Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACACTGCGTAAAAAATACCCGCAATTTGCACAGCAGCATAATAATGTCTACATGCAACAGgttccttctaatcacctacaattaagagtttgtatctactcttgaatttctgtaatgttgttcatcttttttcttttttaaaaaatacag

Basic information

species Zea mays
transcript GRMZM2G017086_T04
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017086_T03 (Zea mays), 5'ss of exon 7
lower sequence: Vv09s0002g02500.t01 (Vitis vinifera), 5'ss of exon 7
ACACTGCGTAAAAAATACCCGCAATTTGCACAGCAGCATAATAATGTCTACATGCAACAGgttcc---ttctaatcacctacaattaagagtttgtatctactcttgaatttct-gtaatgttgttcatcttttttcttttttaaaaaatacag
  | ||||||||||||| || |||||||  |||| |||||||  ||||| |||||||||||||     ||||  |  |   || | |      |||| || || |  |  |  | ||||  |  |||||   ||||     |||  | |     
GTATTGCGTAAAAAATATCCTCAATTTGGCCAGCTGCATAATGGTGTCTTCATGCAACAGgttttcaattcttttgtcacccagtcatagcagtgtaactgctttaaatctgttagtaaattaattcatacattttaaaacttatgacag----
















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|32934266|gb|CF039078.1|CF039078
EST:     AAAAATACCCGCAATTTGCACAGCAGCATAATAATGTCTACATACAACAG                         GATGCAGAAGAATGCTGGACACAGTTGGTGTATACGCTTTCTCAAACTCTT
genomic: AAAAATACCCGCAATTTGCACAGCAGCATAATAATGTCTACATGCAACAGgttccttcta ... aaaaatacagGATGCAGAAGAATGCTGGACACAGTTGGTGTATACGCTTTCTCAAACTCTT
EST: gi|241994792|gb|GR421145.1|GR421145
EST:     AAAAATACCCGCAATTTGCGCAGCAGCATAATAATGTCTACATGCAACAG                         GATGCAGAAGAATGCTGGACACAGTTGGTGTATACGCTTTCTCAAACTCTT
genomic: AAAAATACCCGCAATTTGCACAGCAGCATAATAATGTCTACATGCAACAGgttccttcta ... aaaaatacagGATGCAGAAGAATGCTGGACACAGTTGGTGTATACGCTTTCTCAAACTCTT
EST: gi|32932531|gb|CF037343.1|CF037343
EST:     AAAAATACCCGCAATTTGCACAGCAGCATAATAATGTCTACATGCAACAG                         GATGCAGAAGAATGCTGGACACAGTTGGTGTATACGCTTTCTCAAACTCTT
genomic: AAAAATACCCGCAATTTGCACAGCAGCATAATAATGTCTACATGCAACAGgttccttcta ... aaaaatacagGATGCAGAAGAATGCTGGACACAGTTGGTGTATACGCTTTCTCAAACTCTT
EST: gi|211437528|gb|FK975648.1|FK975648
EST:     AAAAATACCCGCAATTTGCGCAGCAGCATAATAATGTCTACATGCAACAA                         GATGCAGAAGAATGCTGGACACAGTTGGTGTATACGCTTTCTCAAACTCTT
genomic: AAAAATACCCGCAATTTGCACAGCAGCATAATAATGTCTACATGCAACAGgttccttcta ... aaaaatacagGATGCAGAAGAATGCTGGACACAGTTGGTGTATACGCTTTCTCAAACTCTT
EST: gi|32863109|gb|CF002791.1|CF002791
EST:     NNNNNTACCCGCAATTTGCACAGCAGCATAATAATGTCTACATGCAACAG                         GATGCAGAAGAATGCTGGACACAGTTGGTGTATACGCTTTCTCAAACTCTT
genomic: AAAA-TACCCGCAATTTGCACAGCAGCATAATAATGTCTACATGCAACAGgttccttcta ... aaaaatacagGATGCAGAAGAATGCTGGACACAGTTGGTGTATACGCTTTCTCAAACTCTT
EST: gi|32935100|gb|CF039912.1|CF039912
EST:     AAAAATACCCGCAATTTGCACAGCAGCATAATAATGTCTACATGCAACAG                         GATGCAGAAGAATGCTGGACACAGTTGGTGTATACGCTTTC
genomic: AAAAATACCCGCAATTTGCACAGCAGCATAATAATGTCTACATGCAACAGgttccttcta ... aaaaatacagGATGCAGAAGAATGCTGGACACAGTTGGTGTATACGCTTTC
EST: gi|32930082|gb|CF034894.1|CF034894
EST:     AAAAATACCCGCAATTTGCACAGCAGCATAATAATGTCTACATGCAACAG                         GATGCAGAAGGATGCTGGACACAGTTGGTGTATACGCTTTCTCAAACTCTT
genomic: AAAAATACCCGCAATTTGCACAGCAGCATAATAATGTCTACATGCAACAGgttccttcta ... aaaaatacagGATGCAGAAGAATGCTGGACACAGTTGGTGTATACGCTTTCTCAAACTCTT
EST: gi|32945380|gb|CF050199.1|CF050199
EST:     AAAAATACCCGCAATTTGCACAGCAGCATAATAATGTCTACATGCAACAG                         GATGCAGAAGAATGCTGGACACAGTTGGTGTATACGCTTTCTCAAACTCTT
genomic: AAAAATACCCGCAATTTGCACAGCAGCATAATAATGTCTACATGCAACAGgttccttcta ... aaaaatacagGATGCAGAAGAATGCTGGACACAGTTGGTGTATACGCTTTCTCAAACTCTT
EST: gi|32866635|gb|CF006317.1|CF006317
EST:     AAAAATACCCGCAATTTGCACAGCAGCATAATAATGTCTACATGCAACAG                         GATGCAGAAGAATGCTGGACACAGTTGGTGTATACGCTTTCTCAAACTCTT
genomic: AAAAATACCCGCAATTTGCACAGCAGCATAATAATGTCTACATGCAACAGgttccttcta ... aaaaatacagGATGCAGAAGAATGCTGGACACAGTTGGTGTATACGCTTTCTCAAACTCTT
EST: gi|32911302|gb|CF016114.1|CF016114
EST:     AAAAATACCCGCAATTTGCACAGCAGCATAATAATGTCTACATGCAACAG                         GATGCAGAAGAATGCTGGACACAGTTGGTGTATACGCTTTCTCAAACTCTT
genomic: AAAAATACCCGCAATTTGCACAGCAGCATAATAATGTCTACATGCAACAGgttccttcta ... aaaaatacagGATGCAGAAGAATGCTGGACACAGTTGGTGTATACGCTTTCTCAAACTCTT
EST: gi|32932473|gb|CF037285.1|CF037285
EST:     AAAAATACCCGCAATTTGCACAGCAGCATAATAATGTCTACATGCAACAG                         GATGCAGAAGAATGCTGGACACAGTTGGTGTATACGCTTTCTCAAACTCTT
genomic: AAAAATACCCGCAATTTGCACAGCAGCATAATAATGTCTACATGCAACAGgttccttcta ... aaaaatacagGATGCAGAAGAATGCTGGACACAGTTGGTGTATACGCTTTCTCAAACTCTT
EST: gi|74240015|gb|DT647929.1|DT647929
EST:     AAAAATACCCGCAATTTGCACAGCAGCATAATAATGTCTACATGCAACAG                         GATGCAGAAGAATGCTGGACACAGTTGGTGTATACGCTTTCTCAAACTCTT
genomic: AAAAATACCCGCAATTTGCACAGCAGCATAATAATGTCTACATGCAACAGgttccttcta ... aaaaatacagGATGCAGAAGAATGCTGGACACAGTTGGTGTATACGCTTTCTCAAACTCTT
EST: gi|32931528|gb|CF036340.1|CF036340
EST:     AAAAATACCCGCAATTTGCACAGCAGCATAATAATGTCTACATGCAACAG                         GATGCAGAAGAATGCTGGACACAGTTGGTGTATACGCTTTCTCAAACTCTT
genomic: AAAAATACCCGCAATTTGCACAGCAGCATAATAATGTCTACATGCAACAGgttccttcta ... aaaaatacagGATGCAGAAGAATGCTGGACACAGTTGGTGTATACGCTTTCTCAAACTCTT
EST: gi|67017287|gb|CO446036.1|CO446036
EST:     AAAAATACCCGCAATTTGCGCAGCAGCATAATAATGTCTACATGCAACAG                         GATGCAGAAGAATGCTGGACACAGTTGGTGTATACGCTTTCTCAAACTCTT
genomic: AAAAATACCCGCAATTTGCACAGCAGCATAATAATGTCTACATGCAACAGgttccttcta ... aaaaatacagGATGCAGAAGAATGCTGGACACAGTTGGTGTATACGCTTTCTCAAACTCTT
EST: gi|33094903|gb|CF054897.1|CF054897
EST:     AAAAATACCCGCAATTTGCACAGCAGCATAATAATGTCTACATGCAACAG                         GATGCAGAAGAATGCTGGACACAGTTGGTGTATACGCTTTCTCAAACT
genomic: AAAAATACCCGCAATTTGCACAGCAGCATAATAATGTCTACATGCAACAGgttccttcta ... aaaaatacagGATGCAGAAGAATGCTGGACACAGTTGGTGTATACGCTTTCTCAAACT
EST: gi|50332356|gb|CO527482.1|CO527482
EST:     AAAAATACCCGCAATTTGCACAGCAGCATAATAATGTCTACATGCAACAG                         GATGCAGAAGAATGCTGGACACAGTTGGTGTATACGCTTTCTCAAACTCTT
genomic: AAAAATACCCGCAATTTGCACAGCAGCATAATAATGTCTACATGCAACAGgttccttcta ... aaaaatacagGATGCAGAAGAATGCTGGACACAGTTGGTGTATACGCTTTCTCAAACTCTT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 235

ACACTGCGTAAAAAATACCCGCAATTTGCACAGCAGCATAATAATGTCTACATGCAACAGgttccttcta ... aaaaatacagGATGCAGAAGAATGCTGGACACAGTTGGTGTATACGCTTTCTCAAACTCTTACCTCAGATTCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 300

ACACTGCGTAAAAAATACCCGCAATTTGCACAGCAGCATAATAATGTCTACATGCAACAGgttccttcta ... aaaaatacagGATGCAGAAGAATGCTGGACACAGTTGGTGTATACGCTTTCTCAAACTCTTACCTCAGATTCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 203

ACACTGCGTAAAAAATACCCGCAATTTGCACAGCAGCATAATAATGTCTACATGCAACAGgttccttcta ... aaaaatacagGATGCAGAAGAATGCTGGACACAGTTGGTGTATACGCTTTCTCAAACTCTTACCTCAGATTCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 314

ACACTGCGTAAAAAATACCCGCAATTTGCACAGCAGCATAATAATGTCTACATGCAACAGgttccttcta ... aaaaatacagGATGCAGAAGAATGCTGGACACAGTTGGTGTATACGCTTTCTCAAACTCTTACCTCAGATTCAAG