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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatggggtatttttgtttatataaggctttctcattgctttgacgaagcagcgtaaagtgccttccggattcaattgattctttaaattgtttcttacagCTGGCGATTGCGTGCTAATGAGGGCATCTGATGCTTCAAAGCCACCTTATGTGGCAAGAGTTGAGGCAATTGAAGCAGCAGGATCTCGAGGCACCAATGT

Basic information

species Zea mays
transcript GRMZM2G097726_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G097726_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g08880.2 (Oryza sativa), 3'ss of exon 1
-aatggggtatttttgtttatataagg--ctttctcattgctttgacgaagcagcgtaaagtgccttccggattcaattgattctttaaattgtttcttacagCTGGCGATTGCGTGCTAATGAGGGCATCTGATGCTTCAAAGCCACCTTATGTGGCAAGAGTTGAGGCAATTGAAGCAGCAGGATCTCGAGGCACCAATGT
 |||      |||   | |  || | |  |  | ||| |  |||    |||||   |||| |    ||   |      ||||||| | |  |||||||| ||||||| || || ||||||||||||||||||||| | ||||||||||| |||||||||||||||||||| ||||| || ||||| || |||||||| |||||
caataccagctttacatcttgatgatgacccatgtcactattttttataagca---taaaattatctcgatacctgtctgattctcttatatgtttcttgcagCTGGGGACTGTGTGCTAATGAGGGCATCTGATACATCAAAGCCACCCTATGTGGCAAGAGTTGAGGCTATTGAGGCTGCAGGGTCACGAGGCACAAATGT
















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|148940632|gb|EC885443.2|EC885443
EST:     GCGGATCCTCGAGTCCTATACCATCAAGGGTTCGGACAGAGTCATCAAGC                         CTGGCGATTGCGTGCTAATGAGGGCATCTGATGCTTCAAAGCCACCTTATG
genomic: GCGGATCCTCGAGTCCTATACCATCAAGGGTTCGGACAGAGTCATCAAGCgtgagtgccc ... tttcttacagCTGGCGATTGCGTGCTAATGAGGGCATCTGATGCTTCAAAGCCACCTTATG
EST: gi|211072810|gb|FL228287.1|FL228287
EST:     GCGGATCCTCGAGTCCTATACCATCAAGGGTTCGGACAGAGTCATCAAGC                         CTGGCGATTGCGTGCTAATGAGGGCATCTGATGCTTCAAAGCCACCTTATG
genomic: GCGGATCCTCGAGTCCTATACCATCAAGGGTTCGGACAGAGTCATCAAGCgtgagtgccc ... tttcttacagCTGGCGATTGCGTGCTAATGAGGGCATCTGATGCTTCAAAGCCACCTTATG
EST: gi|148942300|gb|EC887317.2|EC887317
EST:     GCGGATCCTCGAGTCCTATACCATCAAGGGTTCGGACAGAGTCATCAAGC                         CTGGCGATTGCGTGCTAATGAGGGCATCTGATGCTTCAAAGCCACCTTATG
genomic: GCGGATCCTCGAGTCCTATACCATCAAGGGTTCGGACAGAGTCATCAAGCgtgagtgccc ... tttcttacagCTGGCGATTGCGTGCTAATGAGGGCATCTGATGCTTCAAAGCCACCTTATG
EST: gi|148941206|gb|EC886093.2|EC886093
EST:     GCGGATCCTCGAGTCCTATACCATCAAGGGTTCGGACAGAGTCATCAAGC                         CTGGCGATTGCGTGCTAATGAGGGCATCTGATGCTTCAAAGCCACCTTATG
genomic: GCGGATCCTCGAGTCCTATACCATCAAGGGTTCGGACAGAGTCATCAAGCgtgagtgccc ... tttcttacagCTGGCGATTGCGTGCTAATGAGGGCATCTGATGCTTCAAAGCCACCTTATG
EST: gi|93282376|gb|EB674640.1|EB674640
EST:     GCGGATCCTCGAGTCCTATACCATCAAGGGTTCGGACAGAGTCATCAAGC                         CTGGCGATTGCGTGCTAATGAGGGCATCTGATGCTTCAAAGCCACCTTATG
genomic: GCGGATCCTCGAGTCCTATACCATCAAGGGTTCGGACAGAGTCATCAAGCgtgagtgccc ... tttcttacagCTGGCGATTGCGTGCTAATGAGGGCATCTGATGCTTCAAAGCCACCTTATG
EST: gi|91874652|gb|EB404609.1|EB404609
EST:     GCGGATCCTCGAGTCCTATACCATCAAGGGTTCGGACAGAGTCATCAAGC                         CTGGCGATTGCGTGCTAATGAGGGCATCTGATGCTTCAAAGCCACCTTATG
genomic: GCGGATCCTCGAGTCCTATACCATCAAGGGTTCGGACAGAGTCATCAAGCgtgagtgccc ... tttcttacagCTGGCGATTGCGTGCTAATGAGGGCATCTGATGCTTCAAAGCCACCTTATG
EST: gi|211075543|gb|FL228301.1|FL228301
EST:     GCGGATCCTCGAGTCCTATACCATCAAGGGTTCGGACAGAGTCATCAAGC                         CTGGCGATTGCGTGCTAATGAGGGCATCTGATGCTTCAAAGCCACCTTATG
genomic: GCGGATCCTCGAGTCCTATACCATCAAGGGTTCGGACAGAGTCATCAAGCgtgagtgccc ... tttcttacagCTGGCGATTGCGTGCTAATGAGGGCATCTGATGCTTCAAAGCCACCTTATG
EST: gi|211075545|gb|FL228303.1|FL228303
EST:     GCGGATCCTCGAGTCCTATACCATCAAGGGTTCGGACAGAGTCATCAAGC                         CTGGCGATTGCGTGCTAATGAGGGCATCTGATGCTTCAAAGCCACCTTATG
genomic: GCGGATCCTCGAGTCCTATACCATCAAGGGTTCGGACAGAGTCATCAAGCgtgagtgccc ... tttcttacagCTGGCGATTGCGTGCTAATGAGGGCATCTGATGCTTCAAAGCCACCTTATG
EST: gi|91872374|gb|EB402331.1|EB402331
EST:     GCGGATCCTCGAGTCCTATACCATCAAGGGTTCGGACAGAGTCATCAAGC                         CTGGCGATTGCGTGCTAATGAGGGCATCTGATGCTTCAAAGCCACCTTATG
genomic: GCGGATCCTCGAGTCCTATACCATCAAGGGTTCGGACAGAGTCATCAAGCgtgagtgccc ... tttcttacagCTGGCGATTGCGTGCTAATGAGGGCATCTGATGCTTCAAAGCCACCTTATG
EST: gi|78082597|gb|DV511009.1|DV511009
EST:     GCGGATCCTCGAGTCCTATACCATCAAGGGTTCGGACAGAGTCATCAAGC                         CTGGCGATTGCGTGCTAATGAGGGCATCTGATGCTTCAAAGCCACCTTATG
genomic: GCGGATCCTCGAGTCCTATACCATCAAGGGTTCGGACAGAGTCATCAAGCgtgagtgccc ... tttcttacagCTGGCGATTGCGTGCTAATGAGGGCATCTGATGCTTCAAAGCCACCTTATG
EST: gi|211072814|gb|FL228291.1|FL228291
EST:     GCGGATCCTCGAGTCCTATACCATCAAGGGTTCGGACAGAGTCATCAAGC                         CTGGCGATTGCGTGCTAATGAGGGCATCTGATGCTTCAAAGCCACCTTATG
genomic: GCGGATCCTCGAGTCCTATACCATCAAGGGTTCGGACAGAGTCATCAAGCgtgagtgccc ... tttcttacagCTGGCGATTGCGTGCTAATGAGGGCATCTGATGCTTCAAAGCCACCTTATG
EST: gi|78074295|gb|DV502729.1|DV502729
EST:     GCGGATCCTCGAGTCCTATACCATCAAGGGTTCGGACAGAGTCATCAAGC                         CTGGCGATTGCGTGCTAATGAGGGCATCTGATGCTTCAAAGCCACCTTATG
genomic: GCGGATCCTCGAGTCCTATACCATCAAGGGTTCGGACAGAGTCATCAAGCgtgagtgccc ... tttcttacagCTGGCGATTGCGTGCTAATGAGGGCATCTGATGCTTCAAAGCCACCTTATG
EST: gi|76927199|gb|DV171172.1|DV171172
EST:     GCGGATCCTCGAGTCCTATACCATCAAGGGTTCGGACAGAGTCATCAAGC                         CTGGCGATTGCGTGCTAATGAGGGCATCTGATGCTTCAAAGCCACCTTATG
genomic: GCGGATCCTCGAGTCCTATACCATCAAGGGTTCGGACAGAGTCATCAAGCgtgagtgccc ... tttcttacagCTGGCGATTGCGTGCTAATGAGGGCATCTGATGCTTCAAAGCCACCTTATG
EST: gi|50336946|gb|CO532072.1|CO532072
EST:     GCGGATCCTCGAGTCCTATACCATCAAGGGTTCGGACAGAGTCATCAAGC                         CTGGCGATTGCGTGCTAATGAGGGCATCTGATGCTTCAAAGCCACCTTATG
genomic: GCGGATCCTCGAGTCCTATACCATCAAGGGTTCGGACAGAGTCATCAAGCgtgagtgccc ... tttcttacagCTGGCGATTGCGTGCTAATGAGGGCATCTGATGCTTCAAAGCCACCTTATG
EST: gi|91872230|gb|EB402187.1|EB402187
EST:     GCGGATCCTCGAGTCCTATACCATCAAGGGTTCGGACAGAGTCATCAAGC                         CTGGCGATTGCGTGCTAATGAGGGCATCTGATGCTTCAAAGCCACCTTATG
genomic: GCGGATCCTCGAGTCCTATACCATCAAGGGTTCGGACAGAGTCATCAAGCgtgagtgccc ... tttcttacagCTGGCGATTGCGTGCTAATGAGGGCATCTGATGCTTCAAAGCCACCTTATG
EST: gi|9733235|gb|BE511987.1|BE511987
EST:     GCGGATCCTCGAGTCCTATACCATCAAGGGTTCGGACAGAGTCATCAAGC                         CTGGCGATTGCGTGCTAATGAGGGCATCTGATGCATCAAAGCCACCTTATG
genomic: GCGGATCCTCGAGTCCTATACCATCAAGGGTTCGGACAGAGTCATCAAGCgtgagtgccc ... tttcttacagCTGGCGATTGCGTGCTAATGAGGGCATCTGATGCTTCAAAGCCACCTTATG
EST: gi|5566990|gb|AI881901.1|AI881901
EST:     GCGGATCCTCGAGTCCTATACCATCAAGGGTTCGGACAGAGTCATCAAGC                         CTGGCGATTGCGTGCTAATGAGGGCATCTGATGCATCAAAGCCACCTTATG
genomic: GCGGATCCTCGAGTCCTATACCATCAAGGGTTCGGACAGAGTCATCAAGCgtgagtgccc ... tttcttacagCTGGCGATTGCGTGCTAATGAGGGCATCTGATGCTTCAAAGCCACCTTATG
EST: gi|148951992|gb|EC897774.2|EC897774
EST:     GCGGATCCTCGAGTCCTATACCATCAAGGGTTCGGACAGAGTCATCAAGC                         CTGGCGATTGCGTGCTAATGAGGGCATCTGATGCTTCAAAGCCACCTTATG
genomic: GCGGATCCTCGAGTCCTATACCATCAAGGGTTCGGACAGAGTCATCAAGCgtgagtgccc ... tttcttacagCTGGCGATTGCGTGCTAATGAGGGCATCTGATGCTTCAAAGCCACCTTATG
EST: gi|148957892|gb|EC904047.2|EC904047
EST:     GCGGATCCTCGAGTCCTATACCATCAAGGGTTCGGACAGAGTCATCAAGC                         CTGGCGATTGCGTGCTAATGAGGGCATCTGATGCTTCAAAGCCACCTTATG
genomic: GCGGATCCTCGAGTCCTATACCATCAAGGGTTCGGACAGAGTCATCAAGCgtgagtgccc ... tttcttacagCTGGCGATTGCGTGCTAATGAGGGCATCTGATGCTTCAAAGCCACCTTATG

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: 308

CCTTCGCCGTCGCGGTCGCGCCCCATGGCGGGGAAGTCGCGACCGCCCAAGCGGATCCTCGAGTCCTATACCATCAAGGGTTCGGACAGAGTCATCAAGCgtgagtgccc ... tttcttacagCTGGCGATTGCGTGCTAATGAGGGCATCTGATGCTTCAAAGCCACCTTATGTGGCAAGAGTTGAGGCAATTGAAGCAGCAGGATCTCGAGGCACCAATGT


Block sizes: 45 (upstream exon), 45 (downstream exon)
Score: 68

CCTTCGCCGTCGCGGTCGCGCCCCATGGCGGGGAAGTCGCGACCGCCCAAGCGGATCCTCGAGTCCTATACCATCAAGGGTTCGGACAGAGTCATCAAGCgtgagtgccc ... tttcttacagCTGGCGATTGCGTGCTAATGAGGGCATCTGATGCTTCAAAGCCACCTTATGTGGCAAGAGTTGAGGCAATTGAAGCAGCAGGATCTCGAGGCACCAATGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 56

CCTTCGCCGTCGCGGTCGCGCCCCATGGCGGGGAAGTCGCGACCGCCCAAGCGGATCCTCGAGTCCTATACCATCAAGGGTTCGGACAGAGTCATCAAGCgtgagtgccc ... tttcttacagCTGGCGATTGCGTGCTAATGAGGGCATCTGATGCTTCAAAGCCACCTTATGTGGCAAGAGTTGAGGCAATTGAAGCAGCAGGATCTCGAGGCACCAATGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 99

CCTTCGCCGTCGCGGTCGCGCCCCATGGCGGGGAAGTCGCGACCGCCCAAGCGGATCCTCGAGTCCTATACCATCAAGGGTTCGGACAGAGTCATCAAGCgtgagtgccc ... tttcttacagCTGGCGATTGCGTGCTAATGAGGGCATCTGATGCTTCAAAGCCACCTTATGTGGCAAGAGTTGAGGCAATTGAAGCAGCAGGATCTCGAGGCACCAATGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagcagcgtaaagtgccttccggattcaattgattctttaaattgtttcttacagCTGGCGATTGCGTGCTAATGAGGGCATCTGATGCTTCAAAGCCACCTTATGTGGCAAGAGTTGAGGCAATTGAAGCAGCAGGATCTCGAGGCACCAATGT
                           aattgat  putative branch site (score: 99)
                                          ttgtttctt  putative PPT
                       attcaattgattcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatggggtatttttgtttatataaggctttctcattgctttgacgaagcagcgtaaagtgccttccggattcaattgattctttaaattgtttcttacagCTGGCGATTGCGTGCTAATGAGGGCATCTGATGCTTCAAAGCCACCTTATGTGGCAAGAGTTGAGGCAATTGAAGCAGCAGGATCTCGAGGCACCAATGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - ttttgtt
- - - - - - - - - - - - - - - - - -tgctttg
- - - - - - - - - - - - - - - - - - - - - - gaagcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgattct