Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctgctatactcttatacatgttgcctaattttctggatataagtttccaccttataatgcaaattactgaaaccagGCTGTGGAGAAGAAGTTCCGAAATCGTGTGAACAGGTATGTGGGCCTATGGTGCTGTGTGGAGTTCCGTGAAATTGGTCACATATATTATGACATGTACT

Basic information

species Zea mays
transcript GRMZM2G011912_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G011912_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g38930.1 (Oryza sativa), 3'ss of exon 9
gtaagctgctatactcttatacatgttgcctaattttctggatataagtttccaccttataatgcaaattactgaaaccagGCTGTGGAGAAGAAGTTCCGAAATCGTGTGAACAGGTATGTGGGCCTATGGTGCTGTGTGGAGTTCCGTGAAATTGGTCACATATATTATGACATGTACT
||||||| | |  ||   | |  | |   ||| ||  ||| ||| |||  | ||  |  |||    | ||  | ||||||||||||||| | ||| || || ||||| || || || |||||||||||||||||||||||| || |||||||||| || ||||||||||||||||||||||
gtaagcttccagtcttcaacaattttgtgctagtt--ctgaataaaaggatgca--tagtaacttta-ttgtttaaaccagGCTGTGGACACGAAATTTCGGAATCGAGTAAAGAGATATGTGGGCCTATGGTGCTGTGTGCAGCTCCGTGAAATAGGGCACATATATTATGACATGTACT

upper sequence: GRMZM2G011912_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA16G08350.2 (Glycine max), 3'ss of exon 11
-------------------------------------gtaagctgctatactcttatacat-gttgcctaattttctggatataa----gtttccaccttataatgcaaattactgaaa--ccagGCTGTGGAGAAGAAGTTCCGAAATCGTGTGAACAGGTATGTGGGCCTATGGTGCTGTGTGGAGTTCCGTGAAATTGGTCACATATATTATGACATGTACT
                                      |  |  | | |||| |  |   |      | || |     || | ||    ||| | |  |  | |||| |   | | |    |||||    |||  | || ||| |||||||||| ||  ||||||||||| ||||||||||||||      |       |||||| ||||||||||| |||||||
gttttactgacaaggcagggacattttgctttttttcatttgaagttttactttgttgagttagcatccaactacaaagaaaaaaaaatgttactatgtgctgatgccatgcatttattttccagGAAAGGGAAGAAAAATTCAGAAATCGTGTTAAGCGGTATGTGGGCATATGGTGCTGTGTGCCAGATCACAGTCCTGGTCATATATATTATGATATGTACT

upper sequence: GRMZM2G011912_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA16G08350.1 (Glycine max), 3'ss of exon 12
-----------------------gtaagctgctatactcttatacat-gttgcctaattttctggatataa----gtttccaccttataatgcaaattactgaaa--ccagGCTGTGGAGAAGAAGTTCCGAAATCGTGTGAACAGGTATGTGGGCCTATGGTGCTGTGTGGAGTTCCGTGAAATTGGTCACATATATTATGACATGTACT
                        |  |  | | |||| |  |   |      | || |     || | ||    ||| | |  |  | |||| |   | | |    |||||    |||  | || ||| |||||||||| ||  ||||||||||| ||||||||||||||      |       |||||| ||||||||||| |||||||
gcagggacattttgctttttttcatttgaagttttactttgttgagttagcatccaactacaaagaaaaaaaaatgttactatgtgctgatgccatgcatttattttccagGAAAGGGAAGAAAAATTCAGAAATCGTGTTAAGCGGTATGTGGGCATATGGTGCTGTGTGCCAGATCACAGTCCTGGTCATATATATTATGATATGTACT

upper sequence: GRMZM2G011912_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv02s0087g00740.t01 (Vitis vinifera), 3'ss of exon 13
------------------------gtaagctgctatactcttatacatgtt--gcctaattttctggatataagtttccaccttataatgcaaattactgaaaccagGCTGTGGAGAAGAAGTTCCGAAATCGTGTGAACAGGTATGTGGGCCTATGGTGCTGTGTGGAGTTCCGTGAAATTGGTCACATATATTATGACATGTACT
                         |    |  || | |   | | || ||  |   | |  ||      | |        | |   ||||||| || ||  | |||     |||| | || ||| |||| || |||||  ||||||| ||  | |||||||| ||| ||    ||||    |||||||||||||||||||||||||
gcaagtttcactctccttcccttatttcattattagagtgacaaatatattatgttcagtaatcatatgctgacaagaagtcgtgccatgcaaaata-tgtgatcagAAAACGGAGGAAAAATTCAGAAAACGGGTGAAGCGGTATGTTGGTATTTGGTGCTGCGTGAAGGGTAGTGATCCGGGTCACATATATTATGACATGTACT

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|71756475|gb|DR954412.1|DR954412
EST:     TCATACAATTCTCATCTATGGTTGATGCCTTCGGTGGTTTTGCTGATGCA                         GCTGTGGAGAAGAAGTTCCGAAATCGTGTGAACAGGTATGTGGGCCTATGG
genomic: TCATACAATTCTCATCTATGGTTGATGCCTTCGGTGGTTTTGCTGATGCAgtaagctgct ... ctgaaaccagGCTGTGGAGAAGAAGTTCCGAAATCGTGTGAACAGGTATGTGGGCCTATGG
EST: gi|71435517|gb|DR816567.1|DR816567
EST:     TCATACAATTCTCATCTATGGTTGATGCCTTCGGTGGTTTTGCTGATGCA                         GCTGTGGAGAAGAAGTTCCGAAATCGTGTGAACAGGTATGTGGGCCTATGG
genomic: TCATACAATTCTCATCTATGGTTGATGCCTTCGGTGGTTTTGCTGATGCAgtaagctgct ... ctgaaaccagGCTGTGGAGAAGAAGTTCCGAAATCGTGTGAACAGGTATGTGGGCCTATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcctaattttctggatataagtttccaccttataatgcaaattactgaaaccagGCTGTGGAGAAGAAGTTCCGAAATCGTGTGAACAGGTATGTGGGCCTATGGTGCTGTGTGGAGTTCCGTGAAATTGGTCACATATATTATGACATGTACT
 gcctaat  putative branch site (score: 3)
                              ttataatgcaaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctgctatactcttatacatgttgcctaattttctggatataagtttccaccttataatgcaaattactgaaaccagGCTGTGGAGAAGAAGTTCCGAAATCGTGTGAACAGGTATGTGGGCCTATGGTGCTGTGTGGAGTTCCGTGAAATTGGTCACATATATTATGACATGTACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG