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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTCACTGCAATCGCTGGGGAGACCGCCTCTGAGCTCCCGGATGCTGTCAGGAAGGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAGgtaatatattagtccctatgtatccttctgcattgtgccggttcatatttagatttcttgaacacctctctgagcttgcactattggccattattgtgcag

Basic information

species Zea mays
transcript GRMZM2G042552_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G042552_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g01810.1 (Oryza sativa), 5'ss of exon 5
CCTCACTGCAATCGCTGGGGAGACCGCCTCTGAGCTCCCGGATGCTGTCAGGAAGGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAGgtaatatatta-gtccctatgtatccttctgcattgtgccggttcatatttagatttcttgaacacctctctgagctt--gcactattggccattattgtgcag-------------------------------
|||| ||||||| ||||||||||| ||||||||||| || || |||||||||||||||||||||||||||||||| ||||||||||||| |||||  |||||||| |   | |   | |  ||||||||  |||| |||   |  |      |  |||||  | | ||||  | | ||    | || ||  |    || || |                                
CCTCTCTGCAATTGCTGGGGAGACTGCCTCTGAGCTTCCAGACGCTGTCAGGAAGGAAAAGGAGAAGATGAAGCAACCTTCAACAAGTGAACCTGCAGAGgtaatgtccaacgattcaacatatccttc-acattttgcaattcta-----gggattcttccatatctctgcgtgtttcaaaaataatgtactgagttctgaaataccttacccggaacttgcgccaatgtgcag
















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|78077138|gb|DV505572.1|DV505572
EST:     AAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAG                         AGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
genomic: AAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAGgtaatatatt ... tattgtgcagAGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
EST: gi|87154823|gb|DY399612.1|DY399612
EST:     GGAAGGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAG                         AGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
genomic: GGAAGGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAGgtaatatatt ... tattgtgcagAGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
EST: gi|44901356|gb|CK827901.1|CK827901
EST:     GGAAGGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGCGGAG                         AGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
genomic: GGAAGGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAGgtaatatatt ... tattgtgcagAGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
EST: gi|76293381|gb|DV032949.1|DV032949
EST:     GGAAGGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAG                         AGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
genomic: GGAAGGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAGgtaatatatt ... tattgtgcagAGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
EST: gi|5740470|gb|AI948160.1|AI948160
EST:     GGAAGGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAG                         AGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
genomic: GGAAGGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAGgtaatatatt ... tattgtgcagAGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
EST: gi|14255660|gb|BG878568.1|BG878568
EST:     GGAAGGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAG                         AGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
genomic: GGAAGGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAGgtaatatatt ... tattgtgcagAGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
EST: gi|6095474|gb|AW120141.1|AW120141
EST:     GGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAG                         AGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
genomic: GGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAGgtaatatatt ... tattgtgcagAGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
EST: gi|113702321|gb|EE679825.1|EE679825
EST:     GGAAGGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGCGGAG                         AGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
genomic: GGAAGGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAGgtaatatatt ... tattgtgcagAGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
EST: gi|113675790|gb|DW831183.1|DW831183
EST:     AAAGGTAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAG                         AGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
genomic: AAAGG-AGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAGgtaatatatt ... tattgtgcagAGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
EST: gi|4646886|gb|AI621961.1|AI621961
EST:     GGAAGGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAG                         AGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
genomic: GGAAGGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAGgtaatatatt ... tattgtgcagAGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
EST: gi|21759932|gb|BQ635473.1|BQ635473
EST:     GGAAGGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTTTACCTGCGGAG                         AGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
genomic: GGAAGGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAGgtaatatatt ... tattgtgcagAGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
EST: gi|60399737|gb|DN232547.1|DN232547
EST:     GGAAGGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAG                         AGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
genomic: GGAAGGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAGgtaatatatt ... tattgtgcagAGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
EST: gi|5929091|gb|AW056383.1|AW056383
EST:     GGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAG                         AGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
genomic: GGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAGgtaatatatt ... tattgtgcagAGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
EST: gi|14311555|gb|BG901310.1|BG901310
EST:     GGAAGGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAG                         AGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
genomic: GGAAGGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAGgtaatatatt ... tattgtgcagAGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG

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), 49 (downstream exon)
Score: 55

CCTCACTGCAATCGCTGGGGAGACCGCCTCTGAGCTCCCGGATGCTGTCAGGAAGGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAGgtaatatatt ... tattgtgcagAGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGGGAAAGGCTTGCCAGAGTGAGGTCATAGAAGATAGCTGAACAAGGTCAGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 101

CCTCACTGCAATCGCTGGGGAGACCGCCTCTGAGCTCCCGGATGCTGTCAGGAAGGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAGgtaatatatt ... tattgtgcagAGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGGGAAAGGCTTGCCAGAGTGAGGTCATAGAAGATAGCTGAACAAGGTCAGA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 116

CCTCACTGCAATCGCTGGGGAGACCGCCTCTGAGCTCCCGGATGCTGTCAGGAAGGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAGgtaatatatt ... tattgtgcagAGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGGGAAAGGCTTGCCAGAGTGAGGTCATAGAAGATAGCTGAACAAGGTCAGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 46

CCTCACTGCAATCGCTGGGGAGACCGCCTCTGAGCTCCCGGATGCTGTCAGGAAGGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAGgtaatatatt ... tattgtgcagAGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGGGAAAGGCTTGCCAGAGTGAGGTCATAGAAGATAGCTGAACAAGGTCAGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTCACTGCAATCGCTGGGGAGACCGCCTCTGAGCTCCCGGATGCTGTCAGGAAGGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAGgtaatatattagtccctatgtatccttctgcattgtgccggttcatatttagatttcttgaacacctctctgagcttgcactattggccattattgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG