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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttattctttgaattgtttctgtaataagaaactcgtatgcatctgtgttcaaatttgaataaattgctgatggttgctttaatttctttcttttgtagTCCGAGCGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCAAGCCAGTTTGCTCTAGGGCTGACTGATGGTGGTGTTTTTGTGTTGGAACCTTTG

Basic information

species Zea mays
transcript GRMZM2G030422_T01
intron # 25
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030422_T03 (Zea mays), 3'ss of exon 26
lower sequence: LOC_Os03g14980.1 (Oryza sativa), 3'ss of exon 25
-----ttttattctttgaattgtttctgtaataagaaactcgtatgcatctgtgttcaaatttgaataaattgctgatggttgctttaatttctttcttttgtagTCCGAGCGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCAAGCCAGTTTGCTCTAGGGCTGACTGATGGTGGTGTTTTTGTGTTGGAACCTTTG
        |||| | |   ||||||    |   |     || | ||  |      | |  ||| |   |   | |  |      | ||  ||| || |||  |||  | |  ||| ||||||| || || |||||||| |||||||||||||  |||||||||||||| ||||||||||||||||||| ||| |||||||| |||
aaagtgcatattatct---ttgtttgctcagccaatgtttcttttg--ttcaaacttatttttaacagacaagttattaaccattatatgttccttgtttcctagCTCAAATGTTTATCCTGTCGTTGTGGCGGCACATCCTTCGGAAGCAAATCAGTTTGCTCTAGGCCTGACTGATGGTGGTGTTTATGTATTGGAACCCTTG
















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|19351107|gb|BM895639.1|BM895639
EST:     AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTTCCTCCAAATATCAG                         TCCGAGCGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCAAGCCA
genomic: AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTTCCTCCAAATATCAGgtattctata ... tcttttgtagTCCGAGCGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCAAGCCA
EST: gi|83278414|gb|DV942422.1|DV942422
EST:     AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTTCCTCCAAATATCAG                         TCTGAGCGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCAAGCCA
genomic: AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTTCCTCCAAATATCAGgtattctata ... tcttttgtagTCCGAGCGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCAAGCCA
EST: gi|32908130|gb|CF012943.1|CF012943
EST:     AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTTCCTCCAAATATCAG                         TCCGAGCGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCAAGCCA
genomic: AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTTCCTCCAAATATCAGgtattctata ... tcttttgtagTCCGAGCGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCAAGCCA
EST: gi|32865780|gb|CF005462.1|CF005462
EST:     AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTTCCTCCAAATATCAG                         TCCGAGCGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCAAGCCA
genomic: AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTTCCTCCAAATATCAGgtattctata ... tcttttgtagTCCGAGCGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCAAGCCA
EST: gi|22473364|gb|BU037844.1|BU037844
EST:     GACTTCAGATGTCGGATTTTTCCAGCTTCGTATCTTCCTCCAAATATCAG                         TCCGAGCGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAA
genomic: GACTTCA-ATGTCGGATTCTTCCAGCTTCGTATCTTCCTCCAAATATCAGgtattctata ... tcttttgtagTCCGAGCGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAA
EST: gi|7227452|gb|AW566093.1|AW566093
EST:     AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTTCCTCCAAATATCAG                         TCCGAGCGTTCATCCTGTT
genomic: AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTTCCTCCAAATATCAGgtattctata ... tcttttgtagTCCGAGCGTTCATCCTGTT
EST: gi|5608394|gb|AI901971.1|AI901971
EST:     TTCGTATCTTCCTCCAAATATCAG                         TCCGAGCGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCAAGCCA
genomic: TTCGTATCTTCCTCCAAATATCAGgtattctata ... tcttttgtagTCCGAGCGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCAAGCCA
EST: gi|6056921|gb|AW091326.1|AW091326
EST:     AGACTTCAATGTCGGATTCTTCCAGCTTCGAATCTTCCTCCAAATATCAG                         TCTGAGCGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCAAGCCA
genomic: AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTTCCTCCAAATATCAGgtattctata ... tcttttgtagTCCGAGCGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCAAGCCA
EST: gi|37393773|gb|CF634152.1|CF634152
EST:     AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTTCCTCCAAATATCAG                         TCCGAGCGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCAAGCCA
genomic: AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTTCCTCCAAATATCAGgtattctata ... tcttttgtagTCCGAGCGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCAAGCCA
EST: gi|7162284|gb|AW519891.1|AW519891
EST:     AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTTCCTCCAAATATCAG                         TCCGAGCGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCAAGCCA
genomic: AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTTCCTCCAAATATCAGgtattctata ... tcttttgtagTCCGAGCGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCAAGCCA
EST: gi|76010934|gb|DT938104.1|DT938104
EST:     AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTTCCTCCAAATATCAG                         TCCGAGCGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCAAGCCA
genomic: AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTTCCTCCAAATATCAGgtattctata ... tcttttgtagTCCGAGCGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCAAGCCA
EST: gi|32908128|gb|CF012941.1|CF012941
EST:     AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTTCCTCCAAATATCAG                         TCCGAGCGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCAAGCCA
genomic: AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTTCCTCCAAATATCAGgtattctata ... tcttttgtagTCCGAGCGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCAAGCCA
EST: gi|32935018|gb|CF039830.1|CF039830
EST:     AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTTCCTCCAAATATCAG                         TCCGAGCGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCAAGCCA
genomic: AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTTCCTCCAAATATCAGgtattctata ... tcttttgtagTCCGAGCGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCAAGCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgttcaaatttgaataaattgctgatggttgctttaatttctttcttttgtagTCCGAGCGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCAAGCCAGTTTGCTCTAGGGCTGACTGATGGTGGTGTTTTTGTGTTGGAACCTTTG
                              ttgctttaatttcttt  CT-rich tract
     tcaaatttgaataaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttattctttgaattgtttctgtaataagaaactcgtatgcatctgtgttcaaatttgaataaattgctgatggttgctttaatttctttcttttgtagTCCGAGCGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCAAGCCAGTTTGCTCTAGGGCTGACTGATGGTGGTGTTTTTGTGTTGGAACCTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG