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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgtttcttataacttgtatatgcagtattgctgtccataaattattacgacttggtgactcttctgatggtttgtatctttgttctttttattcttattacagGAGCCACCCAGAACTCTATCAGGGTTGCCCAA

Basic information

species Zea mays
transcript GRMZM2G135132_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G135132_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g41590.1 (Oryza sativa), 3'ss of exon 3
gtaatgtttcttataacttgtatatgcagtattgctgtccataaattattacgacttggtgactcttctgatggtttgtatctttgttctttttattcttattacagGAGCCACCCAGAACTCTATCAGGGTTGCCCAA
             ||||   | | |   | |     |   | ||  |  | |   ||||||| |||| |||| || |  |||||  || || |    ||| || ||||||||||||||||||||||||||||||| |||
------------gtaacgctt-tgtcttgaacctgagcttacaatatggttcatattggtgaatcttttgattgtcta-atcttcattgttct----cttcttccagGAGCCACCCAGAACTCTATCAGGGTTGCTCAA
















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|211433554|gb|FL254730.1|FL254730
EST:     GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG                         GAGCCACCCAGAACTCTATCAGGGTTGCCCAA
genomic: GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAGgtaatgtttc ... cttattacagGAGCCACCCAGAACTCTATCAGGGTTGCCCAA
EST: gi|211433558|gb|FL254734.1|FL254734
EST:     GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG                         GAGCCACCCAGAACTCTATCAGGGTTGCCCAA
genomic: GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAGgtaatgtttc ... cttattacagGAGCCACCCAGAACTCTATCAGGGTTGCCCAA
EST: gi|211436159|gb|FL254742.1|FL254742
EST:     GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG                         GAGCCACCCAGAACTCTATCAGGGTTGCCCAA
genomic: GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAGgtaatgtttc ... cttattacagGAGCCACCCAGAACTCTATCAGGGTTGCCCAA
EST: gi|211430963|gb|FL254725.1|FL254725
EST:     GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG                         GAGCCACCCAGAACTCTATCAGGGTTGCCCAA
genomic: GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAGgtaatgtttc ... cttattacagGAGCCACCCAGAACTCTATCAGGGTTGCCCAA
EST: gi|87155643|gb|DY400432.1|DY400432
EST:     GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG                         GAGCCACCCAGAACTCTATCAGGGTTGCCCAA
genomic: GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAGgtaatgtttc ... cttattacagGAGCCACCCAGAACTCTATCAGGGTTGCCCAA
EST: gi|211430959|gb|FL254721.1|FL254721
EST:     GTATGATGAGTTGGCTAGCAACAGCAATGNTGAATATATTGCTGGAG                         GAGCCACCCANAACTCTATCAGGGTTGCCCAA
genomic: GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAGgtaatgtttc ... cttattacagGAGCCACCCAGAACTCTATCAGGGTTGCCCAA
EST: gi|211535005|gb|FL000874.1|FL000874
EST:     GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG                         GAGCCACCCAGAACTCTATCAGGGTTGCCCAA
genomic: GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAGgtaatgtttc ... cttattacagGAGCCACCCAGAACTCTATCAGGGTTGCCCAA
EST: gi|211430960|gb|FL254722.1|FL254722
EST:     GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG                         GAGCCACCCAGAACTCTATCAGGGTTGCCCAA
genomic: GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAGgtaatgtttc ... cttattacagGAGCCACCCAGAACTCTATCAGGGTTGCCCAA
EST: gi|211433562|gb|FL254738.1|FL254738
EST:     GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG                         GAGCCACCCAGAACTCTATCAGGGTTGCCCAA
genomic: GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAGgtaatgtttc ... cttattacagGAGCCACCCAGAACTCTATCAGGGTTGCCCAA
EST: gi|211430956|gb|FL254718.1|FL254718
EST:     GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG                         GAGCCACCCAGAACTCTATCAGGGTTGCCCAA
genomic: GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAGgtaatgtttc ... cttattacagGAGCCACCCAGAACTCTATCAGGGTTGCCCAA
EST: gi|211433550|gb|FL254726.1|FL254726
EST:     GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG                         GAGCCACCCAAAACTCTATCAGGGGTGCCCAA
genomic: GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAGgtaatgtttc ... cttattacagGAGCCACCCAGAACTCTATCAGGGTTGCCCAA
EST: gi|211430955|gb|FL254717.1|FL254717
EST:     GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG                         GAGCCACCCAGAACTCTATCAGGGTTGCCCAA
genomic: GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAGgtaatgtttc ... cttattacagGAGCCACCCAGAACTCTATCAGGGTTGCCCAA
EST: gi|26559465|gb|CA831700.1|CA831700
EST:     GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG                         GAGCCACCCAGAACTCTATCAGGGTTGCCCAA
genomic: GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAGgtaatgtttc ... cttattacagGAGCCACCCAGAACTCTATCAGGGTTGCCCAA
EST: gi|32916313|gb|CF021125.1|CF021125
EST:     GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG                         GAGCCACCCAGAACTCTATCAGGGTTGCCCAA
genomic: GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAGgtaatgtttc ... cttattacagGAGCCACCCAGAACTCTATCAGGGTTGCCCAA
EST: gi|211433561|gb|FL254737.1|FL254737
EST:     GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG                         GAGCCACCCAGAACTCTATCAGGGTTGCCCAA
genomic: GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAGgtaatgtttc ... cttattacagGAGCCACCCAGAACTCTATCAGGGTTGCCCAA
EST: gi|211430957|gb|FL254719.1|FL254719
EST:     GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG                         GAGCCACCCAGAACTCTATCAGGGTTGCCCAA
genomic: GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAGgtaatgtttc ... cttattacagGAGCCACCCAGAACTCTATCAGGGTTGCCCAA
EST: gi|22546548|gb|BU098859.1|BU098859
EST:     GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG                         GAGCCACCCAGAACTCTATCAGGGTTGCCCAA
genomic: GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAGgtaatgtttc ... cttattacagGAGCCACCCAGAACTCTATCAGGGTTGCCCAA
EST: gi|211433560|gb|FL254736.1|FL254736
EST:     GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG                         GAGCCACCCAGAACTCTATCAGGGTTGCCCAA
genomic: GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAGgtaatgtttc ... cttattacagGAGCCACCCAGAACTCTATCAGGGTTGCCCAA
EST: gi|211430954|gb|FL254716.1|FL254716
EST:     GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG                         GAGCCACCCAGAACTCTATCAGGGTTGCCCAA
genomic: GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAGgtaatgtttc ... cttattacagGAGCCACCCAGAACTCTATCAGGGTTGCCCAA
EST: gi|211433557|gb|FL254733.1|FL254733
EST:     GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG                         GAGCCACCCAGAACTCTATCAGGGTTGCCCAA
genomic: GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAGgtaatgtttc ... cttattacagGAGCCACCCAGAACTCTATCAGGGTTGCCCAA
EST: gi|31353988|gb|CD438345.1|CD438345
EST:     GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG                         GAGCCACCCAGAACTCTATCAGGGTTGCCCAA
genomic: GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAGgtaatgtttc ... cttattacagGAGCCACCCAGAACTCTATCAGGGTTGCCCAA
EST: gi|211538002|gb|FL000876.1|FL000876
EST:     GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG                         GAGCCACCCAGAACTCTATCAGGGTTGCCCAA
genomic: GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAGgtaatgtttc ... cttattacagGAGCCACCCAGAACTCTATCAGGGTTGCCCAA

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: 47 (upstream exon), 44 (downstream exon)
Score: 84

GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAGgtaatgtttc ... cttattacagGAGCCACCCAGAACTCTATCAGGGTTGCCCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 101

GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAGgtaatgtttc ... cttattacagGAGCCACCCAGAACTCTATCAGGGTTGCCCAA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 208

GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAGgtaatgtttc ... cttattacagGAGCCACCCAGAACTCTATCAGGGTTGCCCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 113

GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAGgtaatgtttc ... cttattacagGAGCCACCCAGAACTCTATCAGGGTTGCCCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacttggtgactcttctgatggtttgtatctttgttctttttattcttattacagGAGCCACCCAGAACTCTATCAGGGTTGCCCAA
             ttctgat  putative branch site (score: 113)
                            tctttgttctttttat  putative PPT
                              tttgttctttttattc  TA-rich tract