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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCGCGATTATTTGTTTCTTGAAGCTGCACGGCGAGATTTAAGAGTAATAATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAGGTTACAAgtgagttcttccatctttctatcctggatagttagttttgttatgtggggataaggtagtagcatctattcttaaacagtgtaatatgtacaattttatg...

Basic information

species Zea mays
transcript GRMZM2G044011_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044011_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os04g56480.3 (Oryza sativa), 5'ss of exon 10
TCCGCGATTATTTGTTTCTTGAAGCTGCACGGCGAGATTTAAGAGTAATAATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAGGTTACAAgtgagttcttccatctttctatcctggatagttagttttgttatgtggggataaggtagtagcatc---tattcttaa-acagtgtaatatgtacaattttatg
||||||||||| ||  ||||||||||||||||||||| |||||| |||||||||||||||| || ||| ||||||| || |||||| | ||||||||||||| || | ||| |||||| |    | || | ||  |    |    | |   ||   |  |  |  |    ||| |    |||    ||  | | |     | ||
TCCGCGATTATATGCATCTTGAAGCTGCACGGCGAGACTTAAGATTAATAATTGAGAACAAACAGCGCATTGTTCTTGCACATGCACCTTCAGGTTACAAgtaagatattctatctttgt----tagacaattgttgccatctactcgacctattctctttcccccctacattttaggtacatcagaacctattctgaactgtg
















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|211495349|gb|FL234479.1|FL234479
EST:     ATTGAGAACAAGCAACGCCTTGTTCTGGCACATGCAACATCAGGTTACAA                         GCATAGTTTAAAGGAAGTTTTGGATACACCAGGTGTGATGGCACTGATAAA
genomic: ATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAGGTTACAAgtgagttctt ... catttgttagGCATAGTTTAAAGGAAGTTTTGGACACACCAGGTGTGATGGCACTGATAAA
EST: gi|91048656|gb|EB159074.1|EB159074
EST:     ATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAGGTTACAA                         GCATAGTTTAAAGGAAGTTTTGGACACACCAGGTGTGATGGCACTGATAAA
genomic: ATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAGGTTACAAgtgagttctt ... catttgttagGCATAGTTTAAAGGAAGTTTTGGACACACCAGGTGTGATGGCACTGATAAA
EST: gi|67018605|gb|CO447354.1|CO447354
EST:     ATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAGGTTACAA                         GCATAGTTTAAAGGAAGTTTTGGATACACCAGGTGTGATGGCACTAATAAA
genomic: ATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAGGTTACAAgtgagttctt ... catttgttagGCATAGTTTAAAGGAAGTTTTGGACACACCAGGTGTGATGGCACTGATAAA
EST: gi|67024357|gb|CO453106.1|CO453106
EST:     ATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAGGTTACAA                         GCATAGTTTAAAGGAAGTTTTGGATACACCAGGTGTGATGGCACTAATAAA
genomic: ATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAGGTTACAAgtgagttctt ... catttgttagGCATAGTTTAAAGGAAGTTTTGGACACACCAGGTGTGATGGCACTGATAAA
EST: gi|40303701|gb|CK348088.1|CK348088
EST:     ATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAGGTTACAA                         GCATAGTTTAAAGGAAGTTTTGGACACACCAGGTGTGATGGCACTGATAAA
genomic: ATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAGGTTACAAgtgagttctt ... catttgttagGCATAGTTTAAAGGAAGTTTTGGACACACCAGGTGTGATGGCACTGATAAA
EST: gi|71763506|gb|DR961443.1|DR961443
EST:     ATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAGGTTACAA                         GCATAGTTTAAAGGAAGTTTTGGACACACCAGGTGTGATGGCACTGATAAA
genomic: ATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAGGTTACAAgtgagttctt ... catttgttagGCATAGTTTAAAGGAAGTTTTGGACACACCAGGTGTGATGGCACTGATAAA
EST: gi|74236267|gb|DT644181.1|DT644181
EST:     ATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAGGTTACAA                         GCATAGTTTAAAGGAAGTTTTGGGCACACCAGGTGTGATGGCACTGATAAA
genomic: ATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAGGTTACAAgtgagttctt ... catttgttagGCATAGTTTAAAGGAAGTTTTGGACACACCAGGTGTGATGGCACTGATAAA
EST: gi|71442136|gb|DR823186.1|DR823186
EST:     ATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAGGTTACAA                         GCATAGTTTAAAGGAAGTTTTGGACACACCAGGTGTGATGGCACTGATAAA
genomic: ATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAGGTTACAAgtgagttctt ... catttgttagGCATAGTTTAAAGGAAGTTTTGGACACACCAGGTGTGATGGCACTGATAAA
EST: gi|50333168|gb|CO528294.1|CO528294
EST:     ATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAGGTTACAA                         GCATAGTTTAAAGGAAGTTTTGGACACACCAGGTGTGATGGCACTGATAAA
genomic: ATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAGGTTACAAgtgagttctt ... catttgttagGCATAGTTTAAAGGAAGTTTTGGACACACCAGGTGTGATGGCACTGATAAA
EST: gi|67021632|gb|CO450381.1|CO450381
EST:     ATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAGGTTACAA                         GCATAGTTTAAAGGAAGTTTTGGATACACCAGGTGTGATGGCACTAATAAA
genomic: ATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAGGTTACAAgtgagttctt ... catttgttagGCATAGTTTAAAGGAAGTTTTGGACACACCAGGTGTGATGGCACTGATAAA
EST: gi|71302744|gb|DR787484.1|DR787484
EST:     ATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAGGTTACAA                         GCATAGTTTAAAGGAAGTTTTGGACACACCAGGTGTGATGGCACTGATAAA
genomic: ATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAGGTTACAAgtgagttctt ... catttgttagGCATAGTTTAAAGGAAGTTTTGGACACACCAGGTGTGATGGCACTGATAAA
EST: gi|76016282|gb|DT943452.1|DT943452
EST:     ATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAGGTTACAA                         GCATAGTTTAAAGGAAGTTTTGGACACACCAGGTGTGATGGCACTGATAAA
genomic: ATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAGGTTACAAgtgagttctt ... catttgttagGCATAGTTTAAAGGAAGTTTTGGACACACCAGGTGTGATGGCACTGATAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCGCGATTATTTGTTTCTTGAAGCTGCACGGCGAGATTTAAGAGTAATAATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAGGTTACAAgtgagttcttccatctttctatcctggatagttagttttgttatgtggggataaggtagtagcatctattcttaaacagtgtaatatgtacaattttatg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA