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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgttcttaatttcccttctacgtttaagattagcccttcttctgaaatagagtctcttatcccatctgatggcaattcttcctggtcccttgtacagATAAAAATGAGATCCAGGATTTGAGGGATGTGGTTTCTGTTGAACAAGAGGAGAAAAAGGACATTCACAGGAAGCTTCAGAATGTGGAAAACGAGT

Basic information

species Zea mays
transcript GRMZM2G067350_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G067350_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g05520.1 (Oryza sativa), 3'ss of exon 6
gtaatgttcttaatttcccttctacgtttaagattagcccttcttctgaaatagagtctcttatcccatctgatggcaattcttcctggtcccttgtacagATAAAAATGAGATCCAGGATTTGAGGGATGTGGTTTCTGTTGAACAAGAGGAGAAAAAGGACATTCACAGGAAGCTTCAGAATGTGGAAAACGAGT
|||||| ||| |||  || ||| | ||  |||||||    ||| | || ||||   ||||| | | | | |||||   ||  |||||||  |||  || ||||||||| |||||||||||| ||| |||||| ||   ||||||||| ||||||||||| ||||| || |||||||||||||||   ||||| || |
gtaatgctctaaat--cctttccatgtgaaagattaaa--ttcctttggaatacgctctct-agctcttatgatgcacatatttcctggctcctactatagATAAAAACGAGATCCAGGATCTGAAGGATGTAGTCATTGTTGAACAGGAGGAGAAAAATGACATGCATAGGAAGCTTCAGAATACTGAAAATGAAT
















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|60355827|gb|DN222800.1|DN222800
EST:     CATGTTAGGTAGCAGGTTGGAGCAGGTTACTAATGACGTGCATTCGCAGT                         ATAAAAATGAGATCCAGGATTTGAGGGATGTGGTTTCTGTTGAACAAGAGG
genomic: CATGTTAGGTAGCAGGTTGGAGCAGGTTACTAATGACGTGCATTCGCAGTgtaatgttct ... ccttgtacagATAAAAATGAGATCCAGGATTTGAGGGATGTGGTTTCTGTTGAACAAGAGG
EST: gi|149016977|gb|EE045644.2|EE045644
EST:     CATGTTAGGTAGCAGGTTGGAGCAGGTTACTAATGACGTGCATTCGCAGT                         ATAAAAATGAGATCCAGGATTTGAGGGATGTGGTTTCTGTTGAACAAGAGG
genomic: CATGTTAGGTAGCAGGTTGGAGCAGGTTACTAATGACGTGCATTCGCAGTgtaatgttct ... ccttgtacagATAAAAATGAGATCCAGGATTTGAGGGATGTGGTTTCTGTTGAACAAGAGG
EST: gi|211056573|gb|FL481095.1|FL481095
EST:     CATGTTAGGTAGCAGGTTGGAGCAGGTTACTGATGGCGTGCATTCGCAGT                         ATAAAAATGAGATCCAGGATTTGAGGGATGTGGTTTCTGTTGAACAAGAGG
genomic: CATGTTAGGTAGCAGGTTGGAGCAGGTTACTAATGACGTGCATTCGCAGTgtaatgttct ... ccttgtacagATAAAAATGAGATCCAGGATTTGAGGGATGTGGTTTCTGTTGAACAAGAGG
EST: gi|149016976|gb|EE154303.2|EE154303
EST:     AATGACGGGCATTCGCAGT                         ATAAAAATGAGATCCAGGATTTGAGGGATGTGGTTTCTGTTGAACAAGAGG
genomic: AATGACGTGCATTCGCAGTgtaatgttct ... ccttgtacagATAAAAATGAGATCCAGGATTTGAGGGATGTGGTTTCTGTTGAACAAGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaatagagtctcttatcccatctgatggcaattcttcctggtcccttgtacagATAAAAATGAGATCCAGGATTTGAGGGATGTGGTTTCTGTTGAACAAGAGGAGAAAAAGGACATTCACAGGAAGCTTCAGAATGTGGAAAACGAGT
                     atctgat  putative branch site (score: 4)
                                 ttcttcctggtccctt  putative PPT
                               aattctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgttcttaatttcccttctacgtttaagattagcccttcttctgaaatagagtctcttatcccatctgatggcaattcttcctggtcccttgtacagATAAAAATGAGATCCAGGATTTGAGGGATGTGGTTTCTGTTGAACAAGAGGAGAAAAAGGACATTCACAGGAAGCTTCAGAATGTGGAAAACGAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA