Skip to another splice site:
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGGGCACTGATGATGAGTATGCTAACTCAAACTACTACTATTCGTTGTCTGCCAATCGACTAGGAGACGAGGAAAAGGAAGAAATAATAGGTTTGGCTc

Basic information

species Zea mays
transcript GRMZM2G065496_T04
intron # 4
splice site 5'
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|78108961|gb|DV527378.1|DV527378
EST:     CTGCCAATCGACTAGGAGACGAGGAAAAGGAAGAAATAATAGGTTTGGCT                         CCCATCCGACCGAACAATCCTGTATTTGTGACCCTTCTGAGGAAAAACCAT
genomic: CTGCCAATCGACTAGGAGACGAGGAAAAGGAAGAAATAATAGGTTTGGCTc ... cCCCATCCGACCGAACAATCCTGTATTTGTGACCCTTCTGAGGAAAAACCATGTTCAGCGCAGAAACAAC
EST: gi|91054726|gb|EB165144.1|EB165144
EST:     ATCGACTAGGAGACGAGGAAAAGGAAGAAATAATAGGTTTGGGT                         CCCATCCGACCGAACAATCCTGTATTTGTGACCCTTCTGAGGAAAAACCAT
genomic: ATCGACTAGGAGACGAGGAAAAGGAAGAAATAATAGGTTTGGCTc ... cCCCATCCGACCGAACAATCCTGTATTTGTGACCCTTCTGAGGAAAAACCATGTTCAGCGCAGAAACAAC
EST: gi|101399912|gb|EB821803.1|EB821803
EST:     CTGCCAATCGACTAGGAGACGAGGAAAAGGAAGAAATAATAAGTTTGGCT                         CCCATCCGACCGAACAATCCTGTATTTGTGACCCTTCTGAGGAAAA-CCAT
genomic: CTGCCAATCGACTAGGAGACGAGGAAAAGGAAGAAATAATAGGTTTGGCTc ... cCCCATCCGACCGAACAATCCTGTATTTGTGACCCTTCTGAGGAAAAACCATGTTCAGCGCAGAAACAAC
EST: gi|71444232|gb|DR825282.1|DR825282
EST:     CTGCCAATCGACTAGGAGACGAGGAAAAGGAAGAAATAATAGGTTTGGCT                         CCCATCCGACCGAACAATCCTGTATTTGTGACCCTT
genomic: CTGCCAATCGACTAGGAGACGAGGAAAAGGAAGAAATAATAGGTTTGGCTc ... cCCCATCCGACCGAACAATCCTGTATTTGTGACCCTT
EST: gi|89760970|gb|DY689169.1|DY689169
EST:     CTGCCAATCGACTAGGAGACGAGGAAAAGGAAGAAATAATAGGTTTGGCT                         CCCATCCGACCGAACAATCCTGTATTTGTGACCCTTCTGAGGAAAAAC-AT
genomic: CTGCCAATCGACTAGGAGACGAGGAAAAGGAAGAAATAATAGGTTTGGCTc ... cCCCATCCGACCGAACAATCCTGTATTTGTGACCCTTCTGAGGAAAAACCATGTTCAGCGCAGAAACAAC
EST: gi|71308093|gb|DR790262.1|DR790262
EST:     CTGCCAATCGACTAGGAGACGAGGAAAAGGAAGAAATAATAGGTTTGGCT                         CCCATCCGACCGAACAATCCTGTATTTGTGACCCTTCTGAGGAAAAACCAT
genomic: CTGCCAATCGACTAGGAGACGAGGAAAAGGAAGAAATAATAGGTTTGGCTc ... cCCCATCCGACCGAACAATCCTGTATTTGTGACCCTTCTGAGGAAAAACCATGTTCAGCGCAGAAACAAC
EST: gi|91054727|gb|EB165145.1|EB165145
EST:     CTGCCAATCGACTAGGAGACGAGGAAAAGGAAGAA-TAATAGGTTTGGCT                         CCCATCCGACCGAACAATCCTGTATTTGTGACCCTTCTGAGGAAAAAC-AT
genomic: CTGCCAATCGACTAGGAGACGAGGAAAAGGAAGAAATAATAGGTTTGGCTc ... cCCCATCCGACCGAACAATCCTGTATTTGTGACCCTTCTGAGGAAAAACCATGTTCAGCGCAGAAACAAC
EST: gi|76286535|gb|DV026103.1|DV026103
EST:     CTGCCAATCGACTAGGAGACGAGGAAAAGGAAGAAATAATAGGTTTGGCT                         CCCATCCGACCGAACAATCCTGTATTTGTGACCCTTCTGAGGAAAAACCAT
genomic: CTGCCAATCGACTAGGAGACGAGGAAAAGGAAGAAATAATAGGTTTGGCTc ... cCCCATCCGACCGAACAATCCTGTATTTGTGACCCTTCTGAGGAAAAACCATGTTCAGCGCAGAAACAAC
EST: gi|74232418|gb|DT640332.1|DT640332
EST:     AGGAAGAAATAATAGGTTTGGCT                         CCCATCCGACCGAACAATCCTGTATTTGTGACCCTTCTGAGGAAAAACCAT
genomic: AGGAAGAAATAATAGGTTTGGCTc ... cCCCATCCGACCGAACAATCCTGTATTTGTGACCCTTCTGAGGAAAAACCATGTTCAGCGCAGAAACAAC
EST: gi|71428131|gb|DR809181.1|DR809181
EST:     AGGAAAAGGAAGAAATAATAGGTTTGGCT                         CCCATCCGACCGAACAATCCTGTATTTGTGACCCTTCTGAGGAAAAACCAT
genomic: AGGAAAAGGAAGAAATAATAGGTTTGGCTc ... cCCCATCCGACCGAACAATCCTGTATTTGTGACCCTTCTGAGGAAAAACCATGTTCAGCGCAGAAACAAC
EST: gi|74232419|gb|DT640333.1|DT640333
EST:     CTGCCAATCGACTAGGAGACGAGGAAAAGGAAGAAATAATAGGTTTGGCT                         CCCATCCGACCGAACAATCCTGTATTTGT
genomic: CTGCCAATCGACTAGGAGACGAGGAAAAGGAAGAAATAATAGGTTTGGCTc ... cCCCATCCGACCGAACAATCCTGTATTTGT
EST: gi|89760968|gb|DY689168.1|DY689168
EST:     TAGGAGACGAGGAAAAGGAAGAAATAATAGGTTTGGCT                         CCCATCCGACCGAACAATCCTGTATTTGTGACCCTTCTGAGGAAAAACCAT
genomic: TAGGAGACGAGGAAAAGGAAGAAATAATAGGTTTGGCTc ... cCCCATCCGACCGAACAATCCTGTATTTGTGACCCTTCTGAGGAAAAACCATGTTCAGCGCAGAAACAAC
EST: gi|101399910|gb|EB821802.1|EB821802
EST:     CTGCCAATCGACTAGGAGACGAGGAAAAGGAAGAAATAATAGGTTTGGCT                         CCCATCCGACCGAACAATCCTGTATTTGTGACCCTTCTGAGGAAAAACCAT
genomic: CTGCCAATCGACTAGGAGACGAGGAAAAGGAAGAAATAATAGGTTTGGCTc ... cCCCATCCGACCGAACAATCCTGTATTTGTGACCCTTCTGAGGAAAAACCATGTTCAGCGCAGAAACAAC

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), 48 (downstream exon)
Score: 149

AGAGGGCACTGATGATGAGTATGCTAACTCAAACTACTACTATTCGTTGTCTGCCAATCGACTAGGAGACGAGGAAAAGGAAGAAATAATAGGTTTGGCTc ... cCCCATCCGACCGAACAATCCTGTATTTGTGACCCTTCTGAGGAAAAACCATGTTCAGCGCAGAAACAACTGTCTG


Block sizes: 27 (upstream exon), 23 (downstream exon)
Score: 1

AGAGGGCACTGATGATGAGTATGCTAACTCAAACTACTACTATTCGTTGTCTGCCAATCGACTAGGAGACGAGGAAAAGGAAGAAATAATAGGTTTGGCTc ... cCCCATCCGACCGAACAATCCTGTATTTGTGACCCTTCTGAGGAAAAACCATGTTCAGCGCAGAAACAACTGTCTG


Block sizes: 27 (upstream exon), 38 (downstream exon)
Score: 4

AGAGGGCACTGATGATGAGTATGCTAACTCAAACTACTACTATTCGTTGTCTGCCAATCGACTAGGAGACGAGGAAAAGGAAGAAATAATAGGTTTGGCTc ... cCCCATCCGACCGAACAATCCTGTATTTGTGACCCTTCTGAGGAAAAACCATGTTCAGCGCAGAAACAACTGTCTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 11

AGAGGGCACTGATGATGAGTATGCTAACTCAAACTACTACTATTCGTTGTCTGCCAATCGACTAGGAGACGAGGAAAAGGAAGAAATAATAGGTTTGGCTc ... cCCCATCCGACCGAACAATCCTGTATTTGTGACCCTTCTGAGGAAAAACCATGTTCAGCGCAGAAACAACTGTCTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGGGCACTGATGATGAGTATGCTAACTCAAACTACTACTATTCGTTGTCTGCCAATCGACTAGGAGACGAGGAAAAGGAAGAAATAATAGGTTTGGCTc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA