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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctcctagcctctctcatagaaatagatgtgtgttcaatataggttcagtcttgtttatatagttaaaactgtactgaatattggccttgttctcaacagCAAGTTCAGAACTTTGGAGAACCTTTTTTTATGGTTATTCGTGAGGATGAGACCCTATCTTCTATCAAAGAACGTATACAGAAAAAGCTTAAGGTTCCAG

Basic information

species Zea mays
transcript GRMZM5G864266_T01
intron # 31
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G864266_T01 (Zea mays), 3'ss of exon 31
lower sequence: LOC_Os07g06950.1 (Oryza sativa), 3'ss of exon 29
--tctcctagcctctctcatagaaatagatgtgtgttcaatataggttcagtcttgtttatatagttaaaactgtactgaatattggccttgttctcaacagCAAGTTCAGAACTTTGGAGAACCTTTTTTTATGGTTATTCGTGAGGATGAGACCCTATCTTCTATCAAAGAACGTATACAGAAAAAGCTTAAGGTTCCAG
     |  |   |   |     |  |      ||  |  || ||    ||  ||| | ||| |||| |||  | | |||| ||||   | || | || |||||||||||||||||||||||||||||| ||||||||||||||||||||||| ||||| |||||||| |||||||| ||||||||||| || || |||||||
gggaacacaatattgttagccaattttagca-gttctgcatctaacagcatacttctatatctagtaaaacttatgctga-tatttatcctgatttctacagCAAGTTCAGAACTTTGGAGAACCTTTCTTTATGGTTATTCGTGAGGATGAAACCCTTTCTTCTATTAAAGAACGGATACAGAAAAAACTAAAAGTTCCAG
















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|60348260|gb|DN215233.1|DN215233
EST:     TCATGTATATCATTTTACAAAAGACACTCAAAACCAAACG                         CAAGTTCAGAACTTTGGAGAACCNNNNNNNATGGTTATTCGTGAGGATGAG
genomic: TCATGTATATCATTTTACAAAAGACACTCAAAACCAAACGgtaatgatgg ... ttctcaacagCAAGTTCAGAACTTTGGAGAACCTTTTTTTATGGTTATTCGTGAGGATGAG
EST: gi|61118763|gb|DN559724.1|DN559724
EST:     ATCGTTTGATTCATGTATATCATTTTACAAAAGACACTCAAAACCAAACG                         CAAGTTCAGAACTTTGGAGAACCNNNNNNNATGGTTATTCGTGAGGATGAG
genomic: ATCGTTTGATTCATGTATATCATTTTACAAAAGACACTCAAAACCAAACGgtaatgatgg ... ttctcaacagCAAGTTCAGAACTTTGGAGAACCTTTTTTTATGGTTATTCGTGAGGATGAG
EST: gi|60400274|gb|DN233081.1|DN233081
EST:     AAAAGACACTCAAAACCAAACG                         CAAGTTCAGAACTTTGGAGAACCNNNNNNNATGGTTATTCGTGAGGATGAG
genomic: AAAAGACACTCAAAACCAAACGgtaatgatgg ... ttctcaacagCAAGTTCAGAACTTTGGAGAACCTTTTTTTATGGTTATTCGTGAGGATGAG
EST: gi|78106266|gb|DV524684.1|DV524684
EST:     ATCGTTTGATTCATGTATATCATTTTACAAAAGACACTCAAAACCAAACG                         CAAGTTCAGAACTTTGGAGAACCNNNNNNNATGGTTATTCGTGAGGATGAG
genomic: ATCGTTTGATTCATGTATATCATTTTACAAAAGACACTCAAAACCAAACGgtaatgatgg ... ttctcaacagCAAGTTCAGAACTTTGGAGAACCTTTTTTTATGGTTATTCGTGAGGATGAG
EST: gi|60394863|gb|DN227732.1|DN227732
EST:     ATCGTTTGATTCATGTATATCATTTTACAAAAGACACTCAAAACCAAACG                         CAAGTTCAGAACTTTGGAGAACCNNNNNNNATGGTTATTCGTGAGGATGAG
genomic: ATCGTTTGATTCATGTATATCATTTTACAAAAGACACTCAAAACCAAACGgtaatgatgg ... ttctcaacagCAAGTTCAGAACTTTGGAGAACCTTTTTTTATGGTTATTCGTGAGGATGAG
EST: gi|211394943|gb|FL031667.1|FL031667
EST:     ATCGTTTGATTCATGTATATCATTTTACAAAAGACACTCAAAACCAAACG                         CAAGTTCAGAACTTTGGAGAACCNNNNNNNATGGTTATTCGTGAGGATGAG
genomic: ATCGTTTGATTCATGTATATCATTTTACAAAAGACACTCAAAACCAAACGgtaatgatgg ... ttctcaacagCAAGTTCAGAACTTTGGAGAACCTTTTTTTATGGTTATTCGTGAGGATGAG
EST: gi|67014431|gb|CO443180.1|CO443180
EST:     ATCGTTTGATTCATGTATATCATTTTACAAAAGACACTCAAAACCAAACG                         CAAGTTCAGAACTTTGGAGAACCNNNNNNNATGGTTATTCGTGAGGATGAG
genomic: ATCGTTTGATTCATGTATATCATTTTACAAAAGACACTCAAAACCAAACGgtaatgatgg ... ttctcaacagCAAGTTCAGAACTTTGGAGAACCTTTTTTTATGGTTATTCGTGAGGATGAG
EST: gi|67020350|gb|CO449099.1|CO449099
EST:     ATCGTTTGATTCATGTATATCATTTTACAAAAGACACTCAAAACCAAACG                         CAAGTTCAGAACTTTGGAGAACCNNNNNNNATGGTTATTCGTGAGGATGAG
genomic: ATCGTTTGATTCATGTATATCATTTTACAAAAGACACTCAAAACCAAACGgtaatgatgg ... ttctcaacagCAAGTTCAGAACTTTGGAGAACCTTTTTTTATGGTTATTCGTGAGGATGAG

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: 234

GTTCCAGAGGAGGAGAAAAATCTTGGCCCCTTCGATCGTTTGATTCATGTATATCATTTTACAAAAGACACTCAAAACCAAACGgtaatgatgg ... ttctcaacagCAAGTTCAGAACTTTGGAGAACCTTTTTTTATGGTTATTCGTGAGGATGAGACCCTATCTTCTATCAAAGAACGTATACAGAAAAAGCTTAAGGTTCCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 94

GTTCCAGAGGAGGAGAAAAATCTTGGCCCCTTCGATCGTTTGATTCATGTATATCATTTTACAAAAGACACTCAAAACCAAACGgtaatgatgg ... ttctcaacagCAAGTTCAGAACTTTGGAGAACCTTTTTTTATGGTTATTCGTGAGGATGAGACCCTATCTTCTATCAAAGAACGTATACAGAAAAAGCTTAAGGTTCCAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 128

GTTCCAGAGGAGGAGAAAAATCTTGGCCCCTTCGATCGTTTGATTCATGTATATCATTTTACAAAAGACACTCAAAACCAAACGgtaatgatgg ... ttctcaacagCAAGTTCAGAACTTTGGAGAACCTTTTTTTATGGTTATTCGTGAGGATGAGACCCTATCTTCTATCAAAGAACGTATACAGAAAAAGCTTAAGGTTCCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 185

GTTCCAGAGGAGGAGAAAAATCTTGGCCCCTTCGATCGTTTGATTCATGTATATCATTTTACAAAAGACACTCAAAACCAAACGgtaatgatgg ... ttctcaacagCAAGTTCAGAACTTTGGAGAACCTTTTTTTATGGTTATTCGTGAGGATGAGACCCTATCTTCTATCAAAGAACGTATACAGAAAAAGCTTAAGGTTCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagtcttgtttatatagttaaaactgtactgaatattggccttgttctcaacagCAAGTTCAGAACTTTGGAGAACCTTTTTTTATGGTTATTCGTGAGGATGAGACCCTATCTTCTATCAAAGAACGTATACAGAAAAAGCTTAAGGTTCCAG
                                        ccttgttctc  CT-rich tract
      ttgtttatatagttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctcctagcctctctcatagaaatagatgtgtgttcaatataggttcagtcttgtttatatagttaaaactgtactgaatattggccttgttctcaacagCAAGTTCAGAACTTTGGAGAACCTTTTTTTATGGTTATTCGTGAGGATGAGACCCTATCTTCTATCAAAGAACGTATACAGAAAAAGCTTAAGGTTCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - -catagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtactg