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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTATTTCCAAGCTGAACCCCTTTCCGGCAATGAAGCATCTCGATGTGGCTGGTGGAACAGgtaatatctatccccttctctcattgctttcagatgcaccatagaaataacaaatacacttttttactagtatcataaacattattaattctatcttgat...

Basic information

species Zea mays
transcript GRMZM2G438673_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G438673_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g74520.1 (Oryza sativa), 5'ss of exon 3
GCTTATTTCCAAGCTGAACCCCTTTCCGGCAATGAAGCATCTCGATGTGGCTGGTGGAACAGgtaatatctatccccttctctcattgctttcagatgcaccatagaaataacaaataca-cttttttactagtatcataaacattattaattctatcttgat
||| || || ||||| || || ||||| |  ||||||||||| |||||||||||||||||||||| | |   |  | | |  |||    |  ||     |      |  || ||   | | |||  | ||       |  || |  ||    |   |  | | 
GCTCATCTCAAAGCTTAATCCTTTTCCTGGGATGAAGCATCTAGATGTGGCTGGTGGAACAGgtattcttcctttcttaccttcagcattaacatcctaagatgccatgtaccatgcatagcttactgacccacccgactaaaaacatagccttgctagtca-

upper sequence: GRMZM2G438673_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g74520.2 (Oryza sativa), 5'ss of exon 2
--------------------------------------GCTTATTTCCAAGCTGAACCCCTTTCCGGCAATGAAGCATCTCGATGTGGCTGGTGGAACAGgtaatatctatccccttctctcattgctttcagatgcaccatagaaataacaaataca-cttttttactagtatcataaacattattaattctatcttgat
                                      ||| || || ||||| || || ||||| |  ||||||||||| |||||||||||||||||||||| | |   |  | | |  |||    |  ||     |      |  || ||   | | |||  | ||       |  || |  ||    |   |  | | 
TGTCAGGCTTACCACATTCCTCTTCTCTATTTTTTAAGGCTCATCTCAAAGCTTAATCCTTTTCCTGGGATGAAGCATCTAGATGTGGCTGGTGGAACAGgtattcttcctttcttaccttcagcattaacatcctaagatgccatgtaccatgcatagcttactgacccacccgactaaaaacatagccttgctagtca-

upper sequence: GRMZM2G438673_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA08G22890.1 (Glycine max), 5'ss of exon 3
GCTTATTTCCAAGCTGAACCCCTTTCCGGCAATGAAGCATCTCGATGTGGCTGGTGGAACAGgtaatatctatccccttctctcattgctttcagatgcaccatagaaataacaaatacacttttttactagtatcataaacattattaattctatcttgat--------
| |  ||||||||||||| || ||||| | |||||||||||| |||||||||||||||||||||     || |  | || || |  || |||    ||   | |     ||  | ||    ||      | | |     |     ||| || |  ||| |          
GTTAGTTTCCAAGCTGAATCCGTTTCCTGGAATGAAGCATCTTGATGTGGCTGGTGGAACAGgt-----ctgtttcattgtcactatgttttatactgtgtcttctgtgtagtagat---tttagaagattgcaatgcgagttaaattgatgcagtctggcaaaatatgt

upper sequence: GRMZM2G438673_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA07G03210.2 (Glycine max), 5'ss of exon 2
GCTTATTTCCAAGCTGAACCCCTTTCCGGCAATGAAGCATCTCGATGTGGCTGGTGGAACAGgt--aatatctatccccttctctcattgctttcagatgcaccatagaaataacaaatacacttttttactagtatcataaacattattaattctatcttgat
| |  |||| |||||||| || ||||| | |||||||||||| ||||| |||||||| ||||||    ||  | | | ||    |   | || ||         ||||   | | ||     |  |   | |   ||        |    ||   ||| ||   
GTTAGTTTCGAAGCTGAATCCATTTCCTGGAATGAAGCATCTTGATGTTGCTGGTGGCACAGgtctgttacattttcactatgttttatactgtctttctgtgtataggttttagaagattgcaatgcgagttaaattgatgcagtctggaaaaatatgtta--

upper sequence: GRMZM2G438673_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv16s0039g01590.t01 (Vitis vinifera), 5'ss of exon 4
GCTTATTTCCAAGCTGAACCCCTTTCCGGCAATGAAGCATCTCGATGTGGCTGGTGGAACAGgtaatatctatccccttctctcattgctttcagatgcacca-tagaaataacaaatacacttttttactagtatcataaacattattaattctatcttgat-
| |  | || ||  || | || ||||| | |||||||||||| ||||||||||||||||||||| |    || |   | |  | |||   |  ||         | |   |   |  || |     | | |  | | |   |  | |  ||   |      |  
GTTGGTCTCTAAATTGCATCCATTTCCTGGAATGAAGCATCTTGATGTGGCTGGTGGAACAGgtta-gcataccttgtacaattattatatgtagtctttttgcttggtgttttaggtagatagggtaaatgat-tgagggagctcaacaaggatggggcaaga

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|5296335|gb|AI783105.1|AI783105
EST:     GCTGAACCCCTTTCCGGCAATGAAGCATCTCGATGTGGCTGGTGGAACAG                         GTGATGTTGCTTTTCGTGTACTGGAAAGAATTAAGAGTGTGAGTCACAGAG
genomic: GCTGAACCCCTTTCCGGCAATGAAGCATCTCGATGTGGCTGGTGGAACAGgtaatatcta ... ttgacttcagGTGATGTTGCTTTTCGTGTACTGGAAAGAATTAAGAGTGTGAGTCACAGAG
EST: gi|76012774|gb|DT939944.1|DT939944
EST:     GCTGAACCCCTTTCCGGCAATGAAGCATCTCGATGTGGCTGGTGGAACAG                         GTGATGTTGCTTTTCGTGTACTGGAAAGAATTAAGAGTGTGAGTCACAGAG
genomic: GCTGAACCCCTTTCCGGCAATGAAGCATCTCGATGTGGCTGGTGGAACAGgtaatatcta ... ttgacttcagGTGATGTTGCTTTTCGTGTACTGGAAAGAATTAAGAGTGTGAGTCACAGAG
EST: gi|8367775|gb|BE050720.1|BE050720
EST:     CTGAACCCCTTTCCGGCGATGAAGCATCTCGATGTGGCTGGTGGAACCAG                         GTGATGTTGCTTTTCGTGTACTGGAAAGAATTAAGAGTGTGAGTCACAGA
genomic: CTGAACCCCTTTCCGGCAATGAAGCATCTCGATGTGGCTGGTGGAAC-AGgtaatatcta ... ttgacttcagGTGATGTTGCTTTTCGTGTACTGGAAAGAATTAAGAGTGTGAGTCACAGA
EST: gi|5846957|gb|AW000036.1|AW000036
EST:     GCTGAACCCCTTTCCGGCAATGAAGCATCTCGATGTGGCTGGTGGAACAG                         GTGATGTTGCTTTTCGTGTACTGGAAAGAATTAAGAGTGTGAGTCACAGAG
genomic: GCTGAACCCCTTTCCGGCAATGAAGCATCTCGATGTGGCTGGTGGAACAGgtaatatcta ... ttgacttcagGTGATGTTGCTTTTCGTGTACTGGAAAGAATTAAGAGTGTGAGTCACAGAG
EST: gi|76919519|gb|DV167756.1|DV167756
EST:     GCTGACCCCCTTTCCGGCAATGAAGCATCTCGATGTGGCTGGTGGAACAG                         GTGATGTTGCTTTTCGTGTACTGGAAAGAATTAAGAGTGTGAGTCACAGAG
genomic: GCTGAACCCCTTTCCGGCAATGAAGCATCTCGATGTGGCTGGTGGAACAGgtaatatcta ... ttgacttcagGTGATGTTGCTTTTCGTGTACTGGAAAGAATTAAGAGTGTGAGTCACAGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTTATTTCCAAGCTGAACCCCTTTCCGGCAATGAAGCATCTCGATGTGGCTGGTGGAACAGgtaatatctatccccttctctcattgctttcagatgcaccatagaaataacaaatacacttttttactagtatcataaacattattaattctatcttgat

- - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agaaataa