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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catgaattagtcctgcattcctatacaggcaatagttctgttacttcagctatataatttatatggcaaatacacgttacaaagttgcatttcttcacagCCATATCTTCATGAGTCCCGACATCGTCATGCCATGAAACGGGCTCGTGGATCAGGAGGACGGTTCCTCAACACAAAGCAGCTCCAGGAGCAGAACCAGC

Basic information

species Zea mays
transcript GRMZM2G040349_T02
intron # 6
splice site 3'
intron type U2

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|78108019|gb|DV526437.1|DV526437
EST:     AAACACGTGCTAAATTGGAGGCCCAGAACAAGATGGTGAAAAATCGGAAG                         CCATATCTTCATGAGTCCCGACATCGTCATGCCATGAAAC
genomic: AAACACGTGCTAAATTGGAGGCCCAGAACAAGATGGTGAAAAATCGGAAGgtaatacata ... ttcttcacagCCATATCTTCATGAGTCCCGACATCGTCATGCCATGAAAC
EST: gi|149028984|gb|EE286170.2|EE286170
EST:     AAACACGTGCTAAATTGGAGGCCCAGAACAAGATGGTGAAAAATCGGAAG                         CCATATCTTCATGAGTCCCGACATCGTCATGCCATGGAACGGGCTCGTGGA
genomic: AAACACGTGCTAAATTGGAGGCCCAGAACAAGATGGTGAAAAATCGGAAGgtaatacata ... ttcttcacagCCATATCTTCATGAGTCCCGACATCGTCATGCCATGAAACGGGCTCGTGGA
EST: gi|76015258|gb|DT942428.1|DT942428
EST:     AAACACGTGCTAAATTGGAGGCCCAGAACAAGATGGTGAAAAATCGGAAG                         CCATATCTTCATGAGTCCCGACATCGTCATGCCATGAAACGGGCTCGTGGA
genomic: AAACACGTGCTAAATTGGAGGCCCAGAACAAGATGGTGAAAAATCGGAAGgtaatacata ... ttcttcacagCCATATCTTCATGAGTCCCGACATCGTCATGCCATGAAACGGGCTCGTGGA
EST: gi|31910573|gb|CD651492.1|CD651492
EST:     ATTGGAGGCCCAGAACAAGATGGTGAAAAATCGGAAG                         CCATATCTTCATGAGTCCCGACATCGTCATGCCATGAAACGGGCTCGTGGA
genomic: ATTGGAGGCCCAGAACAAGATGGTGAAAAATCGGAAGgtaatacata ... ttcttcacagCCATATCTTCATGAGTCCCGACATCGTCATGCCATGAAACGGGCTCGTGGA
EST: gi|31362883|gb|CD447240.1|CD447240
EST:     AAACACGTGCTAAATTGGAGGCCCAGAACAAGATGGTGAAAAATCGGAAG                         CCATATCTTCATGAGTCCCGACATCGTCATGCCATGAAACGGGCTCGTGGA
genomic: AAACACGTGCTAAATTGGAGGCCCAGAACAAGATGGTGAAAAATCGGAAGgtaatacata ... ttcttcacagCCATATCTTCATGAGTCCCGACATCGTCATGCCATGAAACGGGCTCGTGGA
EST: gi|60396679|gb|DN229547.1|DN229547
EST:     AGGCCCAGAACAAGATGGTGAAAAATCGGAAG                         CCATATCTTCATGAGTCCCGACATCGTCATGCCATGAAACGGGCTCGTGGA
genomic: AGGCCCAGAACAAGATGGTGAAAAATCGGAAGgtaatacata ... ttcttcacagCCATATCTTCATGAGTCCCGACATCGTCATGCCATGAAACGGGCTCGTGGA
EST: gi|74246448|gb|DT654362.1|DT654362
EST:     TTGGAGGCCCAGAACAAGATGGTGAAAAATCGGAAG                         CCATATCTTCATGAGTCCCGACATCGTCATGCCATGAAACGGGCTCGTGGA
genomic: TTGGAGGCCCAGAACAAGATGGTGAAAAATCGGAAGgtaatacata ... ttcttcacagCCATATCTTCATGAGTCCCGACATCGTCATGCCATGAAACGGGCTCGTGGA
EST: gi|74233445|gb|DT641359.1|DT641359
EST:     AAACACGTGCTAAATTGGAGGCCCAGAACAAGATGGTGAAAAATCGGAAG                         CCATATCTTCATGAGTCCCGACATCGTCATGCCATGAAACGGGCTCGTGGA
genomic: AAACACGTGCTAAATTGGAGGCCCAGAACAAGATGGTGAAAAATCGGAAGgtaatacata ... ttcttcacagCCATATCTTCATGAGTCCCGACATCGTCATGCCATGAAACGGGCTCGTGGA
EST: gi|30088406|gb|CB886611.1|CB886611
EST:     AAAAATCGGAAG                         CCATATCTTCATGAGTCCCGACATCGTCATGCCATGAAACGGGCTCGTGGA
genomic: AAAAATCGGAAGgtaatacata ... ttcttcacagCCATATCTTCATGAGTCCCGACATCGTCATGCCATGAAACGGGCTCGTGGA
EST: gi|24767374|gb|CA402517.1|CA402517
EST:     AATTGGAGGCCCAGAACAAGATGGTGAAAAATCGGAAG                         CCATATCTTCATGAGTCCCGACATCGTCATGCCATGAAACGGGCTCGTGGA
genomic: AATTGGAGGCCCAGAACAAGATGGTGAAAAATCGGAAGgtaatacata ... ttcttcacagCCATATCTTCATGAGTCCCGACATCGTCATGCCATGAAACGGGCTCGTGGA
EST: gi|74233446|gb|DT641360.1|DT641360
EST:     AAACACGTGCTAAATTGGAGGCCCAGAACAAGATGGTGAAAAATCGGAAG                         CCATATCTTCATGAGTCCCGACATCGTCATGCCATGAAACGGGCTCGTGGA
genomic: AAACACGTGCTAAATTGGAGGCCCAGAACAAGATGGTGAAAAATCGGAAGgtaatacata ... ttcttcacagCCATATCTTCATGAGTCCCGACATCGTCATGCCATGAAACGGGCTCGTGGA

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 3 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 42

ACCAATATATGTTAATGCAAAACAATACCATGCAATCCTTAGGAGGAGGCAAACACGTGCTAAATTGGAGGCCCAGAACAAGATGGTGAAAAATCGGAAGgtaatacata ... ttcttcacagCCATATCTTCATGAGTCCCGACATCGTCATGCCATGAAACGGGCTCGTGGATCAGGAGGACGGTTCCTCAACACAAAGCAGCTCCAGGAGCAGAACCAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 3

ACCAATATATGTTAATGCAAAACAATACCATGCAATCCTTAGGAGGAGGCAAACACGTGCTAAATTGGAGGCCCAGAACAAGATGGTGAAAAATCGGAAGgtaatacata ... ttcttcacagCCATATCTTCATGAGTCCCGACATCGTCATGCCATGAAACGGGCTCGTGGATCAGGAGGACGGTTCCTCAACACAAAGCAGCTCCAGGAGCAGAACCAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 17

ACCAATATATGTTAATGCAAAACAATACCATGCAATCCTTAGGAGGAGGCAAACACGTGCTAAATTGGAGGCCCAGAACAAGATGGTGAAAAATCGGAAGgtaatacata ... ttcttcacagCCATATCTTCATGAGTCCCGACATCGTCATGCCATGAAACGGGCTCGTGGATCAGGAGGACGGTTCCTCAACACAAAGCAGCTCCAGGAGCAGAACCAGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagctatataatttatatggcaaatacacgttacaaagttgcatttcttcacagCCATATCTTCATGAGTCCCGACATCGTCATGCCATGAAACGGGCTCGTGGATCAGGAGGACGGTTCCTCAACACAAAGCAGCTCCAGGAGCAGAACCAGC
                                          catttcttc  CT-rich tract
     tatataatttatatgg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catgaattagtcctgcattcctatacaggcaatagttctgttacttcagctatataatttatatggcaaatacacgttacaaagttgcatttcttcacagCCATATCTTCATGAGTCCCGACATCGTCATGCCATGAAACGGGCTCGTGGATCAGGAGGACGGTTCCTCAACACAAAGCAGCTCCAGGAGCAGAACCAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
catgaat
- - - - - - -tgcattc
- - - - - - - - - - - - -caggcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaataca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agttgca