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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatctgttttgtgtacccttttgatttccctaatgaattgtatttgtatttttctaatatatgttcatctgcatggttctgaataccttcgtcgcagAGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGACAGACAGAAACGTGAACAACAACGAGAAGAGAAGGAGCTGGCAAAAATTG

Basic information

species Zea mays
transcript GRMZM2G075551_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G075551_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os04g02500.1 (Oryza sativa), 3'ss of exon 4
-------------------------------------gtaatctgttttgtgtacccttttgatttcccta-atgaattgtatttgtattttt--ctaatatatgttcatctgcatggttctgaatacct--------tcgtcgcagAGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGT---CGAGATGACAGACAGAAACGTGAACAACAACGAGAAGAGAAGGAGCTGGCAAAAATTG
                                      |    | | || |||    | | | |   | || ||  |||     |  | | ||   || ||  ||||||     ||  ||||||  |  |        |     |||||||| |||||||||| ||||||||| ||||||||  | ||    || |||||||| ||||||||||| || |||||||||||||||||||||||||||    
gtaatgtgtttacttggtgcagcgaacttctcttctactgccttttcttttgtgaagtatgggtgcacatacatatattcccccttcactcttacatattaattgttcaggactatatttctgataagttcactgtggttacaacagAGGTTCAAGGAAATGAAAGAAATGCAAAGCAGCAGCAGCAGCAGCCGTGATGACAGGCAGAAACGTGAGCAGCAACGAGAAGAGAAGGAGCTGGCAAAAT---

upper sequence: GRMZM2G075551_T03 (Zea mays), 3'ss of exon 4
lower sequence: Vv14s0060g00320.t01 (Vitis vinifera), 3'ss of exon 6
gtaatctgttttgtgtaccct------tttgatttccctaatgaattgtatttgtatttttctaatatatgttcatctgcatggttctgaatacct-tcgtcgcagAGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGACAGACAGAAACGTGAACAACAACGAGAAGAGAAGGAGCTGGCAAAAATTG---
|| |  || ||| | ||| ||      |||  ||   |     |||| | |||| | ||      | | | |  ||||  |   | ||   ||     | | ||||||||||||||||||||||||||||||   | | | | | ||||| |||||  | || ||||| |||||||||||  |||||  |||| |||| ||  |||   
gtgaa-tgctttttatactctgaaaaattttgttggtcaggaaaattatttttgaagttcaaggctttctctaaatctaaagtttgcttggtatgggcctttgcagAGGTTTAAGGAAATGAGAGAAATGCA---CGGTACTAGCAGTCGTGATGATCGGCAAAAACGAGAACAACAACGTCAAGAGCGGGAGATGGCTAAGTTTGCTC
















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|71433465|gb|DR814515.1|DR814515
EST:     CTCATGAATTTGAGAGTCACTTGAGCTCATATGACCACAATCATAGGAAG                         AGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGAC
genomic: CTCATGAATTTGAGAGTCACTTGAGCTCATATGACCACAATCATAGGAAGgtaatctgtt ... ttcgtcgcagAGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGAC
EST: gi|74234698|gb|DT642612.1|DT642612
EST:     CTCATGAATTTGAGAGTCACTTGAGCTCATATGACCACAATCATAGGAAG                         AGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGA
genomic: CTCATGAATTTGAGAGTCACTTGAGCTCATATGACCACAATCATAGGAAGgtaatctgtt ... ttcgtcgcagAGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGA
EST: gi|74244524|gb|DT652438.1|DT652438
EST:     CTCATGAATTTGAGAGTCACTTGAGCTCATATGACCACAATCATAGGAAG                         AGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGAC
genomic: CTCATGAATTTGAGAGTCACTTGAGCTCATATGACCACAATCATAGGAAGgtaatctgtt ... ttcgtcgcagAGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGAC
EST: gi|71422270|gb|DR805672.1|DR805672
EST:     CTCATGAATTTGAGAGTCACTTGAGCTCATATGACCACAATCATAGGAAG                         AGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGAC
genomic: CTCATGAATTTGAGAGTCACTTGAGCTCATATGACCACAATCATAGGAAGgtaatctgtt ... ttcgtcgcagAGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGAC
EST: gi|71324316|gb|DR798859.1|DR798859
EST:     CTCATGAATTTGAGAGTCACTTGAGCTCATATGACCACAATCATAGGAAG                         AGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGAC
genomic: CTCATGAATTTGAGAGTCACTTGAGCTCATATGACCACAATCATAGGAAGgtaatctgtt ... ttcgtcgcagAGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGAC
EST: gi|93281364|gb|EB673628.1|EB673628
EST:     CTCATGAATTTGAGAGTCACTTGAGCTCATATGACCACAATCATAGGAAG                         AGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGAC
genomic: CTCATGAATTTGAGAGTCACTTGAGCTCATATGACCACAATCATAGGAAGgtaatctgtt ... ttcgtcgcagAGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGAC
EST: gi|76290174|gb|DV029742.1|DV029742
EST:     CTCATGAATTTGAGAGTCACTTGAGCTCATATGACCACAATCATAGGAAG                         AGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGAC
genomic: CTCATGAATTTGAGAGTCACTTGAGCTCATATGACCACAATCATAGGAAGgtaatctgtt ... ttcgtcgcagAGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtatttttctaatatatgttcatctgcatggttctgaataccttcgtcgcagAGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGACAGACAGAAACGTGAACAACAACGAGAAGAGAAGGAGCTGGCAAAAATTG
         ttctaat  putative branch site (score: 2)
                                           ccttcgtc  putative PPT
     atttttctaatatatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatctgttttgtgtacccttttgatttccctaatgaattgtatttgtatttttctaatatatgttcatctgcatggttctgaataccttcgtcgcagAGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGACAGACAGAAACGTGAACAACAACGAGAAGAGAAGGAGCTGGCAAAAATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT