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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttatttaatcattgtgatgtacctagttgcaactaaagccaaactcagaactaaagcacagcataaaaaaattgtgttcacactatttttatgtgcagTTCTTCTGTGGCTGCTGACAGCAGCCTGCATAAAGACTGGTCGGCCACAAATGGCAAAACGTGCCATTGAGCTCGCAGAGTCAAGGCTGCTCAAGGACGG

Basic information

species Zea mays
transcript GRMZM2G115451_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G115451_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os11g07440.3 (Oryza sativa), 3'ss of exon 4
--gtttatttaatcattgtgatgtacctagttgcaactaaagccaaactcagaactaaagcacagcataaaaaaattgtgttcacactatttttatgtgcagTTCTTCTGTGGCTGCTGACAGCAGCCTGCATAAAGACTGGTCGGCCACAAATGGCAAAACGTGCCATTGAGCTCGCAGAGTCAAGGCTGCTCAAGGACGG
  | |  ||     | ||||||     |  |  |||| |||| ||  || |   || |  |  ||     ||   || |||      |  |   || ||||||||| |||||||||||||||||||||||||| |||||||| || || || ||||| || || |||||||||||||| ||||| ||||| || ||||||||
tagatagttggcgaaatgtgattctgatgttcacaaccaaagtcac-ctgaatcctcattccaagatcttaacgtttatgtgtgtgtt-ctcccatctgcagTTCTCCTGTGGCTGCTGACAGCAGCCTGCATCAAGACTGGGCGTCCGCAGATGGCGAAGCGCGCCATTGAGCTCGCCGAGTCCAGGCTACTGAAGGACGG
















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|40337326|gb|CK371396.1|CK371396
EST:     TGACCCCAAAAACACCCGGTGGAGTTACCACAATGGAGGATCTTGGCCAG                         TTCTTCTGTGGCTGCTGACAGCAGCCTGCATAAAGACTGGTCGGCCACAAA
genomic: TGACCCCAAAAACACCCGGTGGAGTTACCACAATGGAGGATCTTGGCCAGgtatcgtctc ... ttatgtgcagTTCTTCTGTGGCTGCTGACAGCAGCCTGCATAAAGACTGGTCGGCCACAAA
EST: gi|18450454|gb|BM428732.1|BM428732
EST:     TGACCCCAAAAACACCCGGNGGAGTTACCACAATGGAGGATCTTGGCCAG                         TTCTTCTGTGGCTGCTGACAGCAGCCTGCATAAAGACTGGNCGGCCACAAA
genomic: TGACCCCAAAAACACCCGGTGGAGTTACCACAATGGAGGATCTTGGCCAGgtatcgtctc ... ttatgtgcagTTCTTCTGTGGCTGCTGACAGCAGCCTGCATAAAGACTGGTCGGCCACAAA
EST: gi|18649535|gb|BM498354.1|BM498354
EST:     TGACCCCAAAAACACCCGGNGGAGTTACCACAATGGAGGATCTTGGCCAG                         TTCTTCTGTGGCTGCTGACAGCAGCCTGCATAAAGAC
genomic: TGACCCCAAAAACACCCGGTGGAGTTACCACAATGGAGGATCTTGGCCAGgtatcgtctc ... ttatgtgcagTTCTTCTGTGGCTGCTGACAGCAGCCTGCATAAAGAC
EST: gi|19822585|gb|BQ048609.1|BQ048609
EST:     TGACCCCAAAAACACCCGGTGGAGTTACCACAATGGAGGATCTTGGCCAG                         TTCTTCTGTGGCTGCTGACAGCAGCCTGCATAAAGACTGGTCGGCCACAAA
genomic: TGACCCCAAAAACACCCGGTGGAGTTACCACAATGGAGGATCTTGGCCAGgtatcgtctc ... ttatgtgcagTTCTTCTGTGGCTGCTGACAGCAGCCTGCATAAAGACTGGTCGGCCACAAA
EST: gi|18649229|gb|BM498048.1|BM498048
EST:     TGACCCCAAAAACACCCGGTGGAGTTACCACAATGGAGGATCTTGGCCAG                         TTCTTCTGTGGCTGCTGACAGCAGCCTGCATAAAGACTGGTCGGCCACAAA
genomic: TGACCCCAAAAACACCCGGTGGAGTTACCACAATGGAGGATCTTGGCCAGgtatcgtctc ... ttatgtgcagTTCTTCTGTGGCTGCTGACAGCAGCCTGCATAAAGACTGGTCGGCCACAAA
EST: gi|18450395|gb|BM428673.1|BM428673
EST:     TGACCCCAAAAACACCCGGTGGAGTTACCACAATGGAGGATCTTGGCCAG                         TTCTTCTGTGGCTGCTGACAGCAGCCTGCATAAAGACTGGTCGGCCACAAA
genomic: TGACCCCAAAAACACCCGGTGGAGTTACCACAATGGAGGATCTTGGCCAGgtatcgtctc ... ttatgtgcagTTCTTCTGTGGCTGCTGACAGCAGCCTGCATAAAGACTGGTCGGCCACAAA
EST: gi|18648812|gb|BM497631.1|BM497631
EST:     TGACCCCAAAAACACCCGGTGGAGTTACCACAATGGAGGATCTTGGCCAG                         TTCTTCTGTGGCTGCTGACAGCAGCCTGCATAAAGACTGGNCGGCCACAAA
genomic: TGACCCCAAAAACACCCGGTGGAGTTACCACAATGGAGGATCTTGGCCAGgtatcgtctc ... ttatgtgcagTTCTTCTGTGGCTGCTGACAGCAGCCTGCATAAAGACTGGTCGGCCACAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcagaactaaagcacagcataaaaaaattgtgttcacactatttttatgtgcagTTCTTCTGTGGCTGCTGACAGCAGCCTGCATAAAGACTGGTCGGCCACAAATGGCAAAACGTGCCATTGAGCTCGCAGAGTCAAGGCTGCTCAAGGACGG
     aactaaa  putative branch site (score: 2)
                                       ctattttt  putative PPT
                   ataaaaaaattgtgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttatttaatcattgtgatgtacctagttgcaactaaagccaaactcagaactaaagcacagcataaaaaaattgtgttcacactatttttatgtgcagTTCTTCTGTGGCTGCTGACAGCAGCCTGCATAAAGACTGGTCGGCCACAAATGGCAAAACGTGCCATTGAGCTCGCAGAGTCAAGGCTGCTCAAGGACGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - tgtgatg
- - - - - - - - - - - - - - - -caactaa
- - - - - - - - - - - - - - - - aactaaa
- - - - - - - - - - - - - - - - - - - - - aaactca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcacagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgtgtt