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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtccccaattcttctcaaatggtctttcaagagcactctttctatgtctttccattatcatatgaccctgtgaacatcaaattattctgcagGTTAGATTTTTAGATATGTGGGAACCAGCTATTTTGGCAATAAAGAGGGAAGGTTACAGCGTTAAGTGTAATGGACAGCGCGGTGTCGTTGTCATGGAGA

Basic information

species Zea mays
transcript GRMZM2G104377_T03
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G104377_T03 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os05g01060.1 (Oryza sativa), 3'ss of exon 17
gtatgtccccaattcttctcaaat-ggtctttcaagagcactctttctatgtctttccattatcatatgaccctgtgaacatcaaattattctgcagGTTAGATTTTTAGATATGTGGGAACCAGCTATTTTGGCAATAAAGAGGGAAGGTTACAGCGTTAAGTGTAATGGACAGCGCGGTGTCGTTGTCATGGAGA
||||||      | ||| | | || | | | ||||     |||     |  |||||   || |||||| ||| |  ||  |||||    |  |||||||||| ||| |||||||||||||||||||| | ||||||||||||||||||||||||||| ||||||||||||| ||||| ||||| ||| | |  || |
gtatgttatatttcctttttatattgatatgtcaatcattctcacgacacttctttt-gttgtcatataaccattggactatcaa----tcttgcagGTTAGGTTTCTAGATATGTGGGAACCAGCTGTATTGGCAATAAAGAGGGAAGGTTACAGCATTAAGTGTAATGGCCAGCGTGGTGTTGTTATTACAGAAA

upper sequence: GRMZM2G104377_T03 (Zea mays), 3'ss of exon 16
lower sequence: Vv07s0130g00420.t01 (Vitis vinifera), 3'ss of exon 17
---------------------------------------gtatgtccccaattcttctcaaatggtctt-tcaagagcac-tctttctatgtctttccattatcatatgaccctgtgaacatcaaattattctgcagGTTAGATTTTTAGATATGTGGGAACCAGCTATTTTGGCAATAAAGAGGGAAGGTTACAGCGTTAAGTGTAATGGACAGCGCGGTGTCGTTGTCATGGAGA
                                        | |    |   || | ||   |  ||||| ||| || ||  | ||| | |   ||  | || | | |   |   |     |||   | ||| |||||| | ||| | | ||||| ||||||||||||| |||||| || |||||||||||||||||| | ||||||| |||||   | ||||  || |||   ||||
gtatgactattacaacaaatacccctagtttataattctttgttgatcttgttttgctatcaaagtcttatcaggaacatatgtttttttaatttcaccttcttaaagagcttagcctgaatcttttaattttgcagGCTGGATATCTTGATATATGGGAACCAGCTACTTTGGCCATTAAGAGGGAAGGTTACAGCATCAAGTGTACTGGACCTAGTGGTGCTGTAGTCTCTGAGA
















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|78021163|gb|DV489550.1|DV489550
EST:     TTAAGAAAATTCTCTCTCTGGGGCATGTCTCTTATGAAGTTCTATTACCT                         GTTAGATTTTTAGATATGTGGGAACCAGCTATTTTGGCAATAAAGAGGGAA
genomic: TTAAGAAAATTCTCTCTCTGGGGCATGTCTCTTATGAAGTTCTATTACCTgtatgtcccc ... tattctgcagGTTAGATTTTTAGATATGTGGGAACCAGCTATTTTGGCAATAAAGAGGGAA
EST: gi|17921450|gb|BM259101.1|BM259101
EST:     TGTCTCTTATGAAGTTCTATTACCT                         GTTAGATTTTTAGATATGTGGGAACCAGNNNNNNNGGCAATAAAGAGGGAA
genomic: TGTCTCTTATGAAGTTCTATTACCTgtatgtcccc ... tattctgcagGTTAGATTTTTAGATATGTGGGAACCAGCTATTTTGGCAATAAAGAGGGAA
EST: gi|5714191|gb|AI944176.1|AI944176
EST:     TTAAGAAAATTCTCTCTCTGGGGCATGTCTCTTATGAAGTTCTATTACCT                         GTTAGATTTTTAGATATGTGGGAACCAGCTATTTTGGCAATAAAGAGGGAA
genomic: TTAAGAAAATTCTCTCTCTGGGGCATGTCTCTTATGAAGTTCTATTACCTgtatgtcccc ... tattctgcagGTTAGATTTTTAGATATGTGGGAACCAGCTATTTTGGCAATAAAGAGGGAA
EST: gi|5296168|gb|AI783043.1|AI783043
EST:     TTAAGAAAATTCTCTCTCTGGGGCATGTCTCTTATGAAGTTCTATTACCT                         GTTAGATTTTTAGATATGTGGGAACCAGCTATTTTGGCAATAAAGAGGGAA
genomic: TTAAGAAAATTCTCTCTCTGGGGCATGTCTCTTATGAAGTTCTATTACCTgtatgtcccc ... tattctgcagGTTAGATTTTTAGATATGTGGGAACCAGCTATTTTGGCAATAAAGAGGGAA
EST: gi|60351693|gb|DN218666.1|DN218666
EST:     TTAAGAAAATTCTCTCTCTGGGGCATGTCTCTTATGAAGTTCTATTACCT                         GTTAGATTTTTAGATATGTGGGAACCAGCTATTTTGGCAATAAAGAGGGAA
genomic: TTAAGAAAATTCTCTCTCTGGGGCATGTCTCTTATGAAGTTCTATTACCTgtatgtcccc ... tattctgcagGTTAGATTTTTAGATATGTGGGAACCAGCTATTTTGGCAATAAAGAGGGAA
EST: gi|60355764|gb|DN222737.1|DN222737
EST:     TTAAGAAAATTCTCTCTCTGGGGCATGTCTCTTATGAAGTTCTATTACCT                         GTTAGATTTTTAGATATGTGGGAACCAGCTATTTTGGCAATAAAGAGGGAA
genomic: TTAAGAAAATTCTCTCTCTGGGGCATGTCTCTTATGAAGTTCTATTACCTgtatgtcccc ... tattctgcagGTTAGATTTTTAGATATGTGGGAACCAGCTATTTTGGCAATAAAGAGGGAA
EST: gi|31353499|gb|CD437856.1|CD437856
EST:     TTAAGAAAATTCTCTCTCTGGGGCATGTCTCTTATGAAGTTCTATTACCT                         GTTAGATTTTTAGATATGTGGGGACCAGCTATTTTGGCA
genomic: TTAAGAAAATTCTCTCTCTGGGGCATGTCTCTTATGAAGTTCTATTACCTgtatgtcccc ... tattctgcagGTTAGATTTTTAGATATGTGGGAACCAGCTATTTTGGCA
EST: gi|17921770|gb|BM259421.1|BM259421
EST:     CATGTCTCTTATGAAGTTCTATTACCT                         GTTAGATTTTTAGATATGTGGGAACCAGCTATTTTGGCAATAAAGAGGGAA
genomic: CATGTCTCTTATGAAGTTCTATTACCTgtatgtcccc ... tattctgcagGTTAGATTTTTAGATATGTGGGAACCAGCTATTTTGGCAATAAAGAGGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttctatgtctttccattatcatatgaccctgtgaacatcaaattattctgcagGTTAGATTTTTAGATATGTGGGAACCAGCTATTTTGGCAATAAAGAGGGAAGGTTACAGCGTTAAGTGTAATGGACAGCGCGGTGTCGTTGTCATGGAGA
                                            ttattct  CT-rich tract
                                   aacatcaaattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtccccaattcttctcaaatggtctttcaagagcactctttctatgtctttccattatcatatgaccctgtgaacatcaaattattctgcagGTTAGATTTTTAGATATGTGGGAACCAGCTATTTTGGCAATAAAGAGGGAAGGTTACAGCGTTAAGTGTAATGGACAGCGCGGTGTCGTTGTCATGGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA