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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttgttcttcatacacaacttaacagtattcgatctttcatttgatgaataaatatactgaatgatacttaaattctctttgaacaatatgatggtatacaattacttgagatatctgacatgcgaggtagttgatgctaaagttaccctcctatgcagAATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAGGTTGCTAGCTTATCAGAATAAG

Basic information

species Zea mays
transcript GRMZM2G374881_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G374881_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os06g04800.1 (Oryza sativa), 3'ss of exon 3
gtaagtttgttctt---catacacaacttaacagtattcgatctttcattt---gatgaataaat--atactgaatgat---------acttaaattctctttgaacaatatgatggtata-caattacttgagatatctgacatgcgaggtagttgatgctaaagttaccctcc-tatgcagAATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAGGTTGCTAGCTTATCAGAATAAG
||||||||||||||    |   | ||  || |  |    | ||| || |||   | | | ||       |||||||||          ||||| ||| || || |  || |   ||   ||  | |||||    |||| ||   ||| || |||   |||||||| || |||||  | |||||||| |||||||| |||||||||||||| ||||||||||| ||||| ||||||||| | ||||||||||| |||
gtaagtttgttcttgtgtaattataatatatctattaatgctctctccttttaagctaagtaggatggcactgaatgaacaataataaacttagatt-tcattaattaacacagtgaactagtagttactgtgaatatttgctgtgcaagatagcccatgctaaattttccctcgatttgcagAATTCAGCTTGGGCAACCAGCTACTGTGAAAGTTGCAGCCAACTTAATTAGGTTGTTGGCTTATCAGAACAAG

upper sequence: GRMZM2G374881_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g53060.1 (Oryza sativa), 3'ss of exon 3
gtaagtttgttcttcatacacaacttaacagtattcgatctttcatttgatgaataaatatactgaatgatacttaaattctctttgaacaatatgatggtatac-aattacttgagatatctgacatgcgaggtagttgatgctaaagttaccctcc-tatgcagAATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAGGTTGCTAGCTTATCAGAATAAG
                                  |   |  | |  ||||  |   ||||    ||| | |   | || |||   |     ||||  || | ||| | ||||| || | || |||  ||| ||  |||| |||||||| || |||||| | | |||||| |||||||| || |||||||| || ||||||||||| ||||| ||||||||| | ||||||||||| |||
---------------------------------gtaagttgtccccttga--agcgaataggaagaa-gttgaatgaactcttcat-----atatattgttctactagttactggaaacatttgatgtgcaagacagttcatgctaaattttccctccattttcagAATTCAGCTTGGGCAGCCAGCTACCGTGAAAGTTGCAGCCAACTTAATTAGGTTGTTGGCTTATCAGAACAAG
















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|71320622|gb|DR797046.1|DR797046
EST:     GTCATTTCGGACTATATACGTTATTTCCTCCACCAACACAC                         AATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAG
genomic: GTCATTTCGGACTATATACGTTATTTCCTCCACCAACACACgtaagtttgt ... tcctatgcagAATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAG
EST: gi|78543575|gb|DV621073.1|DV621073
EST:     GATACACAAGTCATTTCGGACTATGTACGTTATTTCCTCCACCAACACAC                         AATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAG
genomic: GATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACACgtaagtttgt ... tcctatgcagAATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAG
EST: gi|37380555|gb|CF627096.1|CF627096
EST:     ATACACAAGTCATTTCGGACTATGTACGTTATTTCCTCCACCAAACACAC                         AATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTA
genomic: ATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACC-AACACACgtaagtttgt ... tcctatgcagAATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTA
EST: gi|37378375|gb|CF625874.1|CF625874
EST:     GATACACAAGTCATTTCGGACTATGTACGTTATTTCCTCCACCAACACAC                         AATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAG
genomic: GATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACACgtaagtttgt ... tcctatgcagAATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAG
EST: gi|71320624|gb|DR797047.1|DR797047
EST:     GATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACAC                         AATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAG
genomic: GATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACACgtaagtttgt ... tcctatgcagAATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAG
EST: gi|32806791|gb|CD959025.1|CD959025
EST:     GATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACAC                         AATCCAGCTTGGACAACCAGCTACTGTTA
genomic: GATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACACgtaagtttgt ... tcctatgcagAATCCAGCTTGGACAACCAGCTACTGTTA
EST: gi|78109398|gb|DV527814.1|DV527814
EST:     GATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACAC                         AATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAG
genomic: GATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACACgtaagtttgt ... tcctatgcagAATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttgagatatctgacatgcgaggtagttgatgctaaagttaccctcctatgcagAATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAGGTTGCTAGCTTATCAGAATAAG
                               tgctaaa  putative branch site (score: 2)
                                       ttaccctcct  CT-rich tract
                                  taaagtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttgttcttcatacacaacttaacagtattcgatctttcatttgatgaataaatatactgaatgatacttaaattctctttgaacaatatgatggtatacaattacttgagatatctgacatgcgaggtagttgatgctaaagttaccctcctatgcagAATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAGGTTGCTAGCTTATCAGAATAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT