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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaatccatctgaattttaacttttgttactacacagtgagctacctacccaacctgtgtttttctattatatgcattctcctggactgagttgggtctcatctttctgctaaatggctgtaactggtgctgcagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG

Basic information

species Zea mays
transcript GRMZM2G044027_T02
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044027_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os03g16980.5 (Oryza sativa), 3'ss of exon 9
gtaaaatccatctgaattttaacttttgttactacacagtgagctacctacccaacctgtgtttttctattatatgcattctcctggactgagttgggtctcat---ctttctgctaaatggctgtaac---tggtgctgcagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG-------------------------
                                                                                       |   | |||  | |||    |||    ||||||||   |||    | ||| || |||||||||||||||||||||||||||||||||||||||||||                         
------------------------------------------------------------------------------------gtaatgaaattgattttcacgtccttgtcactaaatggtcataatatattgtgttgtaggtgaattcaccatgctggaacttgctgagaatgtgaaggagGTAAGATGAATATCCTGTTGCCGAA

upper sequence: GRMZM2G044027_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os03g16980.2 (Oryza sativa), 3'ss of exon 10
gtaaaatccatctgaattttaacttttgttactacacagtgagctacctacccaacctgtgtttttctattatatgcattctcctggactgag-ttgggtctcatctttctg---ctaaatggctgtaac---tggtgctgcagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
             | |  || || | ||           |        | | | || |||| |  ||| |  ||   || ||   | | |||  |||  | |||  |   ||   ||||||||   |||    | ||| || |||||||||||||||||||||||||||||||||||||||||||
-------------gtagatttacctctgcattcgtttgat------ttttctctacatgtggtaatctgtactagcaatcctgtggtaatgaaattgattttcacgtccttgtcactaaatggtcataatatattgtgttgtagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
















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|32841175|gb|CD980856.1|CD980856
EST:     TAGACTGATGAATGGAAACAACACTGGGCCGATTAACTTGGGGAACCCAG                         GTGAATTCACCATGCCGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAGACTGATGAATGGAAACAACACTGGGCCGATTAACTTGGGGAACCCAGgtaaaatcca ... ggtgctgcagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|14206834|gb|BG840512.1|BG840512
EST:     TAGACTGATGAATGGAAACAACACTGGGCCGATTAACTTGGGGAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAGACTGATGAATGGAAACAACACTGGGCCGATTAACTTGGGGAACCCAGgtaaaatcca ... ggtgctgcagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|32909997|gb|CF014809.1|CF014809
EST:     TAGACTGATGAATGGAAACAACACTGGGCCGATTAACTTGGGGAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAGACTGATGAATGGAAACAACACTGGGCCGATTAACTTGGGGAACCCAGgtaaaatcca ... ggtgctgcagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|32841101|gb|CD980782.1|CD980782
EST:     TAGACTGATGAATGGAAACAACACTGGGCCGATTAACTTGGGGAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGA
genomic: TAGACTGATGAATGGAAACAACACTGGGCCGATTAACTTGGGGAACCCAGgtaaaatcca ... ggtgctgcagGTGAATTCACCATGCTGGAACTTGCTGA
EST: gi|7216734|gb|AW562856.1|AW562856
EST:     TAGGCTGATGAACGGAAACAACACTGGACCGATTAACTTGGGGAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAGACTGATGAATGGAAACAACACTGGGCCGATTAACTTGGGGAACCCAGgtaaaatcca ... ggtgctgcagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|211032180|gb|FL277400.1|FL277400
EST:     TAGGCTGATGAACGGAAACAACACTGGACCGATTAACTTGGGGAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAGACTGATGAATGGAAACAACACTGGGCCGATTAACTTGGGGAACCCAGgtaaaatcca ... ggtgctgcagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|32850262|gb|CD989943.1|CD989943
EST:     TAGACTGATGAATGGAAACAACACTGGGCCGATTAACTTGGGGAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAGACTGATGAATGGAAACAACACTGGGCCGATTAACTTGGGGAACCCAGgtaaaatcca ... ggtgctgcagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|32850632|gb|CD990313.1|CD990313
EST:     TAGACTGATGAATGGAAACAACACTGGGCCGATTAACTTGGGGAACCCAG                         GTGAATTCACCATGCT
genomic: TAGACTGATGAATGGAAACAACACTGGGCCGATTAACTTGGGGAACCCAGgtaaaatcca ... ggtgctgcagGTGAATTCACCATGCT
EST: gi|32850554|gb|CD990235.1|CD990235
EST:     TAGACTGATGAATGGAAACAACACTGGGCCGATTAACTTGGGGAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAGACTGATGAATGGAAACAACACTGGGCCGATTAACTTGGGGAACCCAGgtaaaatcca ... ggtgctgcagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|166541132|gb|EG308414.1|EG308414
EST:     GATTAACTTGGGGAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: GATTAACTTGGGGAACCCAGgtaaaatcca ... ggtgctgcagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|32866186|gb|CF005868.1|CF005868
EST:     TAGACTGATGAATGGAAACAACACTGGGCCGATTAACTTGGGGAACCCAG                         GTGAACTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAGACTGATGAATGGAAACAACACTGGGCCGATTAACTTGGGGAACCCAGgtaaaatcca ... ggtgctgcagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|32850616|gb|CD990297.1|CD990297
EST:     TAGACTGATGAATGGAAACAACACTGGGCCGATTAACTTGGGGAACCCAG                         GTGAATTCACCATGCTGG
genomic: TAGACTGATGAATGGAAACAACACTGGGCCGATTAACTTGGGGAACCCAGgtaaaatcca ... ggtgctgcagGTGAATTCACCATGCTGG
EST: gi|32840626|gb|CD980307.1|CD980307
EST:     TAGACTGATGAATGGAAACAACACTGGGCCGATTAACTTGGGGAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGGGAAGGAG
genomic: TAGACTGATGAATGGAAACAACACTGGGCCGATTAACTTGGGGAACCCAGgtaaaatcca ... ggtgctgcagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|67013235|gb|CO441984.1|CO441984
EST:     TAGGCTGATGAACGGAAACAACACTGGACCGATTAACTTGGGGAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAANGGAG
genomic: TAGACTGATGAATGGAAACAACACTGGGCCGATTAACTTGGGGAACCCAGgtaaaatcca ... ggtgctgcagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAA-GGAG
EST: gi|213192508|gb|FM182601.1|FM182601
EST:     TAGACTGATGAATGGAAACAACACTGGGCCGATTAACTTGGGGAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAGACTGATGAATGGAAACAACACTGGGCCGATTAACTTGGGGAACCCAGgtaaaatcca ... ggtgctgcagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|166419250|gb|EG304902.1|EG304902
EST:     AACACTGGACCGATTAACTT-GGGAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: AACACTGGGCCGATTAACTTGGGGAACCCAGgtaaaatcca ... ggtgctgcagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|166457737|gb|EG161293.1|EG161293
EST:     AAACAACACTGGACCGATTAACTTGGGGAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: AAACAACACTGGGCCGATTAACTTGGGGAACCCAGgtaaaatcca ... ggtgctgcagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctggactgagttgggtctcatctttctgctaaatggctgtaactggtgctgcagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
                              taaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaatccatctgaattttaacttttgttactacacagtgagctacctacccaacctgtgtttttctattatatgcattctcctggactgagttgggtctcatctttctgctaaatggctgtaactggtgctgcagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG