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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtttttatccttttcatttcatttcattatgatttttatctcatctttctaaaaagtttgaactacctgacagTCTCGTTCAAGCTATACGATATGGATGGCACAGGGTTTATTGAACGAAAGGAG

Basic information

species Zea mays
transcript GRMZM2G107575_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107575_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os10g41510.1 (Oryza sativa), 3'ss of exon 4
gtaggtttttatccttttcatttcatttcattatgatttttatctcatct----ttctaaaaagtttgaactacctgacagTCTCGTTCAAGCTATACGATATGGATGGCACAGGGTTTATTGAACGAAAGGAG
||| ||| ||  | || |  ||| || |||   |  ||  || |  |  |    |||  ||| | |||| |     |||||| || ||||||||||| ||||||||   ||| |||||||||||||||||||||
gtaagttattgccattct-gttttatctcaacttcgttgataccataatttcacttcctaaatgattgaccccttggacagTTTCCTTCAAGCTATATGATATGGACAACACTGGGTTTATTGAACGAAAGGAG
















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|86466680|gb|DY233050.1|DY233050
EST:     AGCTCTAAATGTGTTTCATCCAAATATCCCAATGGAAGAAAAAGTCGATT                         TCTCGTTCAAGCTATACGATATGGATGGCACAGGGTTTATTGAACGAAAGG
genomic: AGCTCTAAATGTGTTTCATCCAAATATCCCAATGGAAGAAAAAGTCGATTgtaggttttt ... tacctgacagTCTCGTTCAAGCTATACGATATGGATGGCACAGGGTTTATTGAACGAAAGG
EST: gi|149079633|gb|EE168627.2|EE168627
EST:     AGCTCTAAATGTGTTTCATCCAAATATCCCAATGGAAGAAAA-GTCGATT                         TCTCGTTCAAGCTATACGATATGGATGGCACAGGGTTTATTG
genomic: AGCTCTAAATGTGTTTCATCCAAATATCCCAATGGAAGAAAAAGTCGATTgtaggttttt ... tacctgacagTCTCGTTCAAGCTATACGATATGGATGGCACAGGGTTTATTG
EST: gi|91053272|gb|EB163690.1|EB163690
EST:     AGCTCTAAATGTGTTTCATCCAAATATCCCAATGGAAGAAAAAGTCGATT                         TCTCGTTCAAGCTATACGATATGGATGGCACAGGGTTTATTGAACGAAAGG
genomic: AGCTCTAAATGTGTTTCATCCAAATATCCCAATGGAAGAAAAAGTCGATTgtaggttttt ... tacctgacagTCTCGTTCAAGCTATACGATATGGATGGCACAGGGTTTATTGAACGAAAGG
EST: gi|78085933|gb|DV514326.1|DV514326
EST:     AGCTCTAAATGTGTTTCATCCAAATATCCCAATGGAAGAAAAAGTCGATT                         TCTCGTTCAAGCTATACGATATGGATGGCACAGGGTTTATTGAACGAAAGG
genomic: AGCTCTAAATGTGTTTCATCCAAATATCCCAATGGAAGAAAAAGTCGATTgtaggttttt ... tacctgacagTCTCGTTCAAGCTATACGATATGGATGGCACAGGGTTTATTGAACGAAAGG
EST: gi|14203857|gb|BG837534.1|BG837534
EST:     AGCTCTAAATGTGTTTCATCCAAATATCCCAATGGAAGAAAAAGTCGATT                         TCTCGTTCAAGCTATACGATATGGATGGCACAGGGTTTATTGAACGAAAGG
genomic: AGCTCTAAATGTGTTTCATCCAAATATCCCAATGGAAGAAAAAGTCGATTgtaggttttt ... tacctgacagTCTCGTTCAAGCTATACGATATGGATGGCACAGGGTTTATTGAACGAAAGG
EST: gi|211199934|gb|FL305445.1|FL305445
EST:     AGCTCTAAATGTGTTTCATCCAAATATCCCAATGGAAGAAAAAGTCGATT                         TCTCGTTCAAGCTATACGATATGGATGGCACAGGGTTTATTGAACGAAAGG
genomic: AGCTCTAAATGTGTTTCATCCAAATATCCCAATGGAAGAAAAAGTCGATTgtaggttttt ... tacctgacagTCTCGTTCAAGCTATACGATATGGATGGCACAGGGTTTATTGAACGAAAGG
EST: gi|149016909|gb|EE045638.2|EE045638
EST:     AGCTCTAAATGTGTTTCATCCAAATATCCCAATGGAAGAAAAAGTCGATT                         TCTCGTTCAAGCTATACGATATGGATGGCACAGGGTTTATTGAACGAAAGG
genomic: AGCTCTAAATGTGTTTCATCCAAATATCCCAATGGAAGAAAAAGTCGATTgtaggttttt ... tacctgacagTCTCGTTCAAGCTATACGATATGGATGGCACAGGGTTTATTGAACGAAAGG
EST: gi|76018012|gb|DT945182.1|DT945182
EST:     AGCTCTAAATGTGTTTCATCCAAATATCCCAATGGAAGAAAAAGTCGATT                         TCTCGTTCAAGCTATACGATATGGATGGCACAGGGTTTATTGAACGAAAGG
genomic: AGCTCTAAATGTGTTTCATCCAAATATCCCAATGGAAGAAAAAGTCGATTgtaggttttt ... tacctgacagTCTCGTTCAAGCTATACGATATGGATGGCACAGGGTTTATTGAACGAAAGG
EST: gi|71427887|gb|DR808937.1|DR808937
EST:     AGCTCTAAATGTGTTTCATCCAAATATCCCAATGGAAGAAAAAGTCGATT                         TCTCGTTCAAGCTATACGATATGGATGGCACAGGGTTTATTGAACGAAAGG
genomic: AGCTCTAAATGTGTTTCATCCAAATATCCCAATGGAAGAAAAAGTCGATTgtaggttttt ... tacctgacagTCTCGTTCAAGCTATACGATATGGATGGCACAGGGTTTATTGAACGAAAGG
EST: gi|20208081|gb|BQ134170.1|BQ134170
EST:     AGCTCTAAATGTGTTTCATCCAAATATCCCAATGGAAGAAAAAGTCGATT                         TCTCGTTCAAGCTATACGATATGGATGGCACAGG
genomic: AGCTCTAAATGTGTTTCATCCAAATATCCCAATGGAAGAAAAAGTCGATTgtaggttttt ... tacctgacagTCTCGTTCAAGCTATACGATATGGATGGCACAGG
EST: gi|78085932|gb|DV514325.1|DV514325
EST:     AATGTGTTTCATCCAAATATCCCAATGGAAGAAAAAGTCGATT                         TTTCGTTCAAGCTATACGATATGGATGGCACAGGGTTTATTGAACGAAAGG
genomic: AATGTGTTTCATCCAAATATCCCAATGGAAGAAAAAGTCGATTgtaggttttt ... tacctgacagTCTCGTTCAAGCTATACGATATGGATGGCACAGGGTTTATTGAACGAAAGG
EST: gi|91052665|gb|EB163083.1|EB163083
EST:     AGCTCTAAATGTGTTTCATCCAAATATCCCAATGGAAGAAAAAGTCGATT                         TCTCGTTCAAGCTATACGATATGGATGGCACAGGGTTTATTGAACGAAAGG
genomic: AGCTCTAAATGTGTTTCATCCAAATATCCCAATGGAAGAAAAAGTCGATTgtaggttttt ... tacctgacagTCTCGTTCAAGCTATACGATATGGATGGCACAGGGTTTATTGAACGAAAGG
EST: gi|71317611|gb|DR795553.1|DR795553
EST:     AGCTCTAAATGTGTTTCATCCAAATATCCCAATGGAAGAAAAAGTCGATT                         TCTCGTTTCA-GCTATACGATATGGATGGCACAGGGTTTATTGAACG
genomic: AGCTCTAAATGTGTTTCATCCAAATATCCCAATGGAAGAAAAAGTCGATTgtaggttttt ... tacctgacagTCTCGTT-CAAGCTATACGATATGGATGGCACAGGGTTTATTGAACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatttcattatgatttttatctcatctttctaaaaagtttgaactacctgacagTCTCGTTCAAGCTATACGATATGGATGGCACAGGGTTTATTGAACGAAAGGAG
                            ttctaaa  putative branch site (score: 2)
     tcattatgatttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggtttttatccttttcatttcatttcattatgatttttatctcatctttctaaaaagtttgaactacctgacagTCTCGTTCAAGCTATACGATATGGATGGCACAGGGTTTATTGAACGAAAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG