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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttttctcagttttaccttataaagcactgctatcatctatataagctgacattgaggccaacccagCATCTCAGGGAATTTCCGGTTGGAATCTTGTTCTCATGGTGACTTTCTTGGTGCTATTCTTGGGACAGGAATAACAAGGGAGAAAGTTGGAGATATTCTT

Basic information

species Zea mays
transcript GRMZM2G105425_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G105425_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g54390.1 (Oryza sativa), 3'ss of exon 4
gttttctcagttttaccttataaagcactgctatcatctatataagctgacattgaggccaacccagCATCTCAGGGAATTTCCGGTTGGAATCTTGTTCTCATGGTGACTTTCTTGGTGCTATTCTTGGGACAGGAATAACAAGGGAGAAAGTTGGAGATATTCTT
||| |||||  ||| |  ||||| ||| | | ||| | |||||||||| || ||||||||  | ||||||||||||||||||| | |||||| | ||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||| |||
gttctctcaaatttgcactataa-gcagttccatcttttatataagctaactttgaggccttctcagCATCTCAGGGAATTTCAGATTGGAACCCTGTTCTCATGGTGACTTTCTTGGTGCTATTCTTGGGACAGGAATAACAAGGGATAAAGTTGGAGATATACTT

upper sequence: GRMZM2G105425_T03 (Zea mays), 3'ss of exon 4
lower sequence: AT1G53120.1 (Arabidopsis thaliana), 3'ss of exon 4
-------------------gttttctcagttttaccttataaagcactgctatca-tctatataagctgacattgaggccaacccagCATCTCAGGGAATTTCCGGTTGGAATCTTGTTCTCATGGTGACTTTCTTGGTGCTATTCTTGGGACAGGAATAACAAGGGAGAAAGTTGGAGATATTCTT
                    | |||||   || |  || |   |  ||  ||| | |||   || | | |  ||         | || ||| ||||||||||| ||||  || |||||||||| |||||||| ||||||||||||||||| || |||||  | ||||| ||| ||||||||||  | 
gtacaggacatgaatggtaatgttctcttcttgaggttttt--gttcttatatgagtctgagtatgtttatgtttgtatt--tctagTATCACAGGGAATTTCGGGTTTCAACCTTGTTCTCACGGTGACTTCCTTGGTGCTATTCTTGGCACGGGAATTTCCAGGGAAAAACTTGGAGATATCTTA

upper sequence: GRMZM2G105425_T03 (Zea mays), 3'ss of exon 4
lower sequence: Vv19s0014g02610.t01 (Vitis vinifera), 3'ss of exon 4
-------------------------------gttttctcagttttaccttataaagcactgctatcatctatataagctgacattgaggccaacccagCATCTCAGGGAATTTCCGGTTGGAATCTTGTTCTCATGGTGACTTTCTTGGTGCTATTCTTGGGACAGGAATAACAAGGGAGAAAGTTGGAGATATTCTT
                                 |||   ||  | ||  ||   |    | |  |  | | |||  | | |             |||| ||| |||| || ||  ||||  |||||||||||||||||||||| ||||| || |||||||| ||||| ||  | ||||| ||  |||| |||||  | 
gtaagtcatactgattaatcacccatttcagactttagtagcatcacagtaggcaatcatacctttgtttgtatttgttaaatgattactttttccagTATCACAGGAAACTTTGGGTTTCAATCTTGTTCTCATGGTGACTTCCTTGGCGCAATTCTTGGTACAGGGATTGCTAGGGAAAAGCTTGGGGATATCATC

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|60339679|gb|DN206652.1|DN206652
EST:     ACGTCATGACAAGTAACCCAGATGTGGTTGCTGCTTTGAG                         CATCTCAGGGAATTTCCGGTTGGAATCTTGTTCTCATGGTGACTTTCTTGG
genomic: ACGTCATGACAAGTAACCCAGATGTGGTTGCTGCTTTGAGgttttctcag ... gccaacccagCATCTCAGGGAATTTCCGGTTGGAATCTTGTTCTCATGGTGACTTTCTTGG
EST: gi|29577131|gb|CB617243.1|CB617243
EST:     GGACACCCGGACGTCATGACAAGTAACCCAGATGTGGTTGCTGCTTTGAG                         CATCTCAGGGAATTTCCGGTTGGAATCTTGTTCTCATGGTGACTTTCTTGG
genomic: GGACACCCGGACGTCATGACAAGTAACCCAGATGTGGTTGCTGCTTTGAGgttttctcag ... gccaacccagCATCTCAGGGAATTTCCGGTTGGAATCTTGTTCTCATGGTGACTTTCTTGG
EST: gi|76292416|gb|DV031984.1|DV031984
EST:     GGACACCCGGACGTCATGACAAGTAACCCAGATGTGGTTGCTGCTTTGAG                         CATCTCAGGGAATTTCCGGTTGGAATCTTGTTCTCATGGTGACTTTCTTGG
genomic: GGACACCCGGACGTCATGACAAGTAACCCAGATGTGGTTGCTGCTTTGAGgttttctcag ... gccaacccagCATCTCAGGGAATTTCCGGTTGGAATCTTGTTCTCATGGTGACTTTCTTGG
EST: gi|67013256|gb|CO442005.1|CO442005
EST:     GGACACCCGGACGTCATGCCAAGTAACCCAGATGTGGTTGCTGCTTTGAG                         CATCTCAGGGAATTTCCGGTTGGAATCTTGTTCTCATGGTGACTTTCTTGG
genomic: GGACACCCGGACGTCATGACAAGTAACCCAGATGTGGTTGCTGCTTTGAGgttttctcag ... gccaacccagCATCTCAGGGAATTTCCGGTTGGAATCTTGTTCTCATGGTGACTTTCTTGG
EST: gi|76292415|gb|DV031983.1|DV031983
EST:     GGACACCCGGACGTCATGACAAGTAACCCAGATGTGGTTGCTGCTTTGAG                         CATCTCAGGGAATTTCCGGTTGGAATCTTGTTCTCATGGTGACTTTCTTGG
genomic: GGACACCCGGACGTCATGACAAGTAACCCAGATGTGGTTGCTGCTTTGAGgttttctcag ... gccaacccagCATCTCAGGGAATTTCCGGTTGGAATCTTGTTCTCATGGTGACTTTCTTGG
EST: gi|78090612|gb|DV518986.1|DV518986
EST:     GGACACCCGGACGTCATGACAAGTAACCCAGATGTGGTTGCTGCTTTGAG                         CATCTCAGGGAATTTCCGGTTGGAATCTTGTTCTCATGGTGACTTTCTTGG
genomic: GGACACCCGGACGTCATGACAAGTAACCCAGATGTGGTTGCTGCTTTGAGgttttctcag ... gccaacccagCATCTCAGGGAATTTCCGGTTGGAATCTTGTTCTCATGGTGACTTTCTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaccttataaagcactgctatcatctatataagctgacattgaggccaacccagCATCTCAGGGAATTTCCGGTTGGAATCTTGTTCTCATGGTGACTTTCTTGGTGCTATTCTTGGGACAGGAATAACAAGGGAGAAAGTTGGAGATATTCTT
                                agctgac  putative branch site (score: 3)
                   tatcatctatataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttctcagttttaccttataaagcactgctatcatctatataagctgacattgaggccaacccagCATCTCAGGGAATTTCCGGTTGGAATCTTGTTCTCATGGTGACTTTCTTGGTGCTATTCTTGGGACAGGAATAACAAGGGAGAAAGTTGGAGATATTCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT