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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAACCAGCTATTTTGGCAATAAAGAGGGAAGGTTACAGCGTTAAGTGTAATGGACAGCGCGGTGTCGTTGTCATGGAGAAATTTCAGCAAGCGATGACCgtatgatttccaaaatcattgtcctcaaaatttctcagtttgtttaatactttatcttctttctttaggaaaaatgtcttgggatttgtagcctcctttt...

Basic information

species Zea mays
transcript GRMZM2G104377_T03
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G104377_T03 (Zea mays), 5'ss of exon 17
lower sequence: LOC_Os05g01060.1 (Oryza sativa), 5'ss of exon 18
GGAACCAGCTATTTTGGCAATAAAGAGGGAAGGTTACAGCGTTAAGTGTAATGGACAGCGCGGTGTCGTTGTCATGGAGAAATTTCAGCAAGCGATGACCgtatgatttccaaaatcattgtcctcaaaatttctcagtttgtttaatactttatcttctttctttaggaaaaatgtcttg--ggatttgtagcctcctttt--------
|||||||||| | ||||||||||||||||||||||||||| ||||||||||||| ||||| ||||| ||| | |  || ||||| |||||||| |   | ||||| |     ||||||||||| |  || || ||      |||    |   | | | |    |  |  ||   || |||     ||||||    |   |||        
GGAACCAGCTGTATTGGCAATAAAGAGGGAAGGTTACAGCATTAAGTGTAATGGCCAGCGTGGTGTTGTTATTACAGAAAAATTCCAGCAAGCCACTGCTgtatg-tcctagaaatcattgtctttgaatttact------gttctgaa---tgtatgccagttagaaaaagggtgcctttataaatttgtgatatatcttttaggtttg

upper sequence: GRMZM2G104377_T03 (Zea mays), 5'ss of exon 17
lower sequence: Vv07s0130g00420.t01 (Vitis vinifera), 5'ss of exon 18
GGAACCAGCTATTTTGGCAATAAAGAGGGAAGGTTACAGCGTTAAGTGTAATGGACAGCGCGGTGTCGTTGTCATGGAGAAATTTCAGCAAGCGATGACCgtatgatttccaaaatcattgtcctcaaaatttctcagtttgtttaatactttatcttctttctttag------gaaaaatgtcttgggatttgtagcctcctttt-
||||||||||| |||||| || |||||||||||||||||| | ||||||| |||||   | ||||  || |||   ||||| |||     ||| |  |  |||||||| |     | ||| | |||||  ||| ||  || |||| | |   ||||  | |    | |      |||  |  || || | | |   |  |       
GGAACCAGCTACTTTGGCCATTAAGAGGGAAGGTTACAGCATCAAGTGTACTGGACCTAGTGGTGCTGTAGTCTCTGAGAAGTTTTCATCAGCCACAAATgtatgattac-----ttatt-tgctcaatttttttctatt-gtttgaaaagctatccgcataaaatggtggtcagaaggacttcctgtggtcttaggaataacagag
















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:     ATGGACAGCGCGGTGTCGTTGTCATGGAGAAATTTCAGCAAGCGATGACC                         ATCAATATCCCATTTGGGCGTCCTACTGAGTTTTCAATTTTGTCTGCTGAT
genomic: ATGGACAGCGCGGTGTCGTTGTCATGGAGAAATTTCAGCAAGCGATGACCgtatgatttc ... aactttgcagATCAATATCCCATTTGGGCGTCCTACTGAGTTTTCAATTTTGTCTGCTGAT
EST: gi|17921450|gb|BM259101.1|BM259101
EST:     ATGGACAGCGCGGTGTCGTTGTCATGGAGAAATTTCAGCAAGCGATGACC                         ATCAATATCCCATTTGGGCGTCCTACTGAGTTTTCAATTTTGTCTGCTGAT
genomic: ATGGACAGCGCGGTGTCGTTGTCATGGAGAAATTTCAGCAAGCGATGACCgtatgatttc ... aactttgcagATCAATATCCCATTTGGGCGTCCTACTGAGTTTTCAATTTTGTCTGCTGAT
EST: gi|5714191|gb|AI944176.1|AI944176
EST:     ATGGCCAGCGCGGTGTCGTTGTCATGGAGAAATTTCAGCAAGCGATGCCC                         ATCAATATCCCATTTGGGCGTCCTACTGAGTTTTCAATTTTGTCTGCTGAT
genomic: ATGGACAGCGCGGTGTCGTTGTCATGGAGAAATTTCAGCAAGCGATGACCgtatgatttc ... aactttgcagATCAATATCCCATTTGGGCGTCCTACTGAGTTTTCAATTTTGTCTGCTGAT
EST: gi|60351693|gb|DN218666.1|DN218666
EST:     ATGGACAGCGCGGTGTCGTTGTCATGGAGAAATTTCAGCAAGCGATGACC                         ATCAATATCCCATTTGGGCGTCCTACTGAGTTTTCAATTTTGTCTGCTGAT
genomic: ATGGACAGCGCGGTGTCGTTGTCATGGAGAAATTTCAGCAAGCGATGACCgtatgatttc ... aactttgcagATCAATATCCCATTTGGGCGTCCTACTGAGTTTTCAATTTTGTCTGCTGAT
EST: gi|60355764|gb|DN222737.1|DN222737
EST:     ATGGACAGCGCGGTGTCGTTGTCATGGAGAAATTTCAGCAAGCGATGACC                         ATCAATATCCCATTTGGGCGTCCTACTGAGTTTTCAATTTTGTCTGCTGAT
genomic: ATGGACAGCGCGGTGTCGTTGTCATGGAGAAATTTCAGCAAGCGATGACCgtatgatttc ... aactttgcagATCAATATCCCATTTGGGCGTCCTACTGAGTTTTCAATTTTGTCTGCTGAT
EST: gi|17921770|gb|BM259421.1|BM259421
EST:     ATGGACAGCGCGGTGTCGTTGTCATGGAGAAATTTCAGCAAGCGATGACC                         ATCAATATCCCATTTGGGCGTCCTACTGAGTTTTCAATTTTGTCTGCTGAT
genomic: ATGGACAGCGCGGTGTCGTTGTCATGGAGAAATTTCAGCAAGCGATGACCgtatgatttc ... aactttgcagATCAATATCCCATTTGGGCGTCCTACTGAGTTTTCAATTTTGTCTGCTGAT
EST: gi|166455526|gb|EG144780.1|EG144780
EST:     GTCATGGAGAAATTTCAGCAAGCGATGACC                         ATCAATATCCCATTTGGGCGTCCTACTGAGTTTTCAATTTTGTCTGCTGAT
genomic: GTCATGGAGAAATTTCAGCAAGCGATGACCgtatgatttc ... aactttgcagATCAATATCCCATTTGGGCGTCCTACTGAGTTTTCAATTTTGTCTGCTGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAACCAGCTATTTTGGCAATAAAGAGGGAAGGTTACAGCGTTAAGTGTAATGGACAGCGCGGTGTCGTTGTCATGGAGAAATTTCAGCAAGCGATGACCgtatgatttccaaaatcattgtcctcaaaatttctcagtttgtttaatactttatcttctttctttaggaaaaatgtcttgggatttgtagcctcctttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aggaaaaa