTTCAAAAGC
genomic: AAATAAGCTGCTTCTTGATATTGGTCTTTGGCTGACTCA-CAAGATAAAGgtacataact ... ttcctcgtagGACTACTT-CAAAAGC
EST: gi|6031341|gb|AW076198.1|AW076198
EST:     GAAATAAGCTGCTTCTTGATATTGGTCTTTGGCTGACTCACAAGATAAAG                         GACTACTTCAAAAGCAAAAAGATGGAGATGACGATTAAATACATAG
genomic: GAAATAAGCTGCTTCTTGATATTGGTCTTTGGCTGACTCACAAGATAAAGgtacataact ... ttcctcgtagGACTACTTCAAAAGCAAAAAGATGGAGATGACGATTAAATACATAG
EST: gi|211480673|gb|FK996001.1|FK996001
EST:     GAAATAAGCTGCTTCTTGATATTGGTCTTTGGCTGACTCACAAGATAAAG                         GACTACTTCAAAAGCAAAAAGATGGAGATGACGATTAAATACATAG
genomic: GAAATAAGCTGCTTCTTGATATTGGTCTTTGGCTGACTCACAAGATAAAGgtacataact ... ttcctcgtagGACTACTTCAAAAGCAAAAAGATGGAGATGACGATTAAATACATAG
EST: gi|71433706|gb|DR814756.1|DR814756
EST:     GAAATAAGCTGCTTCTTGATATTGGTCTTTGGCTGACTCACAAGATAAAG                         GACTACTTCAAAAGCAAAAAGATGGAGATGACGATTAAATACATAG
genomic: GAAATAAGCTGCTTCTTGATATTGGTCTTTGGCTGACTCACAAGATAAAGgtacataact ... ttcctcgtagGACTACTTCAAAAGCAAAAAGATGGAGATGACGATTAAATACATAG
EST: gi|71761875|gb|DR959812.1|DR959812
EST:     TGATATTGGTCTTTGGCTGACTCACAAGATAAAG                         GACTACTTCAAAAGCAAAAAGATGGAGATGACGATTAAATACATAG
genomic: TGATATTGGTCTTTGGCTGACTCACAAGATAAAGgtacataact ... ttcctcgtagGACTACTTCAAAAGCAAAAAGATGGAGATGACGATTAAATACATAG
EST: gi|60348735|gb|DN215708.1|DN215708
EST:     GAAATAAGCTGCTTCTTGATATTGGTCTTTGGCTGACTCACAAGATAAAG                         GACTACTTCAAAAGCAAAAAGATGGAGATGACGATTAAATACATAG
genomic: GAAATAAGCTGCTTCTTGATATTGGTCTTTGGCTGACTCACAAGATAAAGgtacataact ... ttcctcgtagGACTACTTCAAAAGCAAAAAGATGGAGATGACGATTAAATACATAG
EST: gi|94479652|gb|EB708610.1|EB708610
EST:     GAAATAAGCTGCTTCTTGATATTGGTCTTTGGCTGACTCACAAGATAAAG                         GACTACTTCAAAAGCAAAAAGATGGAGATGACGATTAAATACATAG
genomic: GAAATAAGCTGCTTCTTGATATTGGTCTTTGGCTGACTCACAAGATAAAGgtacataact ... ttcctcgtagGACTACTTCAAAAGCAAAAAGATGGAGATGACGATTAAATACATAG
EST: gi|94479651|gb|EB708609.1|EB708609
EST:     GATATTGTTCTTTGGCTGATTCACAAGATAAAG                         GAATACTTCAAAAGCAAAAAGATGGAGATGACGATTAAATACATAG
genomic: GATATTGGTCTTTGGCTGACTCACAAGATAAAGgtacataact ... ttcctcgtagGACTACTTCAAAAGCAAAAAGATGGAGATGACGATTAAATACATAG
EST: gi|87157419|gb|DY402208.1|DY402208
EST:     GAAATAAGCTGCTTCTTGATATTGGTCTTTGGCTGACTCACAAGATAAAG                         GACTACTTCAAAAGCAAAAAGATGGAGATGACGATTAAATACATAG
genomic: GAAATAAGCTGCTTCTTGATATTGGTCTTTGGCTGACTCACAAGATAAAGgtacataact ... ttcctcgtagGACTACTTCAAAAGCAAAAAGATGGAGATGACGATTAAATACATAG
EST: gi|67037463|gb|CO464279.1|CO464279
EST:     GACTCACAAGATAACG                         GACTACTTCAAAAGCAAAAAGATGGAGATGACGATTAAATACATAG
genomic: GACTCACAAGATAAAGgtacataact ... ttcctcgtagGACTACTTCAAAAGCAAAAAGATGGAGATGACGATTAAATACATAG
EST: gi|60344598|gb|DN211571.1|DN211571
EST:     GAAATAAGCTGCTTCTTGATATTGGTCTTTGGCTGACTCACAAGATAAAG                         GACTACTTCAAAAGCAAAAAGATGGAGATGACGATTAAATACATAG
genomic: GAAATAAGCTGCTTCTTGATATTGGTCTTTGGCTGACTCACAAGATAAAGgtacataact ... ttcctcgtagGACTACTTCAAAAGCAAAAAGATGGAGATGACGATTAAATACATAG
EST: gi|26560069|gb|CA832304.1|CA832304
EST:     CTTTGGCTGACTCACAAGATAAAG                         GACTACTTCAAAAGCAAAAAGATGGAGATGACGATTAAATACATAG
genomic: CTTTGGCTGACTCACAAGATAAAGgtacataact ... ttcctcgtagGACTACTTCAAAAGCAAAAAGATGGAGATGACGATTAAATACATAG
EST: gi|89246745|gb|DY618532.1|DY618532
EST:     GAAATAAGCTGCTTCTTGATATTGGTCTTTGGCTGACTCACAAGATAAAG                         GACTACTTCAAAAGCAAAAAGATGGAGATGACGATTAAATACATAG
genomic: GAAATAAGCTGCTTCTTGATATTGGTCTTTGGCTGACTCACAAGATAAAGgtacataact ... ttcctcgtagGACTACTTCAAAAGCAAAAAGATGGAGATGACGATTAAATACATAG
EST: gi|23199633|gb|BU582198.1|BU582198
EST:     G-AATAAGCTGCTTCTTGATATTGGTCTTTGGCTGACTCACAAGATAAAG                         GACTACTTCAAAAGCAAAAAGATGGAGATGACGATTAAATACATAG
genomic: GAAATAAGCTGCTTCTTGATATTGGTCTTTGGCTGACTCACAAGATAAAGgtacataact ... ttcctcgtagGACTACTTCAAAAGCAAAAAGATGGAGATGACGATTAAATACATAG

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: 46 (upstream exon), 40 (downstream exon)
Score: 71

GGATCTTATCGCGAAAAGTTTAGCCACATCAGATCAACAAGATGCGTCTGGAAATAAGCTGCTTCTTGATATTGGTCTTTGGCTGACTCACAAGATAAAGgtacataact ... ttcctcgtagGACTACTTCAAAAGCAAAAAGATGGAGATGACGATTAAATACATAG


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 83

GGATCTTATCGCGAAAAGTTTAGCCACATCAGATCAACAAGATGCGTCTGGAAATAAGCTGCTTCTTGATATTGGTCTTTGGCTGACTCACAAGATAAAGgtacataact ... ttcctcgtagGACTACTTCAAAAGCAAAAAGATGGAGATGACGATTAAATACATAG


Block sizes: 48 (upstream exon), 40 (downstream exon)
Score: 65

GGATCTTATCGCGAAAAGTTTAGCCACATCAGATCAACAAGATGCGTCTGGAAATAAGCTGCTTCTTGATATTGGTCTTTGGCTGACTCACAAGATAAAGgtacataact ... ttcctcgtagGACTACTTCAAAAGCAAAAAGATGGAGATGACGATTAAATACATAG


Block sizes: 49 (upstream exon), 38 (downstream exon)
Score: 27

GGATCTTATCGCGAAAAGTTTAGCCACATCAGATCAACAAGATGCGTCTGGAAATAAGCTGCTTCTTGATATTGGTCTTTGGCTGACTCACAAGATAAAGgtacataact ... ttcctcgtagGACTACTTCAAAAGCAAAAAGATGGAGATGACGATTAAATACATAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATCTTATCGCGAAAAGTTTAGCCACATCAGATCAACAAGATGCGTCTGGAAATAAGCTGCTTCTTGATATTGGTCTTTGGCTGACTCACAAGATAAAGgtacataactatataactaaaatattcttgctgctggatttgagccacttatcttatgttgtagtttggtattcactgtctcgggtattgcaaatgagctaaatggctccactatactgtatgtggttcttgaaagttttgcttaataggccttgtgctaattcctcgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT