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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCGCTGGCCGTCGCGGCGGCGGCCATGGTGTTGGTCTGGGCCATCTACTTCCGCGGTGGGCTCGCCATCGAGGCCACCAACAAGAACCTCATCTTCAACgtgggtactactgcctctcccctccccgcgctggttgcttcaacgccgacaacttgttttggggacgcgtgttttcccttttgtttgctttctttcccct...

Basic information

species Zea mays
transcript GRMZM2G066885_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G066885_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os02g42890.1 (Oryza sativa), 5'ss of exon 1
CGCGCTGGCCGTCGCGGCGGCGGCCATGGTGTTGGTCTGGGCCATCTACTTCCGCGGTGGGCTCGCCATCGAGGCCACCAACAAGAACCTCATCTTCAACgtgggtact-actgcctctcccctccccgcgctggttgcttcaacgccgacaacttgttttggggacgcgtgttttcccttttgtttgctttctttcccct-
|||||||||||| ||||| ||  |||||||| ||||||||  |||| |||||||||| || |||||| |||||||||| |||||||||||||||||||||||| |||||   | |   ||  | |||||      | | |      |     |     |   | ||     | ||          ||  ||   | || || 
CGCGCTGGCCGTGGCGGCCGCCACCATGGTGCTGGTCTGGTGCATCCACTTCCGCGGCGGCCTCGCCTTCGAGGCCACAAACAAGAACCTCATCTTCAACgtgagtacttgattctcgtctgccccccgtctctctagttatctttctagtgataccgtcccgagatattggattggatggacaatt--ttgggtgccgctg
















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|211288140|gb|FL278509.1|FL278509
EST:     TCCGCGGTGGGCTCGCCATCGAGGCCACCAACAAGAACCTCATCTTCAAC                         GTTCACCCTGTTCTTATGCTTATCGGTTATATTATCATCGGCGGCGAAG
genomic: TCCGCGGTGGGCTCGCCATCGAGGCCACCAACAAGAACCTCATCTTCAACgtgggtacta ... aacattgcagGTTCACCCTGTTCTTATGCTTATCGGTTATATTATCATCGGCGGCGAAG
EST: gi|211288139|gb|FL278508.1|FL278508
EST:     TCCGCGGTGGGCTCGCCATCGAGGCCACCAACAAGAACCTCATCTTCAAC                         GTTCACCCTGTTCTTATGCTTATCGGTTATATTATCATCGGCGGCGAAG
genomic: TCCGCGGTGGGCTCGCCATCGAGGCCACCAACAAGAACCTCATCTTCAACgtgggtacta ... aacattgcagGTTCACCCTGTTCTTATGCTTATCGGTTATATTATCATCGGCGGCGAAG
EST: gi|71424805|gb|DR806443.1|DR806443
EST:     ACAAGAACCTCATTTTCAAC                         GTTCACCCTGTTCTTATGCTTATCGGTTATATTATCATCGGCGGCGAAG
genomic: ACAAGAACCTCATCTTCAACgtgggtacta ... aacattgcagGTTCACCCTGTTCTTATGCTTATCGGTTATATTATCATCGGCGGCGAAG
EST: gi|211055163|gb|FK977534.1|FK977534
EST:     TCCGCGGTGGGCTCGCCATCGAGGCCACCAACAAGAACCTCATCTTCAAC                         GTTCACCCTGTTCTTATGCTTATCGGTTATATTATCATCGGCGGCGAAG
genomic: TCCGCGGTGGGCTCGCCATCGAGGCCACCAACAAGAACCTCATCTTCAACgtgggtacta ... aacattgcagGTTCACCCTGTTCTTATGCTTATCGGTTATATTATCATCGGCGGCGAAG
EST: gi|148965066|gb|EC906072.2|EC906072
EST:     TCCGCGGTGGGCTCGCCATCGAGGCCACCAACAAGAACCTCATCTTCAAC                         GTTCACCCTGTTCTTATGCTTATCGGTTATATTATCATCGGCGGCGAAG
genomic: TCCGCGGTGGGCTCGCCATCGAGGCCACCAACAAGAACCTCATCTTCAACgtgggtacta ... aacattgcagGTTCACCCTGTTCTTATGCTTATCGGTTATATTATCATCGGCGGCGAAG
EST: gi|50323144|gb|CO518270.1|CO518270
EST:     TCCGCGGTGGGCTCGCCATCGAGGCCACCAACAAGAACCTCATCTTCAAC                         GTTCACCCTGTTCTTATGCTTATCGGTTATATTATCATCGGCGGCGAAG
genomic: TCCGCGGTGGGCTCGCCATCGAGGCCACCAACAAGAACCTCATCTTCAACgtgggtacta ... aacattgcagGTTCACCCTGTTCTTATGCTTATCGGTTATATTATCATCGGCGGCGAAG
EST: gi|211055161|gb|FK977532.1|FK977532
EST:     TCCGCGGTGGGCTCGCCATCGAGGCCACCAACAAGAACCTCATCTTCAAC                         GTTCACCCTGTTCTTATGCTTATCGGTTATATTATCATCGGCGGCGAAG
genomic: TCCGCGGTGGGCTCGCCATCGAGGCCACCAACAAGAACCTCATCTTCAACgtgggtacta ... aacattgcagGTTCACCCTGTTCTTATGCTTATCGGTTATATTATCATCGGCGGCGAAG
EST: gi|211288138|gb|FL278507.1|FL278507
EST:     TCCGCGGTGGGCTCGCCATCGAGGCCACCAACAAGAACCTCATCTTCAAC                         GTTCACCCTGTTCTTATGCTTATCGGTTATATTATCATCGGCGGCGAAG
genomic: TCCGCGGTGGGCTCGCCATCGAGGCCACCAACAAGAACCTCATCTTCAACgtgggtacta ... aacattgcagGTTCACCCTGTTCTTATGCTTATCGGTTATATTATCATCGGCGGCGAAG
EST: gi|148946110|gb|EC891404.2|EC891404
EST:     TCCGCGGTGGGCTCGCCATCGAGGCCACCAACAAGAACCTCATCTTCAAC                         GTTCACCCTGTTCTTATGCTTATCGGTTATATTATCATCGGCGGCGAAG
genomic: TCCGCGGTGGGCTCGCCATCGAGGCCACCAACAAGAACCTCATCTTCAACgtgggtacta ... aacattgcagGTTCACCCTGTTCTTATGCTTATCGGTTATATTATCATCGGCGGCGAAG
EST: gi|76287729|gb|DV027297.1|DV027297
EST:     TCCGCGGTGGGCTCGCCATCGAGGCCACCAACAAGAACCTCATCTTCAAC                         GTTCACCCTGTTCTTATGCTTATCGGTTATATTATCATCGGCGGCGAAG
genomic: TCCGCGGTGGGCTCGCCATCGAGGCCACCAACAAGAACCTCATCTTCAACgtgggtacta ... aacattgcagGTTCACCCTGTTCTTATGCTTATCGGTTATATTATCATCGGCGGCGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGCGCTGGCCGTCGCGGCGGCGGCCATGGTGTTGGTCTGGGCCATCTACTTCCGCGGTGGGCTCGCCATCGAGGCCACCAACAAGAACCTCATCTTCAACgtgggtactactgcctctcccctccccgcgctggttgcttcaacgccgacaacttgttttggggacgcgtgttttcccttttgtttgctttctttcccct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccctccc