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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagatcacatactcaacaaaaccaagtgcagcgaatcttaattcttttcgtgaaagaaggtccattcgatcctgagaatcccttttctctgtttgtccagGGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAATGTTCCTCAGCCTCATGCCATACTGTACTATCAGCAGAGGGCGACTAAAGGAGGTCTT

Basic information

species Zea mays
transcript GRMZM2G087192_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G087192_T02 (Zea mays), 3'ss of exon 1
lower sequence: 13113.m00235 (Oryza sativa), 3'ss of exon 2
-tagatc--acatactcaacaaaaccaagtgcagcgaatcttaattcttttcgtgaaagaaggtccattcgatcctgagaatcccttttctctgtttgtccagGGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAATGTTCCTCAGCCTCATGCCATACTGTACTATCAGCAGAGGGCGACTAAAGGAGGTCTT
  |  ||   | ||       |   | ||  |  | || |    |  |||   |     | | ||||||     |  |  |     | | | ||| | || |||||||| |||||||||||||| || ||||| ||||| || ||||||||||||||||||||||| |||||||||||||||||  | || |||||||| |||
acaattcctgcttatgggcttatggctagaactacaaaaccatctcttttatctatgcaatgatccatta---tcaaaatactgaatgtttttgtctttctagGGTAGTTCTCGCACCACTGACAAGGCAGCGATCCTATGGTAATGTTCCTCAGCCTCATGCCATTCTGTACTATCAGCAGAGAACAACCAAAGGAGGCCTT
















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|91878868|gb|EB408825.1|EB408825
EST:     GCCCCCCTCCTCACCCCCTACAAGATGGGAAAATTCGATGTTTCCCACAG                         GGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAATGTTCCTCA
genomic: GCCCCCCTCCTCACCCCCTACAAGATGGGAAAATTCGATGTTTCCCACAGgtacgcccct ... gtttgtccagGGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAATGTTCCTCA
EST: gi|211459461|gb|FL315095.1|FL315095
EST:     GCCCCCCTCCTCACCCCCTACAAGATGGGAAAATTCGATGTTACCCACAG                         GGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAACGTTCCCCA
genomic: GCCCCCCTCCTCACCCCCTACAAGATGGGAAAATTCGATGTTTCCCACAGgtacgcccct ... gtttgtccagGGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAATGTTCCTCA
EST: gi|211046904|gb|FL342230.1|FL342230
EST:     GCCCCCCTCCTCACCCCCTACAAGATGGGAAAATTCGATGTTACCCACAG                         GGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAACGTTCCCCA
genomic: GCCCCCCTCCTCACCCCCTACAAGATGGGAAAATTCGATGTTTCCCACAGgtacgcccct ... gtttgtccagGGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAATGTTCCTCA
EST: gi|211434603|gb|FL306594.1|FL306594
EST:     GCCCCCCTCCTCACCCCCTACAAGATGGGAAAATTCGATGTTACCCACAG                         GGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAACGTTCCCCA
genomic: GCCCCCCTCCTCACCCCCTACAAGATGGGAAAATTCGATGTTTCCCACAGgtacgcccct ... gtttgtccagGGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAATGTTCCTCA
EST: gi|211538244|gb|FL353979.1|FL353979
EST:     GCCCCCCTCCTCACCCCCTACAAGATGGGAAAATTCGATGTTACCCACAG                         GGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAACGTTCCCCA
genomic: GCCCCCCTCCTCACCCCCTACAAGATGGGAAAATTCGATGTTTCCCACAGgtacgcccct ... gtttgtccagGGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAATGTTCCTCA
EST: gi|211438615|gb|FL361924.1|FL361924
EST:     GCCCCCCTCCTCACCCCCTACAAGATGGGAAAATTCGATGTTACCCACAG                         GGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAACGTTCCCCA
genomic: GCCCCCCTCCTCACCCCCTACAAGATGGGAAAATTCGATGTTTCCCACAGgtacgcccct ... gtttgtccagGGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAATGTTCCTCA
EST: gi|78105288|gb|DV523706.1|DV523706
EST:     GCCCCCCTCCTCACCCCCTACAAGATGGGAAAATTCGATGTTTCCCACAG                         GGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAATGTTCCTCA
genomic: GCCCCCCTCCTCACCCCCTACAAGATGGGAAAATTCGATGTTTCCCACAGgtacgcccct ... gtttgtccagGGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAATGTTCCTCA
EST: gi|71766717|gb|DR964654.1|DR964654
EST:     GCCCCCCTCCTCACCCCCTACAAGATGGGAAAATTCGATGTTTCCCACAG                         GGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAATGTTCCTCA
genomic: GCCCCCCTCCTCACCCCCTACAAGATGGGAAAATTCGATGTTTCCCACAGgtacgcccct ... gtttgtccagGGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAATGTTCCTCA
EST: gi|211372990|gb|FL342986.1|FL342986
EST:     GCCCCCCTCCTCACCCCCTACAAGATGGGAAAATTCGATGTTACCCACAG                         GGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAACGTTCCCCA
genomic: GCCCCCCTCCTCACCCCCTACAAGATGGGAAAATTCGATGTTTCCCACAGgtacgcccct ... gtttgtccagGGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAATGTTCCTCA
EST: gi|78110280|gb|DV528695.1|DV528695
EST:     GCCCCCCTCCTCACCCCCTACAAGATGGGAAAATTCGATGTTTCCCACAG                         GGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAATGTTCCTCA
genomic: GCCCCCCTCCTCACCCCCTACAAGATGGGAAAATTCGATGTTTCCCACAGgtacgcccct ... gtttgtccagGGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAATGTTCCTCA
EST: gi|71769744|gb|DR967681.1|DR967681
EST:     GCCCCCCTCCTCACCCCCTACAAGATGGGAAAATTCGATGTTTCCCACAG                         GGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAATGTTCCTCA
genomic: GCCCCCCTCCTCACCCCCTACAAGATGGGAAAATTCGATGTTTCCCACAGgtacgcccct ... gtttgtccagGGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAATGTTCCTCA
EST: gi|211004021|gb|FL317949.1|FL317949
EST:     GCCCCCCTCCTCACCCCCTACAAGATGGGAAAATTCGATGTTACCCACAG                         GGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAACGTTCCCCA
genomic: GCCCCCCTCCTCACCCCCTACAAGATGGGAAAATTCGATGTTTCCCACAGgtacgcccct ... gtttgtccagGGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAATGTTCCTCA
EST: gi|211049230|gb|FL320166.1|FL320166
EST:     GCCCCCCTCCTCACCCCCTACAAGATGGGAAAATTCGATGTTACCCACAG                         GGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAACGTTCCCCA
genomic: GCCCCCCTCCTCACCCCCTACAAGATGGGAAAATTCGATGTTTCCCACAGgtacgcccct ... gtttgtccagGGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAATGTTCCTCA
EST: gi|71448418|gb|DR829468.1|DR829468
EST:     GCCCCCCTCCTCACCCCCTACAAGATGGGAAAATTCGATGTTACCCACAG                         GGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAACGTTCCCCA
genomic: GCCCCCCTCCTCACCCCCTACAAGATGGGAAAATTCGATGTTTCCCACAGgtacgcccct ... gtttgtccagGGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAATGTTCCTCA
EST: gi|31363471|gb|CD447828.1|CD447828
EST:     GCCCCCCTCCTCACCCCCTACAAGATGGGAAAATTCGATGTTTCCCACAG                         GGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAATGTTCCTCA
genomic: GCCCCCCTCCTCACCCCCTACAAGATGGGAAAATTCGATGTTTCCCACAGgtacgcccct ... gtttgtccagGGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAATGTTCCTCA
EST: gi|211516970|gb|FL321888.1|FL321888
EST:     GCCCCCCTCCTCACCCCCTACAAGATGGGAAAATTCGATGTTACCCACA-                         GGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAACGTTCCCCA
genomic: GCCCCCCTCCTCACCCCCTACAAGATGGGAAAATTCGATGTTTCCCACAGgtacgcccct ... gtttgtccagGGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAATGTTCCTCA
EST: gi|211086396|gb|FL335516.1|FL335516
EST:     GCCCCCCTCCTCACCCCCTACAAGATGGGAAAATTCGATGTTACCCACAG                         GGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAACGTTCCCCA
genomic: GCCCCCCTCCTCACCCCCTACAAGATGGGAAAATTCGATGTTTCCCACAGgtacgcccct ... gtttgtccagGGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAATGTTCCTCA
EST: gi|76017395|gb|DT944565.1|DT944565
EST:     GCCCCCCTCCTCACCCCCTACAAGATGGGAAAATTCGATGTTTCCCACAG                         GGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAATGTTCCTCA
genomic: GCCCCCCTCCTCACCCCCTACAAGATGGGAAAATTCGATGTTTCCCACAGgtacgcccct ... gtttgtccagGGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAATGTTCCTCA
EST: gi|71431905|gb|DR812955.1|DR812955
EST:     GCCCCCCTCCTCACCCCCTACAAGATGGGAAAATTCGATGTTTCCCACAG                         GGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAATGTTCCTCA
genomic: GCCCCCCTCCTCACCCCCTACAAGATGGGAAAATTCGATGTTTCCCACAGgtacgcccct ... gtttgtccagGGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAATGTTCCTCA
EST: gi|211215728|gb|FL322479.1|FL322479
EST:     GCCCCCCTCCTCACCCCCTACAAGATGGGAAAATTCGATGTTACCCACAG                         GGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAACGTTCCCCA
genomic: GCCCCCCTCCTCACCCCCTACAAGATGGGAAAATTCGATGTTTCCCACAGgtacgcccct ... gtttgtccagGGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAATGTTCCTCA
EST: gi|211399636|gb|FL347340.1|FL347340
EST:     GCCCCCCTCCTCACCCCCTACAAGATGGGAAAATTCGATGTTACCCACAG                         GGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAACGTTCCCCA
genomic: GCCCCCCTCCTCACCCCCTACAAGATGGGAAAATTCGATGTTTCCCACAGgtacgcccct ... gtttgtccagGGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAATGTTCCTCA
EST: gi|76281886|gb|DV021454.1|DV021454
EST:     GCCCCCCTCCTCACCCCCTACAAGATGGGAAAATTCGATGTTTCCCACAG                         GGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAATGTTCCTCA
genomic: GCCCCCCTCCTCACCCCCTACAAGATGGGAAAATTCGATGTTTCCCACAGgtacgcccct ... gtttgtccagGGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAATGTTCCTCA

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: 29

AGAGGACAGAGGAGGAGCAGAGGACGATGGGCAGCGGCGGCGCTAACACTGCCCCCCTCCTCACCCCCTACAAGATGGGAAAATTCGATGTTTCCCACAGgtacgcccct ... gtttgtccagGGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAATGTTCCTCAGCCTCATGCCATACTGTACTATCAGCAGAGGGCGACTAAAGGAGGTCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 3510

AGAGGACAGAGGAGGAGCAGAGGACGATGGGCAGCGGCGGCGCTAACACTGCCCCCCTCCTCACCCCCTACAAGATGGGAAAATTCGATGTTTCCCACAGgtacgcccct ... gtttgtccagGGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAATGTTCCTCAGCCTCATGCCATACTGTACTATCAGCAGAGGGCGACTAAAGGAGGTCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 2943

AGAGGACAGAGGAGGAGCAGAGGACGATGGGCAGCGGCGGCGCTAACACTGCCCCCCTCCTCACCCCCTACAAGATGGGAAAATTCGATGTTTCCCACAGgtacgcccct ... gtttgtccagGGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAATGTTCCTCAGCCTCATGCCATACTGTACTATCAGCAGAGGGCGACTAAAGGAGGTCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 633

AGAGGACAGAGGAGGAGCAGAGGACGATGGGCAGCGGCGGCGCTAACACTGCCCCCCTCCTCACCCCCTACAAGATGGGAAAATTCGATGTTTCCCACAGgtacgcccct ... gtttgtccagGGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAATGTTCCTCAGCCTCATGCCATACTGTACTATCAGCAGAGGGCGACTAAAGGAGGTCTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcgtgaaagaaggtccattcgatcctgagaatcccttttctctgtttgtccagGGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAATGTTCCTCAGCCTCATGCCATACTGTACTATCAGCAGAGGGCGACTAAAGGAGGTCTT
                                 tcccttttctctgttt  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagatcacatactcaacaaaaccaagtgcagcgaatcttaattcttttcgtgaaagaaggtccattcgatcctgagaatcccttttctctgtttgtccagGGTAGTCCTCGCACCACTGACGAGACAGCGGTCCTACGGCAATGTTCCTCAGCCTCATGCCATACTGTACTATCAGCAGAGGGCGACTAAAGGAGGTCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - -cacatac
- - - - - - - aacaaaa
- - - - - - - - - - - - -gtgcagc
- - - - - - - - - - - - - - - - - - - - - - - - - -gaaagaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tccattc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatcctg