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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgaatgcaattcttgcattttttagtatatattcatcgatgttttccatacattagtgtgtttgaaaatcatttcagGCAACAGCAGCTTTTGACGGCATTCACTCCTCCAAATGGGAAGAGCCTGATGGAGCCAAAG

Basic information

species Zea mays
transcript GRMZM2G474236_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G474236_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os07g31460.2 (Oryza sativa), 3'ss of exon 12
gtatgtgaatgcaattcttgcattttttagtatatattcatcgatgttttccatacattagtgtgtttgaaaatcatttcagGCAACAGCAGCTTTTGACGGCATTCACTCCTCCAAATGGGAAGAGCCTGATGGAGCCAAAG
||||| |  |||||    |||||| | |  | |  |||||||    ||   | |||| || ||  |||  ||||  ||||||||||| || || ||||| ||||||| ||| |||||||||||||||||||||||||||||||
gtatgagc-tgcaacctgtgcattctcttatgttcattcatcatcattagac-tacaatattg-attttcaaattgtttcagGCAACGGCGGCATTTGATGGCATTCGCTCATCCAAATGGGAAGAGCCTGATGGAGCCAAAG
















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|211120309|gb|FL433022.1|FL433022
EST:     TGCAAGCA-GGAACAACTTCCAATAGGAATT                         GCAACAGCAGCTTTTGACGGCATTCACTCCTCCAAATGGGAAGAGCCTGAT
genomic: TGCAAGCAGGGAACAACTTCCAATAGGAATTgtatgtgaat ... atcatttcagGCAACAGCAGCTTTTGACGGCATTCACTCCTCCAAATGGGAAGAGCCTGAT
EST: gi|26558437|gb|CA830672.1|CA830672
EST:     TATGCTCAGGTTCAGTCCTTGCAAGCAGGGAACAACTTCCAATAGGAATT                         GCAACAGCAGCTTTTGACGGCATTCACTCCTCCAAATGGGAAGAGCCTGAT
genomic: TATGCTCAGGTTCAGTCCTTGCAAGCAGGGAACAACTTCCAATAGGAATTgtatgtgaat ... atcatttcagGCAACAGCAGCTTTTGACGGCATTCACTCCTCCAAATGGGAAGAGCCTGAT
EST: gi|87155597|gb|DY400386.1|DY400386
EST:     TATGCTCAGGTTCAGTCCTTGCAAGCAGGGAACAACTTCCAATAGGAATT                         GCAACAGCAGCTTTTGACGGCATTCACTCCTCCAAATGGGAAGAGCCTGAT
genomic: TATGCTCAGGTTCAGTCCTTGCAAGCAGGGAACAACTTCCAATAGGAATTgtatgtgaat ... atcatttcagGCAACAGCAGCTTTTGACGGCATTCACTCCTCCAAATGGGAAGAGCCTGAT
EST: gi|32863285|gb|CF002967.1|CF002967
EST:     TATGCTCAGGTTCAGTCCTTGCAAGCAGGGAACAACTTCCAATAGGAATT                         GCAACAGCAGCTTTTGACGGTATTCACTCCTCCAAATGGGAAGAGCCTGAT
genomic: TATGCTCAGGTTCAGTCCTTGCAAGCAGGGAACAACTTCCAATAGGAATTgtatgtgaat ... atcatttcagGCAACAGCAGCTTTTGACGGCATTCACTCCTCCAAATGGGAAGAGCCTGAT
EST: gi|76926868|gb|DV171024.1|DV171024
EST:     TATGCTCAGGTTCAGTCCTTGCAAGCAGGGAACAACTTCCAATAGGAATT                         GCAACAGCAGCTTTTGACGGCATTCACTCCTCCAAATGGGAAGAGCCTGAT
genomic: TATGCTCAGGTTCAGTCCTTGCAAGCAGGGAACAACTTCCAATAGGAATTgtatgtgaat ... atcatttcagGCAACAGCAGCTTTTGACGGCATTCACTCCTCCAAATGGGAAGAGCCTGAT
EST: gi|71766468|gb|DR964405.1|DR964405
EST:     TATGCTCAGGTTCAGTCCTTGCAAGCAGGGAACAACTTCCAATAGGAATT                         GCAACAGCAGCTTTTGACGGCATTCACTCCTCCAAATGGGAAGAGCCTGAT
genomic: TATGCTCAGGTTCAGTCCTTGCAAGCAGGGAACAACTTCCAATAGGAATTgtatgtgaat ... atcatttcagGCAACAGCAGCTTTTGACGGCATTCACTCCTCCAAATGGGAAGAGCCTGAT
EST: gi|76919531|gb|DV167764.1|DV167764
EST:     TATGCTCAGGTTCAGTCCTTGCAAGCAGGGAACAACTTCCAATAGGAATT                         GCAACAGCAGCTTTTGACGGCATTCACTCCTCCAAATGGGAAGAGCCTGAT
genomic: TATGCTCAGGTTCAGTCCTTGCAAGCAGGGAACAACTTCCAATAGGAATTgtatgtgaat ... atcatttcagGCAACAGCAGCTTTTGACGGCATTCACTCCTCCAAATGGGAAGAGCCTGAT
EST: gi|83279043|gb|DV943051.1|DV943051
EST:     TATGCTCAGGTTCAGTCCTTGCAAGCAGGGAACAACTTCCAATAGGAATT                         GCAACAGCAGCTTTTGACGGCATTCACTCCTCCAAATGGGAAGAGCCTGAT
genomic: TATGCTCAGGTTCAGTCCTTGCAAGCAGGGAACAACTTCCAATAGGAATTgtatgtgaat ... atcatttcagGCAACAGCAGCTTTTGACGGCATTCACTCCTCCAAATGGGAAGAGCCTGAT
EST: gi|76291468|gb|DV031036.1|DV031036
EST:     TATGCTCAGGTTCAGTCCTTGCAAGCAGGGAACAACTTCCAATAGGAATT                         GCAACAGCAGCTTTTGACGGCATTCACTCCTCCAAATGGGAAGAGCCTGAT
genomic: TATGCTCAGGTTCAGTCCTTGCAAGCAGGGAACAACTTCCAATAGGAATTgtatgtgaat ... atcatttcagGCAACAGCAGCTTTTGACGGCATTCACTCCTCCAAATGGGAAGAGCCTGAT
EST: gi|32935691|gb|CF040503.1|CF040503
EST:     ATGCTCAGGTTCAGTCCTTGCAAGCAGGGAACCAACTTCCAATAGGAATT                         GCAACAGCAGCTTTTGACGGCATTCACTCCTCCAAATGGGAAGAGCCTGAT
genomic: ATGCTCAGGTTCAGTCCTTGCAAGCAGGGAA-CAACTTCCAATAGGAATTgtatgtgaat ... atcatttcagGCAACAGCAGCTTTTGACGGCATTCACTCCTCCAAATGGGAAGAGCCTGAT
EST: gi|32936388|gb|CF041207.1|CF041207
EST:     TATGCTCAGGTTCAGTCCTTGCAAGCAGGGAACAACTTCCAATAGGAATT                         GCAACAGCAGCTTTTGACGTTTTTCACTCCTCCAAATGGGAAGAGCCTGAT
genomic: TATGCTCAGGTTCAGTCCTTGCAAGCAGGGAACAACTTCCAATAGGAATTgtatgtgaat ... atcatttcagGCAACAGCAGCTTTTGACGGCATTCACTCCTCCAAATGGGAAGAGCCTGAT
EST: gi|32837608|gb|CD977286.1|CD977286
EST:     TATGCTCAGGTTCAGTCCTTGCAAGCAGGGAACAACTTTCAATAGGAATT                         GCAACAGCAGCTTTTGACGGCATTCACTCCTCCAAATGGGAAGAGCCTGAT
genomic: TATGCTCAGGTTCAGTCCTTGCAAGCAGGGAACAACTTCCAATAGGAATTgtatgtgaat ... atcatttcagGCAACAGCAGCTTTTGACGGCATTCACTCCTCCAAATGGGAAGAGCCTGAT
EST: gi|22545635|gb|BU097994.1|BU097994
EST:     TATGCTCAGGTTCAGTCCTTGCAAGCAGGGAACAACTTCCAATAGGAATT                         GCAACAGCAGCTTTTGACGGCATTCACTCCTCCAAATGGGAAGAGCCTGAT
genomic: TATGCTCAGGTTCAGTCCTTGCAAGCAGGGAACAACTTCCAATAGGAATTgtatgtgaat ... atcatttcagGCAACAGCAGCTTTTGACGGCATTCACTCCTCCAAATGGGAAGAGCCTGAT
EST: gi|71421571|gb|DR805500.1|DR805500
EST:     TATGCTCAGGTTCAGTCCTTGCAAGCAGGGAACAACTTCCAATAGGAATT                         GCAACAGCAGCTTTTGACGGCATTCACTCCTCCAAATGGGAAGAGCCTGAT
genomic: TATGCTCAGGTTCAGTCCTTGCAAGCAGGGAACAACTTCCAATAGGAATTgtatgtgaat ... atcatttcagGCAACAGCAGCTTTTGACGGCATTCACTCCTCCAAATGGGAAGAGCCTGAT
EST: gi|18168382|gb|BM338222.1|BM338222
EST:     TATGCTCAGGTTCAGTCCTTGCAAGCAGGGAACAACTTCCAATAGGAATT                         GCAACAGCAGCTTTTGACGGCATTCACTCCTCCAAATGGGAAGAGCCTGAT
genomic: TATGCTCAGGTTCAGTCCTTGCAAGCAGGGAACAACTTCCAATAGGAATTgtatgtgaat ... atcatttcagGCAACAGCAGCTTTTGACGGCATTCACTCCTCCAAATGGGAAGAGCCTGAT

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: 214

GAATAATACCTTTTTCACAGAAGGCAATCATTTCCCAAGAGGGAACAGAGTATGCTCAGGTTCAGTCCTTGCAAGCAGGGAACAACTTCCAATAGGAATTgtatgtgaat ... atcatttcagGCAACAGCAGCTTTTGACGGCATTCACTCCTCCAAATGGGAAGAGCCTGATGGAGCCAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 184

GAATAATACCTTTTTCACAGAAGGCAATCATTTCCCAAGAGGGAACAGAGTATGCTCAGGTTCAGTCCTTGCAAGCAGGGAACAACTTCCAATAGGAATTgtatgtgaat ... atcatttcagGCAACAGCAGCTTTTGACGGCATTCACTCCTCCAAATGGGAAGAGCCTGATGGAGCCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 236

GAATAATACCTTTTTCACAGAAGGCAATCATTTCCCAAGAGGGAACAGAGTATGCTCAGGTTCAGTCCTTGCAAGCAGGGAACAACTTCCAATAGGAATTgtatgtgaat ... atcatttcagGCAACAGCAGCTTTTGACGGCATTCACTCCTCCAAATGGGAAGAGCCTGATGGAGCCAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 148

GAATAATACCTTTTTCACAGAAGGCAATCATTTCCCAAGAGGGAACAGAGTATGCTCAGGTTCAGTCCTTGCAAGCAGGGAACAACTTCCAATAGGAATTgtatgtgaat ... atcatttcagGCAACAGCAGCTTTTGACGGCATTCACTCCTCCAAATGGGAAGAGCCTGATGGAGCCAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtatatattcatcgatgttttccatacattagtgtgtttgaaaatcatttcagGCAACAGCAGCTTTTGACGGCATTCACTCCTCCAAATGGGAAGAGCCTGATGGAGCCAAAG
                                              tcatttc  CT-rich tract
                                      tttgaaaatcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgaatgcaattcttgcattttttagtatatattcatcgatgttttccatacattagtgtgtttgaaaatcatttcagGCAACAGCAGCTTTTGACGGCATTCACTCCTCCAAATGGGAAGAGCCTGATGGAGCCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA