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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcaatgttcctttgagattccataccatccacccgttgggtggtttagccgccctcttgtcgctgactctgaaaagctcgttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTCTGCGCTCTCCCTGTCGTCATCGTCAAGAGACACTGAAGGCCTGCCAAAG

Basic information

species Zea mays
transcript GRMZM2G023528_T03
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G023528_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g03740.1 (Oryza sativa), 3'ss of exon 6
gtaagcaatgttcctttgagattccataccatccacccgt-tgggtggtttagccgccctcttgtcgctgactctgaaaagctcgttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTCTGCGCTCTCCCTGTCGTCATCGTCAAGAGACACTGAAGGCCTGCCAAAG
|| ||     || | |  | || ||||| |||     | |     | ||||||  || ||  ||    ||  ||||       |    || ||||||||| |||||| |||||||||||||||||||     |||| || || ||||| ||||| || || ||||| |||||||||||| |||    | |||||
gttagtgccttttcct--acataccatatcatgttttcatgcatcttgtttag--gctctgatgctcatggatctgtctgctcctgcttgatagGCATCGGTTCTTCCTGGACATGGATAAAGAATCTGATACAAAAGCCTTCTCTGCTCTCTCTCTCTCATCATCTTCAAGAGACACTCAAGATGGGTCAAAG
















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|15079808|gb|BI388841.1|BI388841
EST:     TGCTTTCCCCCCAGAATTGACATCAGACTCCAGATG                         GCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
genomic: TGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
EST: gi|6020368|gb|AW065296.1|AW065296
EST:     AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG                         GCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
genomic: AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
EST: gi|71318383|gb|DR795955.1|DR795955
EST:     AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG                         GCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
genomic: AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
EST: gi|5714344|gb|AI944329.1|AI944329
EST:     AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG                         GCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
genomic: AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
EST: gi|5895630|gb|AW036876.1|AW036876
EST:     AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG                         GCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
genomic: AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
EST: gi|32934367|gb|CF039179.1|CF039179
EST:     AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG                         GCATCGTTTCTTCTTGGACATGGAT
genomic: AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGAT
EST: gi|33467208|gb|CF244257.1|CF244257
EST:     AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG                         GCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
genomic: AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
EST: gi|37382875|gb|CF628406.1|CF628406
EST:     AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG                         GCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
genomic: AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
EST: gi|74233030|gb|DT640944.1|DT640944
EST:     AACATCCTCGCAACTGCTTTCCCCCCAGAATTGACATCAGACTCCAGATG                         GCATCGNNNNNNNNNGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTT
genomic: AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
EST: gi|71437533|gb|DR818583.1|DR818583
EST:     AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG                         GCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
genomic: AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
EST: gi|91055148|gb|EB165566.1|EB165566
EST:     AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG                         GCATCGTTTCTTTTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTT
genomic: AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
EST: gi|15215333|gb|BI431244.1|BI431244
EST:     AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG                         GCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
genomic: AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
EST: gi|31359368|gb|CD443725.1|CD443725
EST:     AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG                         GCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
genomic: AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
EST: gi|78021493|gb|DV489880.1|DV489880
EST:     AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG                         GCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
genomic: AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
EST: gi|5804744|gb|AI979714.1|AI979714
EST:     AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG                         GCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTN
genomic: AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
EST: gi|60340407|gb|DN207380.1|DN207380
EST:     AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG                         GCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
genomic: AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
EST: gi|5804728|gb|AI979698.1|AI979698
EST:     AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG                         GCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
genomic: AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
EST: gi|40303169|gb|CK347556.1|CK347556
EST:     AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG                         GCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
genomic: AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
EST: gi|5597195|gb|AI891188.1|AI891188
EST:     CCTCGC-ACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG                         GCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
genomic: CCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
EST: gi|18166881|gb|BM336720.1|BM336720
EST:     AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG                         GCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
genomic: AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgggtggtttagccgccctcttgtcgctgactctgaaaagctcgttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTCTGCGCTCTCCCTGTCGTCATCGTCAAGAGACACTGAAGGCCTGCCAAAG
                          cgctgac  putative branch site (score: 3)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcaatgttcctttgagattccataccatccacccgttgggtggtttagccgccctcttgtcgctgactctgaaaagctcgttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTCTGCGCTCTCCCTGTCGTCATCGTCAAGAGACACTGAAGGCCTGCCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG