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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcttcctgtgccatgccgccttccgcttcttgaccacagcaccggctccgtgccggcagcatcggtccgtttgctgatgtgatgttttgggtccttttttcccccctttcgcttggggactggtgtcgctgtttgcagGGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAACACGCTGCTGCAGTCCCTCTTCGGGACCCGGCTGCCGACGGTCATCGGCG

Basic information

species Zea mays
transcript GRMZM2G437859_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G437859_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g55500.1 (Oryza sativa), 3'ss of exon 2
gtgagcttcctgtgccatgccgccttccgcttcttgaccacagcaccggctccgtgccggcagcatcggtccgtttgctgatgtgatgttttgggtccttttttcccccctttcgcttggggactggtgtcgctgttt---------gcagGGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAACACGCTGCTGCAGTCCCTCTTCGGGACCCGGCTGCCGACGGTCATCGGCG
                                                     |||   || ||  ||| |    |  || ||   |         | ||     || ||  | | ||| | |||    |  ||| ||         ||||||||||||||| |||||||||||||||||||||||||| || || || ||||||||||||||||| || |||||||| || ||||| ||||| |||||||
-----------------------------------------------------gtgagcgccgccgcggccgcactcttgttgatttcccccaatccattcgccaccacccatggtttgagaactcacttttctgctttctgctgtcgcagGGGGACAGGGTGAGGGTGGTGCAGACGCTGCTGTTCGTCACCGGCATCAACACGCTGCTGCAGTCGCTGTTCGGGACGCGCCTGCCCACGGTGATCGGCG
















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|211100340|gb|FL069921.1|FL069921
EST:     CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCCGCGACCAT                         GGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
genomic: CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGATgtgagcttcc ... ctgtttgcagGGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
EST: gi|50339069|gb|CO534195.1|CO534195
EST:     CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGAT                         GGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCATGACGGGGATAAAC
genomic: CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGATgtgagcttcc ... ctgtttgcagGGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
EST: gi|149001123|gb|EE038382.2|EE038382
EST:     CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGAT                         GGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
genomic: CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGATgtgagcttcc ... ctgtttgcagGGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
EST: gi|211102812|gb|FL069930.1|FL069930
EST:     CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGAT                         GGGGACAGGGTCAGGGTGGTGCAAACGCTGCTGTTCGTGA
genomic: CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGATgtgagcttcc ... ctgtttgcagGGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGA
EST: gi|211100342|gb|FL069923.1|FL069923
EST:     CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGAT                         GGGGACAGGGTCAGGGGTGGTGCAGACGCTGCTGTTCGTGACGG
genomic: CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGATgtgagcttcc ... ctgtttgcagGGGGACAGGGTCAGGG-TGGTGCAGACGCTGCTGTTCGTGACGG
EST: gi|71439895|gb|DR820945.1|DR820945
EST:     CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGAT                         GGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
genomic: CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGATgtgagcttcc ... ctgtttgcagGGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
EST: gi|74243489|gb|DT651403.1|DT651403
EST:     CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGAT                         GGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
genomic: CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGATgtgagcttcc ... ctgtttgcagGGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
EST: gi|149071736|gb|EE160129.2|EE160129
EST:     CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGAT                         GGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
genomic: CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGATgtgagcttcc ... ctgtttgcagGGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
EST: gi|211102808|gb|FL069926.1|FL069926
EST:     CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGAT                         GGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAA-C
genomic: CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGATgtgagcttcc ... ctgtttgcagGGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
EST: gi|71431026|gb|DR812076.1|DR812076
EST:     CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGAT                         GGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
genomic: CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGATgtgagcttcc ... ctgtttgcagGGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
EST: gi|74240437|gb|DT648351.1|DT648351
EST:     CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGAT                         GGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
genomic: CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGATgtgagcttcc ... ctgtttgcagGGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
EST: gi|91049745|gb|EB160163.1|EB160163
EST:     CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGAT                         GGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
genomic: CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGATgtgagcttcc ... ctgtttgcagGGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
EST: gi|71449525|gb|DR830575.1|DR830575
EST:     CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGAT                         GGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
genomic: CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGATgtgagcttcc ... ctgtttgcagGGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
EST: gi|211102809|gb|FL069927.1|FL069927
EST:     CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGAT                         GGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
genomic: CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGATgtgagcttcc ... ctgtttgcagGGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
EST: gi|50331687|gb|CO526813.1|CO526813
EST:     CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGAT                         GGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
genomic: CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGATgtgagcttcc ... ctgtttgcagGGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
EST: gi|211100336|gb|FL069917.1|FL069917
EST:     CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGAT                         GGGGACAGGGTCAGGGTGGTGCAG
genomic: CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGATgtgagcttcc ... ctgtttgcagGGGGACAGGGTCAGGGTGGTGCAG
EST: gi|211100341|gb|FL069922.1|FL069922
EST:     CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGAT                         GGGGACAGGGGTCAGGGTGGTGCAGACGCTGCCTGTTCGTGGACGGGGGAT
genomic: CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGATgtgagcttcc ... ctgtttgcagGGGGACAGGG-TCAGGGTGGTGCAGACGCTGC-TGTTCGTG-ACGGGG-AT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttgggtccttttttcccccctttcgcttggggactggtgtcgctgtttgcagGGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAACACGCTGCTGCAGTCCCTCTTCGGGACCCGGCTGCCGACGGTCATCGGCG
           tttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcttcctgtgccatgccgccttccgcttcttgaccacagcaccggctccgtgccggcagcatcggtccgtttgctgatgtgatgttttgggtccttttttcccccctttcgcttggggactggtgtcgctgtttgcagGGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAACACGCTGCTGCAGTCCCTCTTCGGGACCCGGCTGCCGACGGTCATCGGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG