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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactttgtatagcttagttgttttgttaattacacggatgcccatgaacactcctaatgttattcatctatagGTCTTACGTCTTTCTGCAGCAACTCAAGATTTACCAAAGTCTATTGTTTGCAATGTTCATGGTGTTAACCCAAAGTTCCTGAAGATTGGAGAAGAAATAA

Basic information

species Zea mays
transcript GRMZM2G092588_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G092588_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g33580.1 (Oryza sativa), 3'ss of exon 5
gtactttgtatagcttag-ttgttttgttaattacacggatgcccatgaacactcctaatgttattca------tctatagGTCTTACGTCTTTCTGCAGCAACTCAAGATTTACCAAAGTCTATTGTTTGCAATGTTCATGGTGTTAACCCAAAGTTCCTGAAGATTGGAGAAGAAATAA
|| || | | ||||| |  ||||| || || | |   |||||| | | |       || || || | |      | |  |||| |||||||| |||||||||||||| ||| | || ||||||||| ||||||| || |||||||| || ||||||||||| |||||||||||  ||||||
gtgctgtatctagctcaacttgttctggta-tcatctggatgcacttcagtttcagtattgctaatgaatggcttatgcagGTTTTACGTCTGTCTGCAGCAACTCAGGATCTTCCTAAGTCTATTATTTGCAACGTCCATGGTGTAAATCCAAAGTTCCTTAAGATTGGAGATAAAATAA

upper sequence: GRMZM2G092588_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA03G36050.1 (Glycine max), 3'ss of exon 5
------------------gtactttgtatagcttagttgttttgttaa-------ttacacgga-tgcccatgaacactcctaat-gttattcatctatagGTCTTACGTCTTTCTGCAGCAACTCAAGATTTACCAAAGTCTATTGTTTGCAATGTTCATGGTGTTAACCCAAAGTTCCTGAAGATTGGAGAAGAAATAA
                   ||  || | |     |||| |||| | ||        || ||  |      | | ||     || |  | ||| || |  ||||  | ||||| || || || ||||| ||||||||||||||| |  ||||||||||||||||||| || || || ||| |||| ||||||||| | ||  
gttttcgtgtttttgttgataaatt-tgtcatggagttcttttatcaaaaaagaactaaacaaaacaaaaagggactaaattatttatgatttatattcagGTTCTTCGTCTCTCAGCTGCTACTCAGGATTTACCAAAGTCTGTAATTTGCAATGTTCATGGTGTGAATCCCAAATTCTTGAAAATTGGAGAAAAGATTG

upper sequence: GRMZM2G092588_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA19G38720.1 (Glycine max), 3'ss of exon 5
-----------------gtactttgtatagcttagttgttttgtta--attacacggatgcccatgaacactc-ctaa------tgttattcatctatagGTCTTACGTCTTTCTGCAGCAACTCAAGATTTACCAAAGTCTATTGTTTGCAATGTTCATGGTGTTAACCCAAAGTTCCTGAAGATTGGAGAAGAAATAA
                  |   |  |  || |   |  |  |   |  | || | | |     |  || |    ||||      | | ||| || |  ||||  | ||||| || || || ||||| ||||||||||||||| |  ||||||||||||||||||| || || || ||| |||| ||||||||| | ||  
ggtgtttttgttgataaatttgtcatggagttctttcatcataaaagaactaaatgaaacaagacaaaaagggactaaattatttatgatttatattcagGTTCTTCGTCTCTCAGCTGCTACTCAGGATTTACCAAAGTCTGTAATTTGCAATGTTCATGGTGTGAATCCCAAATTCTTGAAAATTGGAGAAAAGATTG

upper sequence: GRMZM2G092588_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT3G11670.2 (Arabidopsis thaliana), 3'ss of exon 5
--------------gtactttgtatagcttagttgttttgttaattacacggatgcccatgaacactcc------taatg----ttattcatctat---agGTCTTACGTCTTTCTGCAGCAACTCAAGATTTACCAAAGTCTATTGTTTGCAATGTTCATGGTGTTAACCCAAAGTTCCTGAAGATTGGAGAAGAAATAA
               || ||  |  ||| | ||| | ||| |     |     | |  || || | | |      ||||     || |  |   ||   ||||  | || || ||||| ||||| |||||||||||||||||| |||| |||||||| |||||||| || || |||||||| | |||||| ||  ||||  
gtgaatcatctactctatttcttcaagccttgttctgttgcttgaatcctctttactaataaatagtacacgagctaatacatattttctactcatgaaagGTTCTTCGCCTCTCTGCGGCAACACAAGATTTACCAAAGTCTGTTGTATGCAATGTCCATGGTGTCAATCCCAAGTTCCTTATGATTGGGGAGAAAATTG

upper sequence: GRMZM2G092588_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv08s0105g00260.t01 (Vitis vinifera), 3'ss of exon 5
---------------gtactttgtatagcttagttgttttgtt-aattacacgg---------atgcccatgaacactccta-atgttattcatctatagGTCTTACGTCTTTCTGCAGCAACTCAAGATTTACCAAAGTCTATTGTTTGCAATGTTCATGGTGTTAACCCAAAGTTCCTGAAGATTGGAGAAGAAATAA
                |  ||   | || ||     ||   || ||  | ||||         ||   ||| |||     |  || | ||   | |  ||||  | || ||||| || || || || || ||||| |||||| |  ||||||||||||| ||||| ||||| ||||| ||||| ||||||||  || |  
gagatggtctaagtaatttttccaacagttttacctttgaattcaaacatacgggaccttttcatattcattaactaaattgcatctgatctctatccagGTTCTTCGCCTTTCGGCTGCTACCCAGGACTTACCCAAGTCTGTAATTTGCAATGTTCACGGTGTGAACCCCAAGTTTCTGAAAATTGGAGAGAAACTGG

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|71427681|gb|DR808731.1|DR808731
EST:     TTCTAGTTAAACACATCAACAATTGGGTGACCAGAGCATACTGTGACAAG                         GTCTTACGTCTTTCTGCAGCAACTCAAGATTTACCAAAGTCTATTGTTTGC
genomic: TTCTAGTTAAACACATCAACAATTGGGTGACCAGAGCATACTGTGACAAGgtactttgta ... tcatctatagGTCTTACGTCTTTCTGCAGCAACTCAAGATTTACCAAAGTCTATTGTTTGC
EST: gi|47961892|gb|CN844601.1|CN844601
EST:     TTCTAGTTAAACACATCAACAATTGGGTGACCAGAGCATACTGCGACAAG                         GTCTTACGTCTTTCTGCAGCAACTCAAGATTTACCAAAGTCTATTGTTTGC
genomic: TTCTAGTTAAACACATCAACAATTGGGTGACCAGAGCATACTGTGACAAGgtactttgta ... tcatctatagGTCTTACGTCTTTCTGCAGCAACTCAAGATTTACCAAAGTCTATTGTTTGC
EST: gi|211377158|gb|FL183054.1|FL183054
EST:     TTCTAGTTAAACACATCAACAATTGGGTGACCAGAGCATACTGCGACAAG                         GTCTTACGTCTTTCTGCAGCAACTCAAGATTTACCAAAGTCTATTGTTTGC
genomic: TTCTAGTTAAACACATCAACAATTGGGTGACCAGAGCATACTGTGACAAGgtactttgta ... tcatctatagGTCTTACGTCTTTCTGCAGCAACTCAAGATTTACCAAAGTCTATTGTTTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttttgttaattacacggatgcccatgaacactcctaatgttattcatctatagGTCTTACGTCTTTCTGCAGCAACTCAAGATTTACCAAAGTCTATTGTTTGCAATGTTCATGGTGTTAACCCAAAGTTCCTGAAGATTGGAGAAGAAATAA
                                 tcctaat  putative branch site (score: 2)
                                            ttcatct  putative PPT
                                    taatgttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactttgtatagcttagttgttttgttaattacacggatgcccatgaacactcctaatgttattcatctatagGTCTTACGTCTTTCTGCAGCAACTCAAGATTTACCAAAGTCTATTGTTTGCAATGTTCATGGTGTTAACCCAAAGTTCCTGAAGATTGGAGAAGAAATAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA