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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcaattttcttctgtttatttgtttatctacgctgtcaaatttatgcgcactattgtatcatgctggtttaatcttgtgaattgcattttttgacacagATGGGCAACAAGGGTGCATTTATTCGCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTG

Basic information

species Zea mays
transcript GRMZM2G126435_T02
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G126435_T02 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os05g11550.1 (Oryza sativa), 3'ss of exon 11
-----------------------------------------------------------gtcaattttcttctgtttatttgtttatctacgctgtcaaatttatgcgcactattgtatcatgctggtttaatcttgtgaattgcattttttgacacagATGGGCAACAAGGGTGCATTTATTCGCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTG
                                                           |  | || | | ||| | | || | |     || | |     |||     | |||   |||||||   ||  ||||||||||||||  |||| || ||||||||| |||||||||||||  ||||| ||||||||||||||| | |||||| |||||    |||||||||| |||
gtttgcgacaatagaactatagttggttgcacaaactaataattgcaccataaggatatggaagttgtttcctggtcaattttatgctcccgatattcttctta-----aatatctaatcatgccttttacatcttgtgaattgcgatttt-gatacagATGGGTAACAAGGGTGCATACATTCGGTTCACAGCTCCAGAACTAAAACCAAATATTTCCTCTTTCTCAGCGGTG

upper sequence: GRMZM2G126435_T02 (Zea mays), 3'ss of exon 10
lower sequence: Vv12s0142g00720.t01 (Vitis vinifera), 3'ss of exon 5
gtcaattttcttctgtttatttgtttatct-acgctgtca-aatttatgcgcactat--tgtatcatgctggtttaatcttgtgaattgcattttttgacacagATGGGCAACAAGGGTGCATTTATTCGCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTG
    ||||||   |  || |   || || | ||    | |  || | |    | |||  || |  |   |   |  | |||| | ||   |||   ||   |||||||||||||||||||| |||||||| ||   ||| |||||  |||| ||| | ||||| || || ||||| |||
----attttcagataattttgcattgattttacatacttatgatgtgttttaattatgatgcaagagattacatataacttgggtatgtgattggctgttgcagATGGGCAACAAGGGTGCTTTTATTCGTTTTGAAGCCCCAGATCTGAAGCCAAACATTGTCACATTTTCAGCAGTG
















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|166684247|gb|EG135448.1|EG135448
EST:     TGATGGAAAGCTTATAACAGTCTTCTCTGCGCCTAATTACTGTGACCAG                         ATGGGCAACAAGGGTGCATTTATTCGCTTCACAGCTCCAGAAATGA
genomic: TGATGGAAAGCTTATAACAGTCTTCTCTGCGCCTAATTACTGTGACCAGgtataggtgt ... tttgacacagATGGGCAACAAGGGTGCATTTATTCGCTTCACAGCTCCAGAAATGA
EST: gi|61118887|gb|DN559848.1|DN559848
EST:     ATGATGGAAAGCTTATAACAGTCTTCTCTGCGCCTAATTACTGTGACCAG                         ATGGGCAACAAGGGTGCATTTATTCGCTTCACAGCTCCAGAAATGAAACCA
genomic: ATGATGGAAAGCTTATAACAGTCTTCTCTGCGCCTAATTACTGTGACCAGgtataggtgt ... tttgacacagATGGGCAACAAGGGTGCATTTATTCGCTTCACAGCTCCAGAAATGAAACCA
EST: gi|211035489|gb|FK976708.1|FK976708
EST:     ATGATGGAAAGCTTATAACAGTCTTCTCTGCGCCTAATTACTGTGACCAG                         ATGGGCAACAAGGGTGCATTTAT
genomic: ATGATGGAAAGCTTATAACAGTCTTCTCTGCGCCTAATTACTGTGACCAGgtataggtgt ... tttgacacagATGGGCAACAAGGGTGCATTTAT
EST: gi|4688476|gb|AI637146.1|AI637146
EST:     ATGATGGAAAGCTTATAACAGTCTTCTCTGCGCCTAATTACTGTGACCAG                         ATGGGCAACAAGGGTGCATTTATTCGCTTCACAGCTCCAGAAATGAAACCA
genomic: ATGATGGAAAGCTTATAACAGTCTTCTCTGCGCCTAATTACTGTGACCAGgtataggtgt ... tttgacacagATGGGCAACAAGGGTGCATTTATTCGCTTCACAGCTCCAGAAATGAAACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcgcactattgtatcatgctggtttaatcttgtgaattgcattttttgacacagATGGGCAACAAGGGTGCATTTATTCGCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTG
                                            ttttgac  putative branch site (score: 3)
                                        catttttt  CT-rich tract
                       tttaatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcaattttcttctgtttatttgtttatctacgctgtcaaatttatgcgcactattgtatcatgctggtttaatcttgtgaattgcattttttgacacagATGGGCAACAAGGGTGCATTTATTCGCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG