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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcagagttgatcaccaaatattcacctcttattacgcagctaactaaatgtgatgatgcttctacacctgctgagggtacctttcttaattgttatgcagGTATACTAGAGCCAATAAGAGCTGACATGAGAGATGCAAAATTAGGTGTTGGGAAGCAAGAGGAAGATGACTTCTTCACATCTGAAGAGAATGTGCAACG

Basic information

species Zea mays
transcript GRMZM2G075551_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G075551_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g02500.2 (Oryza sativa), 3'ss of exon 2
-gcagagttgatcaccaaatattcacctcttattacgcagctaacta--aatgtgatgatgcttctacacctgctgagggtacctttcttaattgttatgcagGTATACTAGAGCCAATAAGAGCTGACATGAGAGATGCAAAATTAGGTGTTGGGAAGCAAGAGGAAGATGACTTCTTCACATCTGAAGAGAATGTGCAACG
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actatcattgattaaaaaaaaaacagtcatcgctttaatattttctgctaaaattctggcaccttcacgacaat---gcccttttctctttaatgttatatagGTATAACAGAGCCAATAAAAGCTGGTATCAGAGATGCAAAATTGGGTGTGGGGAAGCAAGAGCAAGATGACTTCTTCACATCAGAAGATAATGTGCAAAG
















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|211069021|gb|FL413437.1|FL413437
EST:     GCAGAAGATGGGCTGGAAGACCGGCAAGGGGCTCGGCAAGAACGAGCAAG                         GTATACTAGAGCCAATAAGAGCTGACATGAGAGATGCAAAATTAGGTGTTG
genomic: GCAGAAGATGGGCTGGAAGACCGGCAAGGGGCTCGGCAAGAACGAGCAAGgtatcttcct ... tgttatgcagGTATACTAGAGCCAATAAGAGCTGACATGAGAGATGCAAAATTAGGTGTTG
EST: gi|71433465|gb|DR814515.1|DR814515
EST:     GCAGAAGATGGGCTGGAAGACCGGCAAGGGGCTCGGCAAGAACGAGCAAG                         GTATACTAGAGCCAATAAGAGCTGACATGAGAGATGCAAAATTAGGTGTTG
genomic: GCAGAAGATGGGCTGGAAGACCGGCAAGGGGCTCGGCAAGAACGAGCAAGgtatcttcct ... tgttatgcagGTATACTAGAGCCAATAAGAGCTGACATGAGAGATGCAAAATTAGGTGTTG
EST: gi|211431309|gb|FL387541.1|FL387541
EST:     GCAGAAGATGGGCTGGAAGACCGGCAAGGGGCTCGGCAAGAACGAGCAAG                         GTATACTAGAGC
genomic: GCAGAAGATGGGCTGGAAGACCGGCAAGGGGCTCGGCAAGAACGAGCAAGgtatcttcct ... tgttatgcagGTATACTAGAGC
EST: gi|74234698|gb|DT642612.1|DT642612
EST:     GCAGAAGATGGGCTGGAAGACCGGCAAGGGGCTCGGCAAGAACGAGCAAG                         GTATACTAGAGCCAATAAGAGCTGACATGAGAGATGCAAAATTAGGTGTTG
genomic: GCAGAAGATGGGCTGGAAGACCGGCAAGGGGCTCGGCAAGAACGAGCAAGgtatcttcct ... tgttatgcagGTATACTAGAGCCAATAAGAGCTGACATGAGAGATGCAAAATTAGGTGTTG
EST: gi|211426224|gb|FL393456.1|FL393456
EST:     CAGAAGATGGGCTGGAAGAACCGGCAAGGGGCTCGGCAAGAACGAGCAAG                         GTATACTAGAGCC
genomic: CAGAAGATGGGCTGGAAGA-CCGGCAAGGGGCTCGGCAAGAACGAGCAAGgtatcttcct ... tgttatgcagGTATACTAGAGCC
EST: gi|74244524|gb|DT652438.1|DT652438
EST:     GCAGAAGATGGGCTGGAAGACCGGCAAGGGGCTCGGCAAGAACGAGCAAG                         GTATACTAGAGCCAATAAGAGCTGACATGAGAGATGCAAAATTAGGTGTTG
genomic: GCAGAAGATGGGCTGGAAGACCGGCAAGGGGCTCGGCAAGAACGAGCAAGgtatcttcct ... tgttatgcagGTATACTAGAGCCAATAAGAGCTGACATGAGAGATGCAAAATTAGGTGTTG
EST: gi|76932418|gb|DV173042.1|DV173042
EST:     GCAGAAGATGGGCTGGAAGACCGGCAAGGGGCTCGGCAAGAACGAGCAAG                         GTATACTAGAGCCAATAAGAGCTGACATGAGAGATGCAAAATTAGGTGTTG
genomic: GCAGAAGATGGGCTGGAAGACCGGCAAGGGGCTCGGCAAGAACGAGCAAGgtatcttcct ... tgttatgcagGTATACTAGAGCCAATAAGAGCTGACATGAGAGATGCAAAATTAGGTGTTG
EST: gi|211013868|gb|FL375768.1|FL375768
EST:     GCAGAAGATGGGCTGGAAGACCGGCAAGGGGCTCGGCAAGAACGAGCAAG                         GTATACTAGAGCCAATAAGAGCTGAC
genomic: GCAGAAGATGGGCTGGAAGACCGGCAAGGGGCTCGGCAAGAACGAGCAAGgtatcttcct ... tgttatgcagGTATACTAGAGCCAATAAGAGCTGAC
EST: gi|91879045|gb|EB409002.1|EB409002
EST:     GCAGAAGATGGGCTGGAAGACCGGCAAGGGGCTCGGCAAGAACGAGCAAG                         GTATACTAGAGCCAATAAGAGCTGACATGAGAGATGCAAAATTAGGTGTTG
genomic: GCAGAAGATGGGCTGGAAGACCGGCAAGGGGCTCGGCAAGAACGAGCAAGgtatcttcct ... tgttatgcagGTATACTAGAGCCAATAAGAGCTGACATGAGAGATGCAAAATTAGGTGTTG
EST: gi|89761563|gb|DY689524.1|DY689524
EST:     GCAGAAGATGGGCTGGAAGACCGGCAAGGGGCTCGGCAAGAACGAGCAAG                         GTATACTAGAGCCAATAAGAGCTGACATGAGAGATGCAAAATTAGGTGTTG
genomic: GCAGAAGATGGGCTGGAAGACCGGCAAGGGGCTCGGCAAGAACGAGCAAGgtatcttcct ... tgttatgcagGTATACTAGAGCCAATAAGAGCTGACATGAGAGATGCAAAATTAGGTGTTG
EST: gi|211212015|gb|FL385212.1|FL385212
EST:     GCAGAAGATGGGCTGGAAGACCGGCAAGGGGCTCGGCAAGAACGAGCAAG                         GTATACTAGAGC
genomic: GCAGAAGATGGGCTGGAAGACCGGCAAGGGGCTCGGCAAGAACGAGCAAGgtatcttcct ... tgttatgcagGTATACTAGAGC
EST: gi|71422270|gb|DR805672.1|DR805672
EST:     GCAGAAGATGGGCTGGAAGACCGGCAAGGGGCTCGGCAAGAACGAGCAAG                         GTATACTAGAGCCAATAAGAGCTGACATGAGAGATGCAAAATTAGGTGTTG
genomic: GCAGAAGATGGGCTGGAAGACCGGCAAGGGGCTCGGCAAGAACGAGCAAGgtatcttcct ... tgttatgcagGTATACTAGAGCCAATAAGAGCTGACATGAGAGATGCAAAATTAGGTGTTG
EST: gi|71324316|gb|DR798859.1|DR798859
EST:     GCAGAAGATGGGCTGGAAGACCGGCAAGGGGCTCGGCAAGAACGAGCAAG                         GTATACTAGAGCCAATAAGAGCTGACATGAGAGATGCAAAATTAGGTGTTG
genomic: GCAGAAGATGGGCTGGAAGACCGGCAAGGGGCTCGGCAAGAACGAGCAAGgtatcttcct ... tgttatgcagGTATACTAGAGCCAATAAGAGCTGACATGAGAGATGCAAAATTAGGTGTTG
EST: gi|76283408|gb|DV022976.1|DV022976
EST:     GCAGAAGATGGGCTGGAAGACCGGCAAGGGGCTCGGCAAGAACGAGCAAG                         GTATACTAGAGCCAATAAGAGCTGACATGAGAGATGCAAAATTAGGTGTTG
genomic: GCAGAAGATGGGCTGGAAGACCGGCAAGGGGCTCGGCAAGAACGAGCAAGgtatcttcct ... tgttatgcagGTATACTAGAGCCAATAAGAGCTGACATGAGAGATGCAAAATTAGGTGTTG
EST: gi|93281364|gb|EB673628.1|EB673628
EST:     GCAGAAGATGGGCTGGAAGACCGGCAAGGGGCTCGGCAAGAACGAGCAAG                         GTATACTAGAGCCAATAAGAGCTGACATGAGAGATGCAAAATTAGGTGTTG
genomic: GCAGAAGATGGGCTGGAAGACCGGCAAGGGGCTCGGCAAGAACGAGCAAGgtatcttcct ... tgttatgcagGTATACTAGAGCCAATAAGAGCTGACATGAGAGATGCAAAATTAGGTGTTG
EST: gi|76290174|gb|DV029742.1|DV029742
EST:     GCAGAAGATGGGCTGGAAGACCGGCAAGGGGCTCGGCAAGAACGAGCAAG                         GTATACTAGAGCCAATAAGAGCTGACATGAGAGATGCAAAATTAGGTGTTG
genomic: GCAGAAGATGGGCTGGAAGACCGGCAAGGGGCTCGGCAAGAACGAGCAAGgtatcttcct ... tgttatgcagGTATACTAGAGCCAATAAGAGCTGACATGAGAGATGCAAAATTAGGTGTTG
EST: gi|211030009|gb|FL411228.1|FL411228
EST:     GCAGAAGATGGGCTGGAAGACCGGCAAGGGGCTCGGCAAGAACGAGCAAG                         GTATACTAGAGCCAATAAGAGCTGACATGAGAGATGCAAAATTAGGTGTTG
genomic: GCAGAAGATGGGCTGGAAGACCGGCAAGGGGCTCGGCAAGAACGAGCAAGgtatcttcct ... tgttatgcagGTATACTAGAGCCAATAAGAGCTGACATGAGAGATGCAAAATTAGGTGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatgtgatgatgcttctacacctgctgagggtacctttcttaattgttatgcagGTATACTAGAGCCAATAAGAGCTGACATGAGAGATGCAAAATTAGGTGTTGGGAAGCAAGAGGAAGATGACTTCTTCACATCTGAAGAGAATGTGCAACG
                                    tttcttaattgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcagagttgatcaccaaatattcacctcttattacgcagctaactaaatgtgatgatgcttctacacctgctgagggtacctttcttaattgttatgcagGTATACTAGAGCCAATAAGAGCTGACATGAGAGATGCAAAATTAGGTGTTGGGAAGCAAGAGGAAGATGACTTCTTCACATCTGAAGAGAATGTGCAACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA