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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttacaccatgcaattggtcatctgctcatcgctctcttttggtatcatgcaattctgcttgactgctacactaataaactgttgacttataatcacactatgtatgagatgactatttggggaaataaacaaaatacagtgcatcatcgttccctaagtgcatgtaagtagattttttcatgcttgcagGTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGAT

Basic information

species Zea mays
transcript GRMZM2G149272_T04
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149272_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os02g42520.3 (Oryza sativa), 3'ss of exon 7
gtatttacaccatgcaattggtcatctgctcatcgctctcttttggtatcatgcaattctgcttgactgctacactaataaactgttgacttataatcacactatgtatgagatgactatttggggaaataaacaaaatacagtgcatcatcgttccctaagtgcatgtaagtagattttttcatgcttgcagGTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGAT----
                                                                                          | |  | | |    || |   | || | | ||||     |  | ||  |  |    |||   | |    |   ||||  |   |  | ||||||| ||| |||||  | ||  || | ||  ||||||| |  |||||||| ||||| || ||||||||| | |||||||| || |||||||| |||||||||||||||    
------------------------------------------------------------------------------------------tcaacagctcctgttgcactgg-tgtccaattggtagtttctaaaatcttgatcatatccctgatatacaca-gcataaagacat-tgttttcatactttcagGTGGTGAAGCGGCTGACCAATGGAGGTGCAGATTACTCTTTTGAGTGCGTGGGTGATACAGGAGTAGTGTCGACTGCACTGCAATCATGTTCTGATGTAA

upper sequence: GRMZM2G149272_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os02g42520.2 (Oryza sativa), 3'ss of exon 7
gtatttacaccatgcaattggtcatctgctcatcgctctcttttggtatcatgcaattctgcttgactgctacactaataaactgttgacttataatcacactatgtatgagatgactatttggggaaataaacaaaatacagtgcatcatcgttccctaagtgcatgtaagtagattttttcatgcttgcagGTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGAT
                                                                                          | |  | | |    || |   | || | | ||||     |  | ||  |  |    |||   | |    |   ||||  |   |  | ||||||| ||| |||||  | ||  || | ||  ||||||| |  |||||||| ||||| || ||||||||| | |||||||| || |||||||| |||||||||||||||
------------------------------------------------------------------------------------------tcaacagctcctgttgcactgg-tgtccaattggtagtttctaaaatcttgatcatatccctgatatacaca-gcataaagacat-tgttttcatactttcagGTGGTGAAGCGGCTGACCAATGGAGGTGCAGATTACTCTTTTGAGTGCGTGGGTGATACAGGAGTAGTGTCGACTGCACTGCAATCATGTTCTGAT
















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|71331902|gb|DR802836.1|DR802836
EST:     GTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAACCTGTTCAACAG                         GTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTG
genomic: GTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAACCTGTTCAACAGgtatttacac ... atgcttgcagGTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTG
EST: gi|211510916|gb|FL028116.1|FL028116
EST:     GTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAACCTGTTCAACAG                         GTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTG
genomic: GTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAACCTGTTCAACAGgtatttacac ... atgcttgcagGTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTG
EST: gi|60401092|gb|DN233899.1|DN233899
EST:     GAATTGAGTGAACCTGTTCAACAG                         GTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTG
genomic: GAATTGAGTGAACCTGTTCAACAGgtatttacac ... atgcttgcagGTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTG
EST: gi|14203856|gb|BG837533.1|BG837533
EST:     GTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAACCTGTTCAACAG                         GTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTG
genomic: GTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAACCTGTTCAACAGgtatttacac ... atgcttgcagGTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTG
EST: gi|148958260|gb|EC904476.2|EC904476
EST:     GTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAACCTGTTCAACAG                         GTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTG
genomic: GTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAACCTGTTCAACAGgtatttacac ... atgcttgcagGTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTG
EST: gi|148963165|gb|EE014137.2|EE014137
EST:     GTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAACCTGTTCAACAG                         GTAATCAAAAGGATTACTGATGGAGGGGT
genomic: GTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAACCTGTTCAACAGgtatttacac ... atgcttgcagGTAATCAAAAGGATTACTGATGGAGGGGT
EST: gi|6095609|gb|AW120276.1|AW120276
EST:     CAGATGAATTGAGTGAACCTGTTCAACAG                         GTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTG
genomic: CAGATGAATTGAGTGAACCTGTTCAACAGgtatttacac ... atgcttgcagGTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTG
EST: gi|29945503|gb|CB815672.1|CB815672
EST:     GTGTCCCGGACTTTATTAACCCAGATGAATTGAGTGAACCTGTTCAACAG                         GTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTG
genomic: GTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAACCTGTTCAACAGgtatttacac ... atgcttgcagGTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTG
EST: gi|5296121|gb|AI782996.1|AI782996
EST:     GTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAACCTGTTCAACAG                         GTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTG
genomic: GTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAACCTGTTCAACAGgtatttacac ... atgcttgcagGTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTG
EST: gi|76921975|gb|DV168787.1|DV168787
EST:     TGTCACGGACTTTATTAACCCAGATGAATTGAGTGAACCTGTTTCA-CAG                         GTAATCAAAAGGATTACTGATGAAGGGGTGGATTACTCATTTGAAT
genomic: TGTCACGGACTTTATTAACCCAGATGAATTGAGTGAACCTGTT-CAACAGgtatttacac ... atgcttgcagGTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAAT
EST: gi|89246725|gb|DY618512.1|DY618512
EST:     GTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAACCTGTTCAACAG                         GTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTG
genomic: GTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAACCTGTTCAACAGgtatttacac ... atgcttgcagGTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTG
EST: gi|5847100|gb|AW000179.1|AW000179
EST:     CCTGTTCAACAG                         GTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTG
genomic: CCTGTTCAACAGgtatttacac ... atgcttgcagGTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTG
EST: gi|6194720|gb|AW146824.1|AW146824
EST:     GTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAACCTGTTCAACAG                         GTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTG
genomic: GTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAACCTGTTCAACAGgtatttacac ... atgcttgcagGTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTG
EST: gi|5895803|gb|AW037049.1|AW037049
EST:     GTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAACCTGTTCAACAG                         GTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTG
genomic: GTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAACCTGTTCAACAGgtatttacac ... atgcttgcagGTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTG
EST: gi|5895869|gb|AW037115.1|AW037115
EST:     GTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAACCTGTTCAACAG                         GTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTG
genomic: GTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAACCTGTTCAACAGgtatttacac ... atgcttgcagGTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTG
EST: gi|71769714|gb|DR967651.1|DR967651
EST:     CTGTTCAACAG                         GTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTG
genomic: CTGTTCAACAGgtatttacac ... atgcttgcagGTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTG
EST: gi|211510917|gb|FL028117.1|FL028117
EST:     GTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAACCTGTTCAACAG                         GTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTG
genomic: GTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAACCTGTTCAACAGgtatttacac ... atgcttgcagGTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTG
EST: gi|5901133|gb|AW042233.1|AW042233
EST:     CGGACTTTATTAACCCAGATGAATTGAGTGAACCTGTTCAACAG                         GTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTG
genomic: CGGACTTTATTAACCCAGATGAATTGAGTGAACCTGTTCAACAGgtatttacac ... atgcttgcagGTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTG
EST: gi|78087855|gb|DV516248.1|DV516248
EST:     CGGACTTTATTAACCCAGATGAATTGAGTGAACCTGTTCAACAG                         GTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTG
genomic: CGGACTTTATTAACCCAGATGAATTGAGTGAACCTGTTCAACAGgtatttacac ... atgcttgcagGTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTG
EST: gi|76016067|gb|DT943237.1|DT943237
EST:     GTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAACCTGTTCAACAG                         GTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTAGAATGTGTG
genomic: GTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAACCTGTTCAACAGgtatttacac ... atgcttgcagGTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTG
EST: gi|91873431|gb|EB403388.1|EB403388
EST:     GTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAACCTGTTCAACAG                         GTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTG
genomic: GTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAACCTGTTCAACAGgtatttacac ... atgcttgcagGTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTG
EST: gi|71325642|gb|DR799508.1|DR799508
EST:     GTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAACCTGTTCAACAG                         GTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTG
genomic: GTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAACCTGTTCAACAGgtatttacac ... atgcttgcagGTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTG
EST: gi|6020665|gb|AW065698.1|AW065698
EST:     GTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAACCTGTTCAACAG                         GTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTG
genomic: GTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAACCTGTTCAACAGgtatttacac ... atgcttgcagGTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTG

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), 45 (downstream exon)
Score: 60

GGAAATCATTTGGTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAACCTGTTCAACAGgtatttacac ... atgcttgcagGTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 133

GGAAATCATTTGGTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAACCTGTTCAACAGgtatttacac ... atgcttgcagGTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 150

GGAAATCATTTGGTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAACCTGTTCAACAGgtatttacac ... atgcttgcagGTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 187

GGAAATCATTTGGTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAACCTGTTCAACAGgtatttacac ... atgcttgcagGTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacagtgcatcatcgttccctaagtgcatgtaagtagattttttcatgcttgcagGTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGAT
                                      ttttttcat  CT-rich tract
                              taagtagatttttt  TA-rich tract