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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttctcattttattctacttgcacgccttctataaatagctgcaatcaaaaaaattgcaggattagcatcacgagcttcaatattttcatatttgccatgttgttatgtcactgagtttttctctgcactctttgttagATCGATGAGGGAGTAGTATTTAGGGTCGCAGGTGGTTTGCTGCTTGAACATCCATTGACGCTGCCGTTTGTCGAAGCAGTG

Basic information

species Zea mays
transcript GRMZM2G057056_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G057056_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os11g34770.1 (Oryza sativa), 3'ss of exon 7
---------------------gtatgttctcattttatt--ctacttgc-acgccttctataaatagctgcaatcaaaaa---aattgcaggattagcatcacgagcttcaatattttcatatttgcca-tgttgttatgtcactgagtttttctctgcactcttt--------gttagATCGATGAGGGAGTAGTATTTAGGGTCGCAGGTGGTTTGCTGCTTGAACATCCATTGACGCTGCCGTTTGTCGAAGCAGTG
                      |||||  |   || |||   || |||| |   ||   ||  |||  || |   | |     | ||  |  | || |||||   | | |||| |||  | | |||| | |||| ||||| ||||||  |  |||||  || | ||           ||||||||||||| |||||||||||||||||||||||  || |||||||||||||||||||  | || ||||| |||||||||
gttggcctcgtttattccactctatgtaatatattaattgattatttgctaaatctaacatttataattgtagcaacagtgccagttagaatactatcatcataggatccaatctttaaaaaattgcaaatgtttttatgccactgacctgctctctctacccgtttgaatgtcaacagATCGATGAGGGGGTAGTATTTAGGGTCGCAGGTGGCCTGTTGCTTGAACATCCATTGACATTACCATTTGTTGAAGCAGTG

upper sequence: GRMZM2G057056_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os11g34850.1 (Oryza sativa), 3'ss of exon 7
--------------------------gtatgttctcattttattctacttgcacgccttctataaat--agctgcaat-caaaaaaattgcaggattagcatcacgagcttcaatattttcatat-ttgccatgttgttatgtcactgagtt--tttctctgcactctttgtt------agATCGATGAGGGAGTAGTATTTAGGGTCGCAGGTGGTTTGCTGCTTGAACATCCATTGACGCTGCCGTTTGTCGAAGCAGTG
                           | | || ||   |||||   |        | | ||||  |  ||| ||| | |     |||| |  ||||| |||||   | | ||||||||| | |  ||||  |||| |||||   ||||  |  | ||||| | | |||   |      ||||||||||| | ||||||||||||||||| ||||| ||| |||||||||||||||||||  | || ||||| |||||||||
gttggtctcatttattctactctgtaatttattatctgattatttgccgaatctaacatttatagttgaagcagcagtgctggttaattcctagattatcatcataggatccaatattttaaaaaattgcattgtttttatgcatctgacctgctctctctacccccttgactgtcaacagATCGATGAGAGGGTAGTATTTAGGGTCGCTGGTGGCTTGTTGCTTGAACATCCATTGACATTACCATTTGTTGAAGCAGTG
















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|31664474|gb|CD573407.1|CD573407
EST:     GATATACCAGATGAGGTCATCAAGAGCTTG                         ATCGATGAGGGAGTAGTATTTAGGGTCGCAGGTGGTTTGCTGCTTGAACAT
genomic: GATATACCAGATGAGGTCATCAAGAGCTTGgtatgttctc ... tctttgttagATCGATGAGGGAGTAGTATTTAGGGTCGCAGGTGGTTTGCTGCTTGAACAT
EST: gi|78021738|gb|DV490125.1|DV490125
EST:     CTGTGCAGGTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTG                         ATCGATGAGGGAGTAGTATTTAGGGTCGCAGGTGGTTTGCTGCTTGAACAT
genomic: CTGTGCAGGTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTGgtatgttctc ... tctttgttagATCGATGAGGGAGTAGTATTTAGGGTCGCAGGTGGTTTGCTGCTTGAACAT
EST: gi|32164898|gb|CD670216.1|CD670216
EST:     CTGTGCAGGTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTG                         ATCGATGAGGGAGTAGTATTTAGGGTCGCAGGTGGTTTGCTGCTTGAACAT
genomic: CTGTGCAGGTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTGgtatgttctc ... tctttgttagATCGATGAGGGAGTAGTATTTAGGGTCGCAGGTGGTTTGCTGCTTGAACAT
EST: gi|101393789|gb|EB818827.1|EB818827
EST:     CTGTGCAGGTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTG                         ATCGATGAGGGAGTAGTATTTAGGGTCGCAGGTGGTTTGCTGCTTGAACAT
genomic: CTGTGCAGGTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTGgtatgttctc ... tctttgttagATCGATGAGGGAGTAGTATTTAGGGTCGCAGGTGGTTTGCTGCTTGAACAT
EST: gi|31664475|gb|CD573408.1|CD573408
EST:     CTGTGCAGGTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTG                         ATCGATGAGGGAGTAGTATTTAGGGTCGCAGGTGGTTTGCTGCTTGAACAT
genomic: CTGTGCAGGTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTGgtatgttctc ... tctttgttagATCGATGAGGGAGTAGTATTTAGGGTCGCAGGTGGTTTGCTGCTTGAACAT
EST: gi|32164897|gb|CD670215.1|CD670215
EST:     CTGTGCAGGTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTG                         ATCGATGAGGGAGTAGTATTTAGGGTCGCAGGTGGTTTGCTGCTTGAACAT
genomic: CTGTGCAGGTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTGgtatgttctc ... tctttgttagATCGATGAGGGAGTAGTATTTAGGGTCGCAGGTGGTTTGCTGCTTGAACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcatatttgccatgttgttatgtcactgagtttttctctgcactctttgttagATCGATGAGGGAGTAGTATTTAGGGTCGCAGGTGGTTTGCTGCTTGAACATCCATTGACGCTGCCGTTTGTCGAAGCAGTG
                                tttttctctgcactct  CT-rich tract
                ttgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttctcattttattctacttgcacgccttctataaatagctgcaatcaaaaaaattgcaggattagcatcacgagcttcaatattttcatatttgccatgttgttatgtcactgagtttttctctgcactctttgttagATCGATGAGGGAGTAGTATTTAGGGTCGCAGGTGGTTTGCTGCTTGAACATCCATTGACGCTGCCGTTTGTCGAAGCAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT