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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGAAGTTTCTGCACCTGCGAATGCAGAAGAAGCAAATCGCCCAGACTATGTGTTAAATAAGTACGACTACTTTGGTTATGgtaagacatttcatgtcatgataatttggtttaattatgttcaaactcattctgcatgaaaagatataaaacagtgatgtcttatgtgatttcatttctttaattactgatgctttgcattattttgtag

Basic information

species Zea mays
transcript GRMZM2G344476_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G344476_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os04g47120.1 (Oryza sativa), 5'ss of exon 4
GCTGAAGTTTCTGCACCTGCGAATGCAGAAGAAGCAAATCGCCCAGACTATGTGTTAAATAAGTACGACTACTTTGGTTATGgtaagacatttcatgtcatgataatttggtttaattatgttcaaactcattctgcatgaaaagatataaaaca------gtgatgtcttatgtgatttcatttctttaat-tactgatgctttgcattattttgtag
||||| ||||| || ||||| ||  ||||||||| ||| ||||| |||||||||||||||||||| ||||||||||||||||||||||  | ||||  |||||    |   ||| ||  |  |    ||  || |  || ||   ||||||| ||       | |  |     |    |   |||   || | | || ||  | |||||| ||||||||
GCTGAGGTTTCAGCTCCTGCAAACACAGAAGAAGAAAACCGCCCTGACTATGTGTTAAATAAGTATGACTACTTTGGTTATGgtaagaactatcattacatgacttctgatttttatagtagttc--ctttttttttatcaagt-atataaaccattttttataagatacggagcagctctgtttgcgtactattctaatattctgcattgttttgtag
















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|50337659|gb|CO532785.1|CO532785
EST:     AGCAAATCGCCCAGACTATGTGTTAAATAAGTACGACTACTTTGGTTATG                         GAACTAATAGTTCTGTTCATCAAGTCAATGTTGTTGCACTATCAAAG
genomic: AGCAAATCGCCCAGACTATGTGTTAAATAAGTACGACTACTTTGGTTATGgtaagacatt ... tattttgtagGAACTAATAGTTCTGTTCATCAAGTCAATGTTGTTGCACTATCAAAG
EST: gi|148956464|gb|EC902291.2|EC902291
EST:     AGCAAATCGCCCAGACTATGTGTTAAATAAGTACGACTACTTTGGTTATG                         GAACTAATAGTTCTGTTCATCAAGTCAATGTTGTTGCACTATCAAAG
genomic: AGCAAATCGCCCAGACTATGTGTTAAATAAGTACGACTACTTTGGTTATGgtaagacatt ... tattttgtagGAACTAATAGTTCTGTTCATCAAGTCAATGTTGTTGCACTATCAAAG
EST: gi|74238643|gb|DT646557.1|DT646557
EST:     AGCAAATCGCCCAGACTATGTGTTAAATAAGTACGACTACTTTGGTTATG                         GAACTAATAGTTCTGTTCATCAAGTCAATGTTGTTGCACTATCAAAG
genomic: AGCAAATCGCCCAGACTATGTGTTAAATAAGTACGACTACTTTGGTTATGgtaagacatt ... tattttgtagGAACTAATAGTTCTGTTCATCAAGTCAATGTTGTTGCACTATCAAAG
EST: gi|211119071|gb|FL021982.1|FL021982
EST:     AGCAAATCGCCCAGACTATGTGTTAAATAAGTACGACTACTTTGGTTATG                         GAACTAATAGTTCTGTTCATCAAGTCAATGTTGTTGCACTATCAAAG
genomic: AGCAAATCGCCCAGACTATGTGTTAAATAAGTACGACTACTTTGGTTATGgtaagacatt ... tattttgtagGAACTAATAGTTCTGTTCATCAAGTCAATGTTGTTGCACTATCAAAG
EST: gi|149104205|gb|EE289638.2|EE289638
EST:     AGCAAATCGCCCAGACTATGTGTTAAATAAGTACGACTACTTTGGTTATG                         GAACTAATAGTTCTGTTCATCAAGTCAATGTTGTTGCACTATCAAAG
genomic: AGCAAATCGCCCAGACTATGTGTTAAATAAGTACGACTACTTTGGTTATGgtaagacatt ... tattttgtagGAACTAATAGTTCTGTTCATCAAGTCAATGTTGTTGCACTATCAAAG
EST: gi|148936448|gb|EC880552.2|EC880552
EST:     AGCAAATCGCCCAGACTATGTGTTAAATAAGTACGACTACTTTGGTTATG                         GAACTAATAGTTCTGTTCATCAAGTCAATGTTGTTGCACTATCAAAG
genomic: AGCAAATCGCCCAGACTATGTGTTAAATAAGTACGACTACTTTGGTTATGgtaagacatt ... tattttgtagGAACTAATAGTTCTGTTCATCAAGTCAATGTTGTTGCACTATCAAAG
EST: gi|149112589|gb|EE191373.2|EE191373
EST:     AGCAAATCGCCCAGACTATGTGTTAAATAAGTACGACTACTTTGGTTATG                         GAACTAATAGTTCTGTTCATCAAGTCAATGTTGTTGCACTATCAAAG
genomic: AGCAAATCGCCCAGACTATGTGTTAAATAAGTACGACTACTTTGGTTATGgtaagacatt ... tattttgtagGAACTAATAGTTCTGTTCATCAAGTCAATGTTGTTGCACTATCAAAG
EST: gi|91872284|gb|EB402241.1|EB402241
EST:     AGCAAATCGCCCAGACTATGTGTTAAATAAGTACGACTACTTTGGTTATG                         GAACTAATAGTTCTGTTCATCAAGTCAATGTTGTTGCACTATCAAAG
genomic: AGCAAATCGCCCAGACTATGTGTTAAATAAGTACGACTACTTTGGTTATGgtaagacatt ... tattttgtagGAACTAATAGTTCTGTTCATCAAGTCAATGTTGTTGCACTATCAAAG
EST: gi|50331303|gb|CO526429.1|CO526429
EST:     AGCAAATCGCCCAGACTATGTGTTAAATAAGTACGACTACTTTGGTTATG                         GAACTAATAGTTCTGTTCATCAAGTCAATGTTGTTGCACTATCAAAG
genomic: AGCAAATCGCCCAGACTATGTGTTAAATAAGTACGACTACTTTGGTTATGgtaagacatt ... tattttgtagGAACTAATAGTTCTGTTCATCAAGTCAATGTTGTTGCACTATCAAAG
EST: gi|148958992|gb|EE010517.2|EE010517
EST:     AGCAAATCGCCCAGACTATGTGTTAAATAAGTACGACTACTTTGGTTATG                         GAACTAATAGTTCTGTTCATCAAGTCAATGTTGTTGCACTATCAAAG
genomic: AGCAAATCGCCCAGACTATGTGTTAAATAAGTACGACTACTTTGGTTATGgtaagacatt ... tattttgtagGAACTAATAGTTCTGTTCATCAAGTCAATGTTGTTGCACTATCAAAG
EST: gi|148944150|gb|EC889238.2|EC889238
EST:     AGCAAATCGCCCAGACTATGTGTTAAATAAGTACGACTACTTTGGTTATG                         GAACTAATAGTTCTGTTCATCAAGTCAATGTTGTTGCACTATCAAAG
genomic: AGCAAATCGCCCAGACTATGTGTTAAATAAGTACGACTACTTTGGTTATGgtaagacatt ... tattttgtagGAACTAATAGTTCTGTTCATCAAGTCAATGTTGTTGCACTATCAAAG
EST: gi|4730512|gb|AI649678.1|AI649678
EST:     AGCAAATCGCCCAGACTATGTGTTAAATAAGTACGACTACTTTGGTTATG                         GAACTAATAGTTCTGTTCATCAAGTCAATGTTGTTGCACTATCAAAG
genomic: AGCAAATCGCCCAGACTATGTGTTAAATAAGTACGACTACTTTGGTTATGgtaagacatt ... tattttgtagGAACTAATAGTTCTGTTCATCAAGTCAATGTTGTTGCACTATCAAAG
EST: gi|71315960|gb|DR794668.1|DR794668
EST:     AGCAAATCGCCCAGACTATGTGTTAAATAAGTACGACTACTTTGGTTATG                         GAACTAATAGTTCTGTTCATCAAGTCAATGTTGTTGCACTATCAAAG
genomic: AGCAAATCGCCCAGACTATGTGTTAAATAAGTACGACTACTTTGGTTATGgtaagacatt ... tattttgtagGAACTAATAGTTCTGTTCATCAAGTCAATGTTGTTGCACTATCAAAG
EST: gi|91875931|gb|EB405888.1|EB405888
EST:     AGCAAATCGCCCAGACTATGTGTTAAATAAGTACGACTACTTTGGTTATG                         GAACTAATAGTTCTGTTCATCAAGTCAATGTTGTTGCACTATCAAAG
genomic: AGCAAATCGCCCAGACTATGTGTTAAATAAGTACGACTACTTTGGTTATGgtaagacatt ... tattttgtagGAACTAATAGTTCTGTTCATCAAGTCAATGTTGTTGCACTATCAAAG

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: 34 (upstream exon), 48 (downstream exon)
Score: 65

GCTGAAGTTTCTGCACCTGCGAATGCAGAAGAAGCAAATCGCCCAGACTATGTGTTAAATAAGTACGACTACTTTGGTTATGgtaagacatt ... tattttgtagGAACTAATAGTTCTGTTCATCAAGTCAATGTTGTTGCACTATCAAAG


Block sizes: 35 (upstream exon), 48 (downstream exon)
Score: 67

GCTGAAGTTTCTGCACCTGCGAATGCAGAAGAAGCAAATCGCCCAGACTATGTGTTAAATAAGTACGACTACTTTGGTTATGgtaagacatt ... tattttgtagGAACTAATAGTTCTGTTCATCAAGTCAATGTTGTTGCACTATCAAAG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 69

GCTGAAGTTTCTGCACCTGCGAATGCAGAAGAAGCAAATCGCCCAGACTATGTGTTAAATAAGTACGACTACTTTGGTTATGgtaagacatt ... tattttgtagGAACTAATAGTTCTGTTCATCAAGTCAATGTTGTTGCACTATCAAAG


Block sizes: 36 (upstream exon), 49 (downstream exon)
Score: 63

GCTGAAGTTTCTGCACCTGCGAATGCAGAAGAAGCAAATCGCCCAGACTATGTGTTAAATAAGTACGACTACTTTGGTTATGgtaagacatt ... tattttgtagGAACTAATAGTTCTGTTCATCAAGTCAATGTTGTTGCACTATCAAAG