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

CGTTCCGCGGAGCGCGCACAAGGACTCGCCCGCCGTGGCGGACGTCTGGCCGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggattaacacatctcgttcgtgtgatcgtttttttaaaagattgtgatgcgagcgctagtagtcgatgcagaacataatgtgttccacgttcattt...

Basic information

species Zea mays
transcript GRMZM2G145376_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G145376_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA03G29850.2 (Glycine max), 5'ss of exon 1
CGTTCCGCGGAGCGCGCACAAGGACTCGCCCGCCGTGGCGGACGTCTGGCCGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggattaacacatctcgttcgtgtgatcgttt--ttttaaaagattgtgatgcgagcgctagtagtcgatgcagaacata-atgtgttccacgttcattt-
  | |  | | || |||||||||||||  ||||||| || || |||||||| ||||||||||| ||||| || ||| | ||||| ||||| ||| | |||||  | |||  |   | || ||||     ||  ||   ||| |   |    |||| |     ||     | || | | ||  | |||   | |  |  || |  
GCTCCTCCCGCGCACGCACAAGGACTCCGCCGCCGTCGCCGATGTCTGGCCTTCCACCTCCGCCTTCGACGGCTACTTGTCCGCACTCTCGCCGCTTCAGgt--gaattctccgttttccttcgatccttctattatctttgatgcaagtcgatgtgttgtttaacg--ctattcggcacggagatgctgttcgggaccaatac

upper sequence: GRMZM2G145376_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA19G32740.1 (Glycine max), 5'ss of exon 1
CGTTCCGCGGAGCGCGCACAAGGACTCGCCCGCCGTGGCGGACGTCTGGCCGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggattaacacatctcgttcg--tgtgatcgtttttttaaaagattgtgatgcgagcgctagtagtcgatgcagaacataatg-tgttccacgttcattt
  | |  | | |  |||||||||||||  |||||||  | ||||||||||| ||||||||||| |||||||| ||| | || || ||||| ||| | |||||  | |||  |   | || ||||    |  |  | | ||| | | | |  |||  |   | ||   |    |    |     ||| || | |      ||  
GCTCCTCCCGCGAACGCACAAGGACTCCGCCGCCGTCACCGACGTCTGGCCTTCCACCTCCGCCTTCGATGGCTACTTGTCTGCTCTCTCGCCGCTTCAGgt--gaattctccgttttccttcgatccttgtattctctttgacacaattcgatttgt-tgttaaacgctattaggcacagggatgctgcttcggaccaatac

upper sequence: GRMZM2G145376_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA03G29860.1 (Glycine max), 5'ss of exon 1
CGTTCCGCGGAGCGCGCACAAGGACTCGCCCGCCGTGGCGGACGTCTGGCCGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggattaacacatctcgttcgtgtgatcgtttttttaaaagattgtgatgcga-gcgctagtagtcgatgcagaacataatgtgttccacgttcattt------
  | |  | | || |||||||||||||  ||||||| || || |||||||| ||||||||||| ||||| || ||| | ||||| ||||| ||| | |||||  | |||      | || |||   |  | | |||||         |  || ||| | | || |   || |||     || | |  ||      |  ||       
GCTCCTCCCGCGCACGCACAAGGACTCCGCCGCCGTCGCCGATGTCTGGCCTTCCACCTCCGCCTTCGACGGCTACTTGTCCGCTCTCTCGCCGCTTCAGgt--gaattcttcgttttccttca-atcctagctttttcggtga--cgcaattcgatgtgttattctgcggtgcgc--tattaggcattgaggtgttgttctggagt

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|211288680|gb|FL312631.1|FL312631
EST:     CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAG                         CTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
genomic: CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggatta ... ttttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
EST: gi|148945185|gb|EC890388.2|EC890388
EST:     CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAG                         CTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
genomic: CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggatta ... ttttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
EST: gi|211208734|gb|FL358266.1|FL358266
EST:     CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAG                         CTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
genomic: CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggatta ... ttttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
EST: gi|149071042|gb|EE159445.2|EE159445
EST:     GCCCACCTCCCGCGT-CGATGGGTACCTCTCCGCGCTCTCCCCGATCCAG                         CTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAGGCTGATGAAGAA
genomic: GTCCACCTCC-GCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggatta ... ttttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
EST: gi|211012394|gb|FL319255.1|FL319255
EST:     CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAG                         CTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
genomic: CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggatta ... ttttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
EST: gi|78079827|gb|DV508239.1|DV508239
EST:     CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAG                         CTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
genomic: CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggatta ... ttttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
EST: gi|211347336|gb|FL342021.1|FL342021
EST:     CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAG                         CTTGTTCGCAGCAACAGCCGCCGTTTTATGCTTTCTCAAGCTGATGAAGAA
genomic: CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggatta ... ttttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
EST: gi|211392160|gb|FL368046.1|FL368046
EST:     CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAG                         CTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
genomic: CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggatta ... ttttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
EST: gi|211260626|gb|FL351803.1|FL351803
EST:     CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAG                         CTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
genomic: CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggatta ... ttttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
EST: gi|211089442|gb|FL362867.1|FL362867
EST:     CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAG                         CTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGATGATGAAGAA
genomic: CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggatta ... ttttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
EST: gi|148935831|gb|EC879879.2|EC879879
EST:     CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAG                         CTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
genomic: CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggatta ... ttttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
EST: gi|211158616|gb|FL316326.1|FL316326
EST:     CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAG                         CTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGAT
genomic: CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggatta ... ttttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGAT
EST: gi|211303808|gb|FL321303.1|FL321303
EST:     CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAG                         CTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
genomic: CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggatta ... ttttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
EST: gi|76934101|gb|DV173728.1|DV173728
EST:     CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAG                         CTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
genomic: CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggatta ... ttttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
EST: gi|89762105|gb|DY689855.1|DY689855
EST:     CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAG                         CTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
genomic: CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggatta ... ttttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
EST: gi|148946192|gb|EC891487.2|EC891487
EST:     CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAG                         CTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
genomic: CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggatta ... ttttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
EST: gi|211424273|gb|FL309087.1|FL309087
EST:     CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAG                         CTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
genomic: CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggatta ... ttttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
EST: gi|149011570|gb|EE042404.2|EE042404
EST:     CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAG                         CTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
genomic: CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggatta ... ttttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
EST: gi|211316366|gb|FL341233.1|FL341233
EST:     CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAG                         CTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
genomic: CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggatta ... ttttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
EST: gi|148978503|gb|EE026182.2|EE026182
EST:     CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAG                         CTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
genomic: CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggatta ... ttttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
EST: gi|211263174|gb|FL356041.1|FL356041
EST:     CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAG                         CTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
genomic: CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggatta ... ttttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
EST: gi|211390755|gb|FL310442.1|FL310442
EST:     CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAG                         CTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
genomic: CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggatta ... ttttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA

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: 44 (upstream exon), 39 (downstream exon)
Score: 30

CGTTCCGCGGAGCGCGCACAAGGACTCGCCCGCCGTGGCGGACGTCTGGCCGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggatta ... ttttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAAATTCATCAGTTGTCCTTTCTGCAAAAGCATATGGCGAATATTCTTACTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 52

CGTTCCGCGGAGCGCGCACAAGGACTCGCCCGCCGTGGCGGACGTCTGGCCGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggatta ... ttttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAAATTCATCAGTTGTCCTTTCTGCAAAAGCATATGGCGAATATTCTTACTC


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 37

CGTTCCGCGGAGCGCGCACAAGGACTCGCCCGCCGTGGCGGACGTCTGGCCGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggatta ... ttttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAAATTCATCAGTTGTCCTTTCTGCAAAAGCATATGGCGAATATTCTTACTC


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 50

CGTTCCGCGGAGCGCGCACAAGGACTCGCCCGCCGTGGCGGACGTCTGGCCGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggatta ... ttttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAAATTCATCAGTTGTCCTTTCTGCAAAAGCATATGGCGAATATTCTTACTC