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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGGgtgagaaatctgccaactcttctgtgctctttttacccaacctaccttgaccctgttcaattaacagaatttcttgtgttgcag

Basic information

species Zea mays
transcript GRMZM2G009876_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G009876_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os07g47580.2 (Oryza sativa), 5'ss of exon 7
------------------------------------------------GTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGGgtgagaaatctgccaactcttctg-tgctctttttacccaac--ctaccttgaccctgttcaattaacagaatttcttgtgttgcag
                                                || || || ||||| |||||||||||||| || ||||||||||||||||||||| ||  |||||   | | ||||| |  | ||  |    |||  || ||| || | ||||| || ||      |||||||  |||||
AGACATCCTGCTTTTACCTGTTGGTGCTTACAGACTTTATCTTTTCAGGTGAACGTTAGTGAACTTGGTCTGGTAACCCCTGCTGGAAAAGTTGTTTGGGgtaaggcatctgttgaatgttctgcttattttgctttttaacttctccctggaacttgttccataaaacagcgttcttgtcgtgcag

upper sequence: GRMZM2G009876_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os07g47580.1 (Oryza sativa), 5'ss of exon 8
GTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGGgtgagaaatctgccaactcttctg-tgctctttttacccaac--ctaccttgaccctgttcaattaacagaatttcttgtgttgcag
|| || || ||||| |||||||||||||| || ||||||||||||||||||||| ||  |||||   | | ||||| |  | ||  |    |||  || ||| || | ||||| || ||      |||||||  |||||
GTGAACGTTAGTGAACTTGGTCTGGTAACCCCTGCTGGAAAAGTTGTTTGGGgtaaggcatctgttgaatgttctgcttattttgctttttaacttctccctggaacttgttccataaaacagcgttcttgtcgtgcag

upper sequence: GRMZM2G009876_T01 (Zea mays), 5'ss of exon 8
lower sequence: EFJ37687 (Selaginella moellendorffii), 5'ss of exon 8
GTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGGgtgagaaatctgccaactcttctgtgctctttttacccaacctaccttgaccctgttcaattaacagaatttcttgtgttgcag
|||||||| || ||||| || || |||||||| |||||||||||||| |||||| |||  | || | |  |   ||    | ||||       ||| ||| || |   |    |  |||                 
GTAAATGTTAGCGAGCTCGGACTCGTAACTCCTGCTGGAAAAGTTGTATGGGgtaagat-tttggcgatccgattgaaaacgttttg------ctaactttactcatcttgcctctcag-----------------

upper sequence: GRMZM2G009876_T01 (Zea mays), 5'ss of exon 8
lower sequence: EFJ15002 (Selaginella moellendorffii), 5'ss of exon 8
GTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGGgtgagaaatctgccaactcttctgtgctctttttacccaacctaccttgaccctgttcaattaacagaatttcttgtgttgcag
|||||||| || ||||| || || |||||||| |||||||||||||| |||||| |||  | || | |  |   ||    | ||||       ||| ||| || |   |    |  |||                 
GTAAATGTTAGCGAGCTCGGACTCGTAACTCCTGCTGGAAAAGTTGTATGGGgtaagat-tttggcgatacgattgaaaacgttttg------ctaactttactcatcttgcctctcag-----------------

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|6993959|gb|AW453173.1|AW453173
EST:     GGTAACTCCCGCTGGAAAAGTTGTTTGGG                         GGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATG
genomic: GGTAACTCCCGCTGGAAAAGTTGTTTGGGgtgagaaatc ... tgtgttgcagGGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATG
EST: gi|78027636|gb|DV496023.1|DV496023
EST:     AAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGG                         GGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATG
genomic: AAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGGgtgagaaatc ... tgtgttgcagGGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATG
EST: gi|24764520|gb|CA399684.1|CA399684
EST:     AAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGG                         GGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATG
genomic: AAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGGgtgagaaatc ... tgtgttgcagGGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATG
EST: gi|60344144|gb|DN211117.1|DN211117
EST:     AAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGG                         GGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATG
genomic: AAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGGgtgagaaatc ... tgtgttgcagGGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATG
EST: gi|78087299|gb|DV515692.1|DV515692
EST:     AAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGG                         GGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATG
genomic: AAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGGgtgagaaatc ... tgtgttgcagGGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATG
EST: gi|78025817|gb|DV494204.1|DV494204
EST:     AAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGG                         GGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATG
genomic: AAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGGgtgagaaatc ... tgtgttgcagGGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATG
EST: gi|74232800|gb|DT640714.1|DT640714
EST:     AAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGGAAAGTTGTTTGGG                         GGAAAAATGCTCAAGTTACAAACAACCC
genomic: AAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGGgtgagaaatc ... tgtgttgcagGGAAATATGCTCAAGTTACAAACAACCC
EST: gi|37375342|gb|CF624101.1|CF624101
EST:     AAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGG                         GGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATG
genomic: AAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGGgtgagaaatc ... tgtgttgcagGGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATG
EST: gi|71764848|gb|DR962785.1|DR962785
EST:     AAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGG                         GGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATG
genomic: AAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGGgtgagaaatc ... tgtgttgcagGGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATG
EST: gi|74232799|gb|DT640713.1|DT640713
EST:     AAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGG                         GGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATG
genomic: AAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGGgtgagaaatc ... tgtgttgcagGGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATG
EST: gi|211358243|gb|FL402304.1|FL402304
EST:     AAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGG                         GGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATG
genomic: AAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGGgtgagaaatc ... tgtgttgcagGGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATG
EST: gi|148953095|gb|EE152575.2|EE152575
EST:     ATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGGAAAAGT-GTTTTGGG                         GGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAAT
genomic: ATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGG-AAAAGTTGTTT-GGGgtgagaaatc ... tgtgttgcagGGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAAT
EST: gi|13515938|gb|BG518214.1|BG518214
EST:     AAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGG                         GGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCNNNN
genomic: AAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGGgtgagaaatc ... tgtgttgcagGGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATG
EST: gi|29946116|gb|CB815987.1|CB815987
EST:     AAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGG                         GGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATG
genomic: AAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGGgtgagaaatc ... tgtgttgcagGGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATG
EST: gi|12970034|gb|BG266781.1|BG266781
EST:     AAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGG                         GGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATG
genomic: AAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGGgtgagaaatc ... tgtgttgcagGGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATG
EST: gi|211251420|gb|FL479566.1|FL479566
EST:     AAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGG                         GGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATG
genomic: AAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGGgtgagaaatc ... tgtgttgcagGGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATG
EST: gi|16379907|gb|BI993212.1|BI993212
EST:     AAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGG                         GGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATG
genomic: AAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGGgtgagaaatc ... tgtgttgcagGGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATG
EST: gi|4621612|gb|AI612445.1|AI612445
EST:     AAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGG                         GGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATG
genomic: AAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGGgtgagaaatc ... tgtgttgcagGGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATG
EST: gi|60399997|gb|DN232804.1|DN232804
EST:     AAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGG                         GGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATG
genomic: AAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGGgtgagaaatc ... tgtgttgcagGGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATG
EST: gi|113653950|gb|DW814543.1|DW814543
EST:     GTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGG                         GGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATG
genomic: GTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGGgtgagaaatc ... tgtgttgcagGGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATG
EST: gi|5688512|gb|AI941527.1|AI941527
EST:     AAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGG                         GGAAATATGCTCAAGTTACAACCAACCCGGAGAACGATGGCTGTATCAATG
genomic: AAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGGgtgagaaatc ... tgtgttgcagGGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATG
EST: gi|4621611|gb|AI612444.1|AI612444
EST:     AAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGG                         GGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATG
genomic: AAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGGgtgagaaatc ... tgtgttgcagGGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATG
EST: gi|78026982|gb|DV495369.1|DV495369
EST:     AAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGG                         GGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATG
genomic: AAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGGgtgagaaatc ... tgtgttgcagGGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATG
EST: gi|78026391|gb|DV494778.1|DV494778
EST:     AAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGG                         GGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATG
genomic: AAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGGgtgagaaatc ... tgtgttgcagGGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATG
EST: gi|4776075|gb|AI665078.1|AI665078
EST:     AAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGG                         GGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATG
genomic: AAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGGgtgagaaatc ... tgtgttgcagGGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATG
EST: gi|6865237|gb|AW360587.1|AW360587
EST:     GGTAACTCCCGCTGGAAAAGTTGTTTGGG                         GGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATG
genomic: GGTAACTCCCGCTGGAAAAGTTGTTTGGGgtgagaaatc ... tgtgttgcagGGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATG
EST: gi|71319945|gb|DR796736.1|DR796736
EST:     AAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGG                         GGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATG
genomic: AAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGGgtgagaaatc ... tgtgttgcagGGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATG

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), 48 (downstream exon)
Score: 153

GTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGGgtgagaaatc ... tgtgttgcagGGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATGCTGTTTTGCTAGTGTAGAGCCATAGTGAGATTTTGTTGATGGTGGTGAA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 91

GTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGGgtgagaaatc ... tgtgttgcagGGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATGCTGTTTTGCTAGTGTAGAGCCATAGTGAGATTTTGTTGATGGTGGTGAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 59

GTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGGgtgagaaatc ... tgtgttgcagGGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATGCTGTTTTGCTAGTGTAGAGCCATAGTGAGATTTTGTTGATGGTGGTGAA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 60

GTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGGgtgagaaatc ... tgtgttgcagGGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATGCTGTTTTGCTAGTGTAGAGCCATAGTGAGATTTTGTTGATGGTGGTGAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGGgtgagaaatctgccaactcttctgtgctctttttacccaacctaccttgaccctgttcaattaacagaatttcttgtgttgcag

- - - - - - GAGCTT
- - - - - - - - - - - - - - - -  GCTGGA