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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttcttgtcatgccttttgtttccatacatgcatacttcacatatcctattcccttctattcatttgcatttccaacttgctagGGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTGTCTACTCATTATGCATTTCTTCTATCCGGAAGAACACTGAAGGGATCTA

Basic information

species Zea mays
transcript GRMZM2G149272_T04
intron # 7
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 8
lower sequence: LOC_Os02g42520.2 (Oryza sativa), 3'ss of exon 8
gtaatttcttgtcatgccttttgtttccatacatgcatacttcacatatcctattcccttctattcatttgcatttccaacttgctagGGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTGTCTACTCATTATGCATTTCTTCTATCCGGAAGAACACTGAAGGGATCTA
||||||| |  ||   | ||   || |  ||||     || |    |  ||   |   || | |||  |    |||    |||  |||||||||||  | ||||||||||||||  | ||||||| ||| | ||| || ||| ||||||||||| | ||||| || ||||||||| ||||||| ||| 
gtaatttttattc---ctttccattgcactacaattccacctattctgcccagatatattatcttc--tcatgttttggtcttcttagGGTTGGGGGCTGACTGTAACTCTTGGTGTGCCAAAAGCAAAGCCAGAGGTTTCTGCTCATTATGCACTACTTCTGTCTGGAAGAACATTGAAGGGGTCTT
















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:     GTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGAT                         GGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTG
genomic: GTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGATgtaatttctt ... aacttgctagGGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTG
EST: gi|211510916|gb|FL028116.1|FL028116
EST:     GTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGAT                         GGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTG
genomic: GTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGATgtaatttctt ... aacttgctagGGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTG
EST: gi|6342730|gb|AW165554.1|AW165554
EST:     TCCACTGCACTTCAATCATGTTCTGAT                         GGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTG
genomic: TCCACTGCACTTCAATCATGTTCTGATgtaatttctt ... aacttgctagGGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTG
EST: gi|60401092|gb|DN233899.1|DN233899
EST:     GTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGAT                         GGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTG
genomic: GTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGATgtaatttctt ... aacttgctagGGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTG
EST: gi|14203856|gb|BG837533.1|BG837533
EST:     GTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGAT                         GGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTG
genomic: GTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGATgtaatttctt ... aacttgctagGGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTG
EST: gi|6095609|gb|AW120276.1|AW120276
EST:     GTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGAT                         GGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTG
genomic: GTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGATgtaatttctt ... aacttgctagGGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTG
EST: gi|29945503|gb|CB815672.1|CB815672
EST:     GTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGAT                         GGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTG
genomic: GTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGATgtaatttctt ... aacttgctagGGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTG
EST: gi|5296121|gb|AI782996.1|AI782996
EST:     GTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGAT                         GGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTG
genomic: GTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGATgtaatttctt ... aacttgctagGGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTG
EST: gi|89246725|gb|DY618512.1|DY618512
EST:     GTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGAT                         GGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTG
genomic: GTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGATgtaatttctt ... aacttgctagGGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTG
EST: gi|67012049|gb|CO440798.1|CO440798
EST:     TCATGTTCTGAT                         GGTTGGGGAGTCACTGTAACTCTTGGCTTACCAAAAGGAAAACAAGAAGTG
genomic: TCATGTTCTGATgtaatttctt ... aacttgctagGGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTG
EST: gi|91874802|gb|EB404759.1|EB404759
EST:     GTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGAT                         GGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTG
genomic: GTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGATgtaatttctt ... aacttgctagGGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTG
EST: gi|5847100|gb|AW000179.1|AW000179
EST:     GTGTGGGTGATTCTGGAGTAGTCTCCCCTGCACTTCAATCATGTTCTGAT                         GGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTG
genomic: GTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGATgtaatttctt ... aacttgctagGGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTG
EST: gi|6194720|gb|AW146824.1|AW146824
EST:     GTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGAT                         GGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTG
genomic: GTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGATgtaatttctt ... aacttgctagGGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTG
EST: gi|5895803|gb|AW037049.1|AW037049
EST:     GTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGAT                         GGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAA-CTAGAA-TG
genomic: GTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGATgtaatttctt ... aacttgctagGGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTG
EST: gi|5895869|gb|AW037115.1|AW037115
EST:     GTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGAT                         GGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTG
genomic: GTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGATgtaatttctt ... aacttgctagGGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTG
EST: gi|71769714|gb|DR967651.1|DR967651
EST:     GTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGAT                         GGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTG
genomic: GTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGATgtaatttctt ... aacttgctagGGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTG
EST: gi|211510917|gb|FL028117.1|FL028117
EST:     GTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGAT                         GGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTG
genomic: GTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGATgtaatttctt ... aacttgctagGGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTG
EST: gi|71762504|gb|DR960441.1|DR960441
EST:     GTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGAT                         GGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTG
genomic: GTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGATgtaatttctt ... aacttgctagGGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTG
EST: gi|5901133|gb|AW042233.1|AW042233
EST:     GTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGAT                         GGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGGG
genomic: GTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGATgtaatttctt ... aacttgctagGGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTG
EST: gi|5922168|gb|AW055438.1|AW055438
EST:     GTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGAT                         GGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTG
genomic: GTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGATgtaatttctt ... aacttgctagGGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTG
EST: gi|76016067|gb|DT943237.1|DT943237
EST:     GTGTGGGTGATTCTGGAGTAGTTTCCACTGCACTTCAATCATGTTCTGAT                         GGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTG
genomic: GTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGATgtaatttctt ... aacttgctagGGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTG
EST: gi|211322359|gb|FL445870.1|FL445870
EST:     CACTGCACTTCAATCATGTTCTGAT                         GGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTG
genomic: CACTGCACTTCAATCATGTTCTGATgtaatttctt ... aacttgctagGGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTG
EST: gi|71325642|gb|DR799508.1|DR799508
EST:     GTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGAT                         GGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTG
genomic: GTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGATgtaatttctt ... aacttgctagGGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTG
EST: gi|6020665|gb|AW065698.1|AW065698
EST:     GTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGAT                         GGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTG
genomic: GTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGATgtaatttctt ... aacttgctagGGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTG

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), 47 (downstream exon)
Score: 67

GTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGATgtaatttctt ... aacttgctagGGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTGTCTACTCATTATGCATTTCTTCTATCCGGAAGAACACTGAAGGGATCTA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 102

GTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGATgtaatttctt ... aacttgctagGGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTGTCTACTCATTATGCATTTCTTCTATCCGGAAGAACACTGAAGGGATCTA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 126

GTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGATgtaatttctt ... aacttgctagGGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTGTCTACTCATTATGCATTTCTTCTATCCGGAAGAACACTGAAGGGATCTA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 159

GTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGATgtaatttctt ... aacttgctagGGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTGTCTACTCATTATGCATTTCTTCTATCCGGAAGAACACTGAAGGGATCTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcatacttcacatatcctattcccttctattcatttgcatttccaacttgctagGGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTGTCTACTCATTATGCATTTCTTCTATCCGGAAGAACACTGAAGGGATCTA
                            tattcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatttcttgtcatgccttttgtttccatacatgcatacttcacatatcctattcccttctattcatttgcatttccaacttgctagGGTTGGGGAGTAACTGTAACTCTTGGCTTACCAAAAGGAAAACTAGAAGTGTCTACTCATTATGCATTTCTTCTATCCGGAAGAACACTGAAGGGATCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG